Questions and problems?

MM-PB(GB)/SA error messages


Up to now this FAQ considers only problems concerning the mm_pbsa.pl version, not the mmpbsa.py version.
Collected from the AMBER mailing list archive and supplemented by A. Metz and N. Homeyer.
In case you find an insufficient explanation for your problem please mail to the AMBER mailing list. Help keeping/bringing this FAQ up to date by adding the URL provided in the error message to your email.
Last update: 21.01.2012


General hints


List of error messages


=>> Calculating energy / entropy contributions
<prefix>_<com/rec/lig>.all.out not opened
e.g.: =>> Calculating energy / entropy contributions
        ras_raf_II_wt_com.all.out not opened

The <prefix>_<com/rec/lig>.all.out file could not be opened. This file is created during the MM-PB/SA calculation to collect the data generated for each snapshot. Not being able to open this file might be caused by insufficient user rights. Either the file cannot be created or it already exists and cannot be re-opened.


=>> Calculating energy / entropy contributions
sanmin_<com/rec/lig>.in not found
e.g.: =>> Calculating energy / entropy contributions
        sanmin_com.in not found

The Sander input file sanmin_<com/rec/lig>.in could not be found. This file is used for the minimization before a normal mode calculation in MM-PB/SA.


=>> Calculating energy / entropy contributions
nmode_<com/rec/lig>.in not found
e.g.: =>> Calculating energy / entropy contributions
        nmode_com.in not found

The Nmode input file nmode_<com/rec/lig>.in could not be found. This file is used for the normal mode calculation in MM-PB/SA.


=>> Calculating energy / entropy contributions
<com/rec/lig>.prmtop not found
e.g.: =>> Calculating energy / entropy contributions
        ../ras_raf_II_wt.prmtop not found

The parameter and topology file for either the complex, the receptor, or the ligand could not be found. These are the files actually defined in the MM-PB/SA input file in the @GENERAL section next to the keywords COMPT, RECPT, or LIGPT.


Finished process <fork_manager_id> with PID <system_process_id> has wrong exit code <exit_code>
e.g.: Finished process 256 with PID 9546 has wrong exit code 0.

This message indicates a problem with the parallelization via ForkManager. Try running the MM-PB/SA calculation in non-parallel mode to narrow down the problem.


Process <fork_manager_id> was not successfully analyzed
e.g.: Process 27 was not sucessfully analyzed.

This message indicates a problem with the analysis of the results produced by running the parallelization mode of MM-PB/SA. Try running the calculation in non-parallel mode to narrow down the problem.


Calc MM/GB/SAS
$AMBERHOME/bin/sander -O -i <sander_in_file> -o <sander_out_file> -c <coordinate_file> -p <parmtop_file> not successful
e.g.: sander -O -i sander_lig.in -o sander_lig.155.out -c ./snapshot_lig.crd.155 -p ./mmR18.prmtop not successful

The execution of Sander for the calculation for MM, GB, or SAS was not sucessful. Have a look into the <sander_out_file> for the error messages created by Sander.


Ana MM/GB/SAS
<sander_out_file> not opened
e.g.: sander_com.1.out not opened

The Sander output file that should have been created in the previous MM-PB/SA calculation could not be opened.


Calc PBSA
$AMBERHOME/bin/sander -O -i pbsa_<com/rec/lig>.in -o pbsa_<com/rec/lig>.<number>.out -c <prefix>_<com/rec/lig>.crd.<number> -p <prmtop_file> not successful
e.g.: sander -O -i pbsa_lig.in -o pbsa_lig.155.out -c ./snapshots_lig.crd.155 -p ./mmR18.prmtop not successful

The execution of Sander for the calculation of PB energy was not sucessful. Have a look into the <pbsa_out_file> for the error messages created by Sander. A problem that occures quiet often for small molecules is related to the fillratio value. In this case you will find the following error message in the <pbsa_out_file>

     PB Bomb in setgrd(): focusing grid too large 2
     reset fillratio to a larger number 2.000

You can simply increase this value for small molecules to avoid this problem. Therefor add the line

     print OUT " fillratio=4 \n";

to the subroutine create_pbsa_input in the $AMBERHOME/src/mm_pbsa/mm_pbsa_createinput.pm script. This line should be positioned in the &pb namelist of the section that creates the pbsa_<com/rec/lig>.in file.


Ana PBSA
pbsa_<com/rec/lig>.<number>.out not opened
e.g.: Ana PBSA
        pbsa_com.1.out not opened

The Sander output file that should have been created in the previous MM-PB/SA calculation could not be opened.


Calc Amber/iAPBS
Linking pqr file <com/rec/lig>.pqr failed!
e.g.: Linking pqr file com.pqr failed!

The pqr file from which radii and charges shall be read (RADIOPT=2) could not be linked.


Calc Amber/iAPBS
$AMBERHOME/bin/sander.APBS -O -i iapbs.in -o iapbs_<com/rec/lig>.<number>.out -c <prefix>_<com/rec/lig>.crd.<number> -p $npar not successful.
e.g.: sander.APBS -O -i iapbs.in -o iapbs_com.155.out -c ./snapshot_com.crd.155 -p ./mmR18.prmtop not successful.

The execution of sander.APBS, a Sander version comprising iAPBS (C/C++/Fortran interface to APBS), was not successful. The program sander.APBS can be used for PB/SA calculations by setting PROC to 3 in the @PB section of the MM-PB/SA input file. Prerequisite is a previous installation of APBS and iAPBS, see http://www.poissonboltzmann.org/apbs and http://mccammon.ucsd.edu/iapbs. If APBS and iAPBS are correctly installed on your system, have a look into the <iapbs_out_file> for the error messages created by sander.APBS.


Calc Amber/iAPBS
iapbs_<com/rec/lig>.<number>.out not opened
e.g.: iapbs_com.155.out not opened.

The iAPBS output file that should have been created in the previous MM-PB/SA calculation could not be opened.


Ana Amber/iAPBS
iapbs_<com/rec/lig>.<number>.out not opened
e.g.: iapbs_com.155.out not opened.

The iAPBS output file that should have been created in the previous MM-PB/SA calculation could not be opened.


$DELPHIHOME/bin/delphi delphi.prm.<number>.<number> > <prefix>_<com/rec/lig>.delphilog.<number>.<number> not running properly
e.g.: /usr/msi/2000/irix6m4/exe/delphi delphi.prm.0 > ras_raf_II_wt_com.delphilog.1.0 not running properly

The execution of Delphi is not running properly.


Ana delphi
<prefix>_<com/rec/lig>.delphilog.<number>.<focus>.<number> not opened
e.g.: 2W26_lig.delphilog.1.0.0 not opened.

The delphi output file that should have been created in the previous MM-PB/SA calculation could not be opened.


Minimize structure and calc entropy
$AMBERHOME/bin/mm_pbsa_nabnmode <prefix>_<com/rec/lig>.pdb.<number> <parmtop_file> "ntpr=50, nsnb=999999, cut=999., diel=R, gb=0, dielc=<dielc>" <maxcyc> <drms>
> nmode_<com/rec/lig>.<number>.out 2>&1 not running properly
e.g.: mm_pbsa_nabnmode ./snapshot_com.pdb.155 ./mmR18.prmtop "ntpr=50, nsnb=999999, cut=999., diel=R, gb=0, dielc=<dielc>" 50000 0.0001 > nmode_com.155.out 2>&1 not running properly.

NAB nmode calculation is not running properly. Have a look into the nmode output file for the error message created by the NAB nmode module of AMBER.


Minimize structure
$AMBERHOME/bin/sander -O -i sanmin_<com/rec/lig>.in -o sander_<com/rec/lig>.<number>.out -c <coordinate_file> -p <parmtop_file> sanmin_<com/rec/lig>.<number>.restrt not running properly
e.g.: Minimize structure
        sander -O -i sanmin_com.in -o sanmin_com.1.out -c ./snapshot_com.crd.1 -p ./mm.prmtop -r sanmin_com.1.restrt not running properly

Sander minimization of system before nmode calculation not running properly. Have a look into the <sander_out_file> for the error messages created by sander.


Calc entropy
$AMBERHOME/bin/nmode -O -i nmode_<com/rec/lig>.in -o nmode_<com/rec/lig>.<number>.out -c sanmin_<com/rec/lig>.<number>.restrt -p <parmtop_file> not running properly
e.g.: Calc entropy
        /home/fs/wiest/dwang/bin/amber7/exe/nmode -O -i nmode_lig.in -o nmode_lig.1.out -c sanmin_lig.1.restrt -p ../raf_wt.prmtop not running properly.

Nmode calculation not running properly. Have a look into the <nmode_out_file> for the error message created by nmode.


Ana entropy
nmode_<com/rec/lig>.<number>.out not opened
e.g.: nmode_com.155.out not opened

The nmode output file that should have been created in the previous NMODE calculation could not be opened.


Ana MS
<prefix>_<com/rec/lig>.mslog.<number> not opened
e.g.: snapshot_com.mslog.155 not opened.

The file from which the surface area information is read and that should have been created in the previous MOLSURF calculation could not be opened.


Generate PQR
<prefix>_<com/rec/lig>.pdb-.<number>.pdb not opened
e.g.: snapshot_com.pdb.155 not opened.

PDB file that shall be used for the creation of a corresponding PQR file could not be opened.


Generate PQR
<prefix>_<com/rec/lig>.pqr.<number>.pdb not opened
e.g.: snapshot_com.pqr.155 not opened.

PQR file could not be created. Please ensure that the correct rights are set for the folder in which the PQR file shall be created.


No radius found for $atm $atnum in residue $resname $resno
e.g.: No radius found for F1 4424 in residue TOG 278

Currently the MOLSURF calculation preparation functionality of mm_pbsa.pl supports the elements / ions N, H, C, O, P, S, FE, Na+, Cl-, MG, F, and Br. For all other types of atoms a radius value needs to be added to the hash called %exp_rad in the generate_pqr subroutine of the $AMBERHOME/src/mm_pbsa/mm_pbsa_calceneent.pm file.


Generate PDB
$command not successful
e.g.: ambpdb -p ./mmR18.prmtop < ./snapshot_com.crd.1 > tmp.pdb.1 not successful.

PDB-file could not be generated based on provided topology and coordinate files. Please ensure that provided topology and coordinate files match. To check if coordinate and toplogy files match, you can run ambpdb as a stand alone program and generate a PDB from an example coordinate file and the corresponding topology file. If the two files do not match, an error message should be printed by ambpdb.


Generate PDB
$tmp_pdb not opened
e.g.: tmp.pdb.155 not opened

Temporary PDB file that should have been created with ambpdb before could not be opened.


Center PDB
$pdb not opened
e.g.: snpahot_com.pdb.155 not opened.

PDB file that shall be read for centering the system could not be opened.


Center PDB
Unrecognized ATOM format in pdb: $line
e.g.: Unrecognized ATOM format in pdb: ATOM    1223  O     MET                      78      44.223   21.374   14.953

PDB file used for centering the system contains a line that does not match the expected format. This error message has not been reported on the AMBER mailing list yet.


Checking atom numbers
$ncrdfile not opened
e.g.: snapshot_com.crd.155 not opened.

Provided coordinate file could not be opened for checking atom number consistency between coordinate and topology file.


Checking atom numbers
$npar not opened
e.g.: ./mmR18_com.prmtop not opened.

Provided topology file could not be opened for checking atom number consistency between coordinate and topology file.


Checking atom numbers
Prmtop $npar and coord.file $ncrdfile have different atom numbers
e.g.: Prmtop ./mmR18_com.prmtop and coord.file ./snapshot_com.crd.1 have different atom numbers.

Atom numbers in provided coordinate and topology files differ. Please ensure that the correct coordinate and topology files are specified in the MM-PB/SA input file. To ensure that coordinate and topology files are matching you can run ambpdb as a stand-alone program.


=>> Creating coordinates
Specify path to zcat in subroutine create_coords in mm_pbsa_createcoords.pm
e.g.: Specify path to zcat in subroutine create_coords in mm_pbsa_createcoords.pm

The mm_pbsa.pl script can handle, i.e. automatically decompress, *.gz trajectory files generated with gzip. The trajectory file you provided has the extension *.Z. Thus the trajectory file has probably been compressed by the UNIX "compress" program. Please specify the program / command that shall be used for decompression of the trajectory in the file $AMBERHOME/src/mm_pbsa/mm_pbsa_createcoords.pm.


Executing makecrd
Open FROM failed: $!
e.g.: Open FROM failed:

Although the trajectory file specified in the MM-PB/SA input file was found, it could not be opened for snapshot extraction. Please ensure that the rights for accessing the trajectory file are correctly set.


Executing makecrd
Open TO failed: $!
e.g.: Open TO failed:

Opening of filehandle to "make_crd_hg" program failed. Ensure that the program is correctly installed on your system. The program should be usually be located in $AMBERHOME/exe.


Executing makecrd
Close TO failed: $?/$!
e.g.: Close To failed: 256/

Closing pipe to "make_crd_hg" program failed. The provided trajectory might be in a format that cannot be processed by "make_crd_hg". Please ensure that the trajectory is complete and is in AMBER trajectory file format (http://ambermd.org/formats.html#trajectory).


Executing makecrd
Close FROM failed: $?/$!
e.g.: Close FROM failed: 256/

Closing of trajectory file after coordinate extraction failed. This is usually a hint that something went wrong in the snapshot extraction step. Look for additional error messages in the <log text> printed to the console. For example "gzip: ./trajectory_001.mdcrd.gz: not in gzip format" is printed to <STDOUT> before Close FROM failed: $?/$!, if the provided trajectory file has the extension *.gz although it is not a compressed file.


=>> Reading input parameters
$file not opened
e.g.: mmpbsa.in not opened.

The MM-PB/SA input file you specified in the program call "perl mm_pbsa.pl" <mmpbsa input file> could not be opened for reading the parameters.


=>> Reading input parameters
At-entry must be first
e.g.: At-entry must be first.

Each section of the MM-PB/SA input file in which the parameters for running mm_pbsa.pl are specified starts with a @<SECTION HEADER>. This error message usually occurs, if the section header of the first section of your input file is missing. Apart from that, it has been reported that this error message was printed when users tried to call mm_pbsa.pl as MPI. Calling mm_pbsa.pl as MPI is not possible. To make use of the forking functionallity of mm_pbsa.pl please specify the number of parallel threads you would like to request via the PARALLEL flag in the MM-PB/SA input file.


Found $key => $value
$key already exists in GEN
e.g.: Found RECEPTOR => 1
        RECEPTOR already exists in GEN

The format of the MM-PB/SA input file you provided is probably not correct. Usually this error occurs if there is a double entry for one of the keywords in the @GENERAL section of the MM-PB/SA input file.


Found $key => $value
$key already exists in DEC
e.g.: Found COMREC => 1-218
        COMREC already exists in DEC

The format of the MM-PB/SA input file> you provided is probably not correct. This error commonly hints at the existence of a double entry for one of the keywords in the @DECOMP section of the <mmpbsa input file>.


Found $key => $value
$key already exists in DEL
e.g.: Found EXDI => 80.0
        EXDI already exists in DEL

The format of the MM-PB/SA input file you provided is probably not correct. Usually this error occurs if there is a double entry for one of the key words in the @PB section of the MM-PB/SA input file.


Found $key => $value
$key already exists in SAN
e.g.: Found DIELC => 1.0
        DIELC already exists in SAN

The format of the MM-PB/SA input file you provided is probably not correct. This error commonly hints at the existence of a double entry for one of the keywords in the @MM section of the MM-PB/SA input file.


Found $key => $value
$key already exists in GBO
e.g.: Found IGB => 2
        IGB already exists in GBO

The format of the MM-PB/SA input file you provided is probably not correct. Usually this error occurs if there is a double entry for one of the keywords in the @GB section of the MM-PB/SA input file.


Found $key => $value
$key already exists in MOL
e.g.: Found PROBE => 1.4
        PROBE already exists in MOL

The format of the MM-PB/SA input file you provided is probably not correct. This error commonly hints at the existence of a double entry for one of the keywords in the @MS section of the MM-PB/SA input file.


Found $key => $value
$key already exists in NMO
e.g.: Found MAXCYC => 10000         MAXCYC already exists in NMO

The format of the MM-PB/SA input file you provided is probably not correct. Usually this error occurs if there is a double entry for one of the keywords in the @NM section of the MM-PB/SA input file.


Found $key => $value
Unknown key $key where TRAJECTORY expected
e.g.: Found MAXCYC => 1000         Unknown key MAXCYC where TRAJECTORY expected

The format of the MM-PB/SA input file you provided is not correct. In the @TRAJECTORY section only entries with the keyword TRAJECTORY are accepted. In your MM-PB/SA input file the @TRAJECTORY section contains an unkown keyword.


Found $key => $value
NUMBER_LIG_GROUPS not yet found
e.g.: NUMBER_LIG_GROUPS not yet found.

The MM-PB/SA input file you provided is not correct. In the section called @MAKECRD the keywords LSTART or LSTOP are given before the number of ligand groups that shall be considered is defined. Please specify the number of ligand groups using the NUMBER_LIG_GROUPS keyword before you define the atom range of the ligand.


Found $key => $value
NUMBER_REC_GROUPS not yet found
e.g.: Found RSTART => 200
        NUMBER_REC_GROUPS not yet found.

The MM-PB/SA input file you provided is not correct. In the @MAKECRD section the keywords RSTART or RSTOP are given before the number of receptor groups that shall be considered is defined. Please specify the number of receptor groups using the NUMBER_REC_GROUPS keyword before you define the atom range of the receptor.


Found $key => $value
$key already exists in MAK
e.g.: NTOTAL => 4211
        NTOTAL already exists in MAK

The format of the MM-PB/SA input file is not correct. Usually this error occurs if there is a double entry for one of the keywords in the @MAKECRD section of the MM-PB/SA input file.


Found $key => $value
NUMBER_MUTANT_GROUPS not yet found
e.g.: NUMBER_MUTANT_GROUPS not yet found

The MM-PB/SA input file you provided is not correct. In the @ALASCAN section of the MM-PB/SA input file the atoms that shall be used for the mutation(s) are given before the total number of residues that shall be mutated is defined. Please make sure that the total number of residues to be mutated is specified by the keyword NUMBER_MUTANT_GROUPS, before the individual atoms that shall be used for the mutation(s) are defined.


Found $key => $value
Found unknown atflg $atflg
e.g.: MUTANT_REFERENCE => 1549 Found unknown atflg PBSA

The format of the MM-PB/SA input file you provided is not correct. Usually this error occurs if there exists a section with an unkown section name in the MM-PB/SA input file, e.g. a section called @PBSA or @PoissonBoltzmannCalculation. Please keep the section names given in the example files, e.g. @PB for the section in which the parameters for the Poisson-Boltzmann calculation are defined.


Checking sanity
Checking GENERAL
Something wrong with COMPLEX/RECEPTOR/LIGAND
e.g.: Something wrong with COMPLEX/RECEPTOR/LIGAND

Something related to the COMPLEX, RECEPTOR, and/or LIGAND specification went wrong. Check the COMPLEX, RECEPTOR, and LIGAND definition in the MM-PB/SA input file.


Checking sanity
Checking GENERAL
START must be smaller than STOP
e.g.: START must be smaller than STOP

The MM-PB/SA input file you provided contains a mistake. The first snapshot that shall be used for the energy calculation has a larger number than the last snapshot that shall be considered in the respective calculation. Please ensure that <START> is smaller than <STOP>.


Checking sanity
Checking GENERAL
OFFSET must be larger than 0
e.g.: OFFSET must be larger than 0

Either no number or a number below zero was assigned to the OFFSET keyword in the MM-PB/SA input file;. The mmpbsa.pl program only accepts an offset of 1 or larger. If you would like to consider every snapshot recorded during a simulation in the calculation, request an OFFSET of 1.


Checking sanity
Checking GENERAL
PARALLEL must be larger than or equal to 0
e.g.: PARALLEL must be larger than or equal to 0

A number below zero was assigned to the PARALLEL keyword in the MM-PB/SA input file. If you want to conduct a serial calculation, please set PARALLEL to 0. In case you want to use the forking functionality of mmpbsa.pl, define the number of parrallel threads you want to process, e.g. PARALLEL  8.


Checking sanity
Checking GENERAL
No route for calculation
e.g.: No route for calculation

No calculation option was set to one in the MM-PB/SA input file, so that the program does not know what to do. Please set at least one of the calculation options GC, AS, DC, MM, NM, PB, GB, or MS to 1.


Checking sanity
Checking GENERAL
Energy decomp is not (yet) possible with GC, AS, MS
e.g.: Energy decomp is not (yet) possible with GC, AS, MS

If energy decomposition is requested by setting DC == 1 in the MM-PB/SA input file, the flags GC, AS, and MS need to be set to 0.


Checking sanity
Checking GENERAL
Energy decomp only works with ICOSA algorithm (i.e. GBSA == 2)
e.g.: Energy decomp only works with ICOSA algorithm (i.e. GBSA == 2)

If an energy decomposition shall be conducted, the solvent accessible surface area can only be calculated with the ICOSA algorithm. This error message is shown when DC == 1 and the LCPO method is requested by GBSA == 1. Please use only GBSA == 2 with DC == 1.


Checking sanity
Checking GENERAL
Energy decomp only works with original nmode (i.e. PROC == 2 in NM section)
e.g.: Energy decomp only works with original nmode (i.e. PROC == 2 in NM section)

If energy decomposition (DC == 1) is requested in conjunction with a normal mode calculation, PROC in the @NM section of the MM-PB/SA input file needs to be set to 2.


Checking sanity
Checking GENERAL
Normal mode decomp only works for DCTYPE == 1 or 2
e.g.: Normal mode decomp only works for DCTYPE == 1 or 2

Normal mode decomposition is only possible by residue yet. DCTYPE == 1 and 2 are equal with respect to the normal mode decomposition and entropy calculation, but affect other energy decompositions normally. This error message has not occured on the AMBER mailing list yet.


Checking sanity
Checking GENERAL
Cannot find directory $r_gen->{"PATH"}
e.g.: Cannot find directory /home/user/mmpbsa_calculations

The directory you specified as PATH in the MM-PB/SA input file does not exist.


Checking sanity
Checking GENERAL
COMPT must be specified (correctly)
e.g.: COMPT must be specified (correctly)

Either the COMPT keyword is missing in the provided MM-PB/SA input file or the specified complex topology file does not exist.


Checking sanity
Checking GENERAL
RECPT must be specified (correctly)
e.g.: RECPT must be specified (correctly)

Either the RECPT keyword is missing in the provided MM-PB/SA input file or the specified receptor topology file does not exist.


Checking sanity
Checking GENERAL
LIGPT must be specified (correctly)
e.g.: LIGPT must be specified (correctly)

Either the LIGPT keyword is missing in the provided MM-PB/SA input file or the specified ligand topology file does not exist.


Checking DC
#COMREC + #COMLIG != #COMPRI
e.g.: #COMREC + #COMLIG != #COMPRI

The definitions in the @DECOMP section of the provided MM-PB/SA input file are not correct. The number of complex residues that shall be considered for output (COMPRI) is not equal to the sum of complex residues assigned to the receptor (COMREC) and ligand (COMLIG). If you would like to run a decomposition analysis for only a subset of the residues, specify the same range of residues in COMREC and COMLIG as in COMPRI, i.e. pretend you have a system consisting only of the subset of residues that shall be regarded in the calculation.


Checking DC
#RECRES != #RECPRI
e.g.: #RECRES != #RECPRI

Incorrect input parameters in the @DECOMP section of the provided MM-PB/SA input file. The number of receptor residues that shall be considered for output (RECPRI) is not equal to the specified number of residues in the receptor molecule (RECRES). If you would like to run a decomposition analysis for only a subset of the receptor residues, specify the same range of residues in RECRES as in RECPRI, i.e. pretend you have a receptor consisting only of the subset of residues that shall be regarded in the calculation.


Checking DC
#RECMAP != #RECPRI
e.g.: #RECMAP != #RECPRI

Wrong input in the @DECOMP section of the provided MM-PB/SA input file. The number of receptor residues that shall be considered for output (RECPRI) differs from the number of receptor residues that are present in the complex molecule (RECMAP). Please ensure that the number of residues in the complex that are equivalent to the residues in the receptor molecule is equal to the number of receptor residues that shall be considered for output.


Checking DC
#LIGRES != #LIGPRI
e.g.: #LIGRES != #LIGPRI

Incorrect input parameters in the @DECOMP section of the provided MM-PB/SA input file. The number of ligand residues that shall be considered for output (LIGPRI) is larger than the specified number of residues in the ligand molecule (LIGRES). If you would like to run a decomposition analysis for only a subset of the ligand residues, specify the same range of residues in LIGRES as in LIGPRI, i.e. pretend you have a ligand consisting only of the subset of residues that shall be regarded in the calculation.


Checking DC
#LIGMAP != #LIGPRI
e.g.: #LIGMAP != #LIGPRI

Wrong input in the @DECOMP section of the provided MM-PB/SA input file. The number of ligand residues that shall be considered for output (LIGPRI) differs from the number of ligand residues that are present in the complex molecule (LIGMAP). Please ensure that the number of residues in the complex that are equivalent to the residues in the ligand molecule is equal to the number of ligand residues that shall be considered for output.


Checking DC
#RECMAP + #LIGMAP != #COMPRI
e.g.: #RECMAP + #LIGMAP != #COMPRI

Incorrect input parameters in the @DECOMP section of the MM-PB/SA input file. The number of complex residues that shall be considered for output need to be equal to the sum of the number of complex residues that are defined as equivalent to residues in the receptor and the ligand.


Checking TRAJ
TRAJECTORY not defined
e.g.: TRAJECTORY not defined

Information missing in the @TRAJECTORY section of the MM-PB/SA input file. Although snapshot extraction was requested, no trajectory file information could be read from the @TRAJECTORY section. Either no trajectory was specified in the MM-PB/SA input file or the trajectory definition could not be recognized.


Checking TRAJ
$traj not found
e.g.: /home/user/trajectories/trajectory_001.mdcrd.gz not found

The trajectory file shown in the error message which was specified in the MM-PB/SA input file could not be found. Please ensure that you provided the correct name and path for the respective trajectory file.


Checking NM
If IGB>0, IGB must be 1 in NM section
e.g.: If IGB>0, IGB must be 1 in NM section

Wrong input in @NM section of provided MM-PB/SA input file. The NAB implementation of nmode can only be used with IGB == 0 or IGB == 1.


Checking NM
SALTCON and EXTDIEL and SURFTEN must be set for IGB>0 in NM section
e.g.: SALTCON and EXTDIEL and SURFTEN must be set for IGB>0 in NM section

Incorrect input parameters in the @NM section of the MM-PB/SA input file. If the NAB nmode implementation is used (PROC == 1) and IGB is set to 1, then SALTCON, EXTDIEL, and SURFTEN must be set in the @NM section.


Checking NM
If IGB=0, DIELC must be set in NM section
e.g.: If IGB=0, DIELC must be set in NM section

Wrong input in @NM section of provided MM-PB/SA input file. If the NAB nmode implementation is used (PROC == 1) and IGB is set to 0, then DIELC must be set in the @NM section of the MM-PB/SA input file.


Checking NM
If PROC= 2, IGB must be 0 in NM section
e.g.: If PROC= 2, IGB must be 0 in NM section

Wrong input parameters in the @NM section of the MM-PB/SA input file. If the "original" nmode implementation (PROC == 2) is used, IGB in the @NM section must be set to 0.


Checking NM
If IGB=0, DIELC must be set in NM section
e.g.: If IGB=0, DIELC must be set in NM section

The input parameters in the @NM section of the MM-PB/SA input file are not correct. If the "original" nmode implementation (PROC == 2) is used with IGB == 0, DIELC needs to be set in the @NM section.


Checking NM
PROC parameter in NM section must be 1 or 2
e.g.: PROC parameter in NM section must be 1 or 2

Wrong input parameter in the @NM section of the MM-PB/SA input file. PROC can be either set to 1 (NAB implementation of nmode) or 2 ("original" nmode implementation). Please ensure that PROC is set in the @NM section of the MM-PB/SA input file and that it is equal to 1 or 2.


Checking PB
Nof SCALE parameters wrong
e.g.: Nof SCALE parameters wrong

Wrong input parameters in @PB section of the MM-PB/SA input file. The number of specified SCALE parameter entries is not consistent with the requested number of subsequent focussing calculations.


Checking PB
Nof PERFIL parameters wrong
e.g.: Nof PERFIL parameters wrong

Input parameters in the @PB section of the MM-PB/SA input file are not correct. The number of specified PERFIL parameter entries is not consistent with the requested number of subsequent focussing calculations.


Checking PB
Focussing does not work with REFE > 0
e.g.: Focussing does not work with REFE >

Wrong input parameters in @PB section of the MM-PB/SA input script. If a Delphi focussing calculation is requested REFE needs to be set to 0.


Checking PB
IVCAP == 1,5 only works with PBSA, not DELPHI.
e.g.: IVCAP == 1,5 only works with PBSA, not DELPHI.

Input parameters in @PB section of the provided MM-PB/SA input file are not correct. Delphi was selected as method for solving the Poisson-Boltzmann equation. In this case IVCAP needs to be set to 0. Hybrid model calculations with IVCAP > 0 can only be performed with the PBSA program of AMBER.


Checking PB
PB energy decomp does not work with delphi
e.g.: PB energy decomp does not work with delphi

Wrong input parameters specified in the @PB section of the MM-PB/SA input file. Decomposition cannot be requested if Delphi is used for solving the Poisson-Boltzmann equation. An energy decomposition is only possible with the PBSA program of AMBER (PROC == 2 in @PB section of MM-PB/SA input file).


Checking PB
Parallel computation does not work with delphi
e.g.: Parallel computation does not work with delphi

Running calculations in parallel only works, if the PBSA program of the AMBER suite is used for solving the Poisson-Boltzmann equation (PROC == 2). In all other cases, e.g. PROC == 1, PARALLEL needs to be set to 0.


Checking PB
Without specifying GB, PB calc with Delphi needs SAS calc by MS
e.g. Without specifying GB, PB calc with Delphi needs SAS calc by MS

Wrong input parameter specification in MM-PB/SA input file. If Delphi is used for solving the Poisson-Boltzmann equation, the solvent accessible surface area used for calculation of the nonpolar solvation free energy needs to be determined separaterly. This can either be done be requesting a GB calculation (GB == 1, GBSA == 1 or 2) or by setting MS to 1.


Checking PB
PB calculation with REFE > 0 doesn't work with PROC equals 2
e.g.: PB calculation with REFE > 0 doesn't work with PROC equals 2

Wrong input parameters in the @PB section of the provided MM-PB/SA input file. If the PBSA program is used for solving the Poisson-Boltzmann equation, REFE needs to be set to 0.


Checking PB
For IVCAP == 1, CUTCAP, XCAP, YCAP, and ZCAP must also be given.
e.g.: For IVCAP == 1, CUTCAP, XCAP, YCAP, and ZCAP must also be given.

Information missing in the @PB section of the MM-PB/SA input file. If PROC == 2 and IVCAP == 1, CUTCAP, XCAP, YCAP, and ZCAP need to be set.


Checking PB
For IVCAP == 5, CUTCAP must also be given.
e.g.: For IVCAP == 5, CUTCAP must also be given.

Input parameter specification missing in the @PB section of the MM-PB/SA input file. If PROC == 2 and IVCAP == 5, CUTCAP needs to be set.


Checking PB
For IVCAP == 1,5, MS must be used to determine cavity energy.
e.g.: For IVCAP == 1,5, MS must be used to determine cavity energy.

Wrong input parameters specified in @PB section of provided MM-PB/SA input file. If PROC == 2 and IVCAP is set to 1 or 5, the MOLSURF program (MS == 1) needs to be used to determine the molecular surface area. In the hybrid model calculation this molecular surface area is used to determine the cavity free energy. The total nonpolar solvation free energy is calculated as the sum of the cavity free energy and the van der Waals interaction energy between the solute and solvent atoms. For a detailed explanation see: H. Gohlke, D. A. Case, J Comput Chem 2004, 25: 238250.


Checking PB
For IVCAP == 1,5, MM cannot be used in parallel.
Instead, do an IVCAP == 0 calculation with MM == 1 first, using snapshots without explicit waters.
Then do an IVCAP == 5 calculation with MM == 0, using snapshots with explict waters.
Results of both calculations currently need to be combined manually.
e.g.: See above.

The calculation of molecular mechanics energy (MM == 1) and the computation of the solvation free energy by the hybrid model approach (IVCAP > 0) need to be run separately. The energies from the two calculations can be combined "manually" afterwards.
For an example hybrid calculation see $AMBERHOME/src/mm_pbsa/Examples/07_MMPBSA_Hyb


Checking PB
If INP == 2 then RADIOPT must be set to 1.
e.g.: If INP == 2 then RADIOPT must be set to 1.

Wrong input parameters in the @PB section of the provided MM-PB/SA input file. If the INP == 2 is used for the calculation of the nonpolar solvation energy, RADIOPT needs to be set to 1, i.e. the radii set of Tan & Luo needs to be used for the calculation.


Checking PB
For decomposition with pbsa INP must be set to 0.
e.g.: For decomposition with pbsa INP must be set to 0.

The input parameters specified in the @PB section of the MM-PB/SA input file are not correct. If decomposition by the PBSA program of AMBER is requested, INP needs to be set to 0. The nonpolar solvation energy can be estimated by computing the solvent accessible surface area with the ICOSA method (GB == 1, GBSA == 2).


Checking PB
PB energy decomp does not work with iapbs
e.g.: PB energy decomp does not work with iapbs

Input parameters in the @PB section of the provided MM-PB/SA input file are not correct. If iAPBS is used for solving the Poisson-Boltzmann equation (PROC == 3), no decomposition analysis can be conducted. In this case DC shoud be set to 0.


Checking PB
PROC parameter in PB section must be 1, 2 or 3
e.g.: PROC parameter in PB section must be 1, 2 or 3

The PROC keyword in the @PB section of the MM-PB/SA input file was not correctly specified. If PB == 1, make sure that the PROC keyword is present and that PROC is set to 1, 2, or 3.


Checking PB
INDI != DIELC
e.g.: INDI != DIELC

Wrong input parameters in MM-PB/SA input file. If REFE == 0, the reaction field energy is calculated with EXDI/INDI. Here, INDI must agree with DIELC from MM part.


Checking PB
INDI <= 1.0 does not make sense for REFE > 0
e.g.: INDI <= 1.0 does not make sense for REFE > 0

Input parameters in the MM-PB/SA input file are not correct. When REFE > 0, INDI needs to be > 1. If REFE > 0 && INDI > 1.0, the difference of total energies for combinations EXDI,INDI and 1.0,INDI is calculated. The electrostatic contribution is not taken from Sander here.


Checking PB
ISTRNG > 0.0 does not (yet) work with REFE > 0
e.g.: ISTRNG > 0.0 does not (yet) work with REFE > 0

Input parameters in the MM-PB/SA input file; are not correct. If ISTRNG > 0.0, REFE should be set to 0.


Checking GB
DIELC must be 1.0 if INTDIEL > 1.0
e.g.: DIELC must be 1.0 if INTDIEL > 1.0

The input parameters in the provided MM-PB/SA input file are not correctly specified. If a Generalized Born calculation is conducted with INTDIEL > 1.0, DIELC must be set to 1.0 in the MM-PB/SA input file. Please note that for INTDIEL values other than unity have not exensively been tested. Thus, carefully study the results.


Wrong format for decomp: $str
e.g.: Wrong format for decomp: 309

The residue specification in the @DECOMP section of the MM-PB/SA input file has a wrong format. Residue ranges should be specified using the format:
<residue number>-<residue number>  <residue number>-<residue number>


Param $must does not exist
e.g.: Param PROC does not exist

The parameter $must, e.g. PROC, that needs to exist according to the definitions in mm_pbsa_global.pm, is missing in the MM-PB/SA input file. This error message can occur in very different contexts, but it always hints at a missing input keyword. Please check the definition of the $must parameter in the MM-PB/SA input file. Note that some parameters appear in different sections of the MM-PB/SA input file. Check in which sections the $must parameter needs to be set in the mm_pbsa_global.pm file.


Param $must is not defined
e.g.: Param PROC is not defined

The parameter $must, e.g. PROC, that needs to exist according to the definitions in mm_pbsa_global.pm, is not defined in the MM-PB/SA input file. This error message can occur in very different contexts, but it always hints at a missing input value. Please check the definition of the $must parameter in the MM-PB/SA input file. Note that some parameters appear in different sections of the MM-PB/SA input file. Check in which sections the $must arameter needs to be set in the mm_pbsa_global.pm file.


File $must is not found
e.g.: File MAKE_CRD is not found

One of the files required for the calculation could not be found. The files that are required and the associated aliasses can be found in the file $AMBERHOME/src/mm_pbsa/mm_pbsa_global.pm. Check the existence of the file that is associated with the reported alias, e.g. the alias MAKE_CRD is used for the executable make_crd_hg which is used to extract snapshots from trajectories.


=>> Doing statistics
$statin not opened
e.g.: L15S_statistics.in not opened

The file containing the parameters for statistical analysis could not be opened. This file is usually generated automatically in an MM-PB/SA calculation with the mm_pbsa.pl program. Please ensure that a file with the name given in the error message exists and that the permissions for reading the file are correctly set.


USAGE: mm_pbsa_stat(<calc_delta? 0..2> <calc_dec? 0..2>
                     <input_file> <output_file>
                     [<snap_min> <snap_max>])
e.g.: USAGE: mm_pbsa_statistics.pl <calc_delta? 0..2> <calc_dec? 0..2>
                         <input_file> <output_file>
                         [<snap_min> <snap_max>]

At least one of the parameters needed for statistical analysis is missing. As the parameters are set internally if the MM-PB/SA calculation is conducted with the mm_pbsa.pl program, this error message usually occurs when the parameters are not correctly specified in a call of mm_pbsa_statistics.pl.

<calc_delta? 0..2> :
0 = Single free energy calculation; only free energy of one molecule, e.g. the receptor, shall be calculated
1 = Binding free energy calculation based on single trajectory approach
2 = Binding free energy calculation based on three trajectory approach

<calc_dec? 0..2>
0 = No energy decomposition
1 = Per residue energy decomposition (Note: Results of an analysis with DC == 1 and DCTYPE == 1 or 2 must be available)
2 = Pairwise energy decomposition (Note: Results of an analysis with DC == 1 and DCTYPE == 3 or 4 must be available)

<input_file> : Name of input file for statistical analysis. This file is generated automatically in an MM-PB/SA calculation with the mm_pbsa.pl program and is called <PREFIX>_statistics.in. It needs to contain the names of the *.all.out files that shall be regarded in the statistical analysis. In case an energy decomposition has been conducted it also needs to contain information about the residues that shall be considered in the statistical analysis of the decomposition results.
Example input file:
    mysystem_com.all.out  1-107  108-120
    mysystem_rec.all.out  1-107
    mysystem_lig.all.out  108-120

<output_file> : Name of output file to which the results of the statistical analysis will be written.

<snap_min> <snap_max> : If not all snapshots that were considered in the MM-PB/SA calculation shall be regarded in a statistical analysis, the interval of snapshots that shall be taken into account can be specified, e.g. 200 800 for considering only the snapshots in the intervall 200-800 in the statistical calculation.

Example call of mm_pbsa_statistics.pl for a 3-trajectory analysis with decomposition per residue:
mm_pbsa_statistics.pl 2 1 mysystem_statistics.in mysystem_statistics.out


=>> Print output to $output
$output not opened
e.g.: =>> Print output to mysystem_statistics.out
        mysystem_statistics.out not opened

The output file in which the results of the statistical analysis shall be stored (<PREFIX>_statistics.out) could not be opened for writing. Please ensure that the writing permissions are correctly set, so that the specified file can be created.


=>> Print output to $output
        Missing values for $calc $var
e.g.: =>> Print output to mysystem_statistics.out
        Missing values for MM GAS

Values for at least one energetic component, e.g. the internal energy (GAS) from the molecular mechanics calculation (MM), are missing. This error can have different causes, but it always means that values that shall be printed to the output file are not available.


=>> Print output (snap) to $output
$output not opened
e.g.: =>> Print output (snap) to mysystem_statistics.out.snap
        mysystem_statistics.out.snap not opened

The output file in which the results obtained per snapshot shall be written (<PREFIX>_statistics.out.snap) could not be opened. Please ensure that the permissions for writing are correctly set for the folder in which the output file shall be created.


=>> Print output (snap) to $output
That operation doesn't make sense with calc_delta == 2
e.g.: =>> Print output (snap) to mysystem_statistics.out.snap
         That operation doesn't make sense with calc_delta == 2

When calc_delta is set to 2, then the data of the individual snapshots are averaged before the difference in energies between complex, receptor, and ligand is calculated. This is the correct procedure if the energies were calculated according to the 3-trajectory approach. However, due to this procedure no delta data are available for individual snapshots. Therefore, the results per snapshot cannot be written in the usual format to the snapshot output file. In order to avoid wrong formatting the program ends with this error message and no data are written to the file <PREFIX>_statistics.out.snap. Consequently this error message can be expected, if calc_type is set to 2 in the mm_pbsa_statistics.pl call. When mm_pbsa.pl is called with specification of COMPLEX, RECPTOR, and LIGAND in the MM-PB/SA input file, calc_type is set to 1. Thus, the difference between the energies (G_delta = G_complex - G_receptor - G_ligand) is calculated before averaging and an output file with the energy per snapshot is generated. However, it needs to be considered, that the values in the delta section of the <PREFIX>_statistics.out.snap file are not meainingful if the snapshots were extracted from three separate trajectories. Furthermore, in this case also the standard deviations shown in the delta section of the output file containing the average energies are not reasonable, because they are calculated based on the delta values and not based on the individual energy contributions and are therefore to small. Consequently, if you have performed an analysis according to the three trajectory approach, please use the mm_pbsa_statistics.pl script for the computation of the standard deviation and neglect the error message printed when the output of the snapshot specific energies is prepared.


Snapshot
Missing values for $calc $var
e.g.: Missing values for MM GAS

Values for at least one of the energetic components, e.g. the internal energy (GAS) from the molecular mechanics calculation (MM), are missing. This error can have different causes, but it always means that values that shall be printed to the snapshot specific output file <PREFIX>_statistics.out.snap are not available.


Snapshot
Non-equal no. of snapshots: $snap != scalar(@{$DATA->[$i]->{$calc}->{$var}})
e.g.: Non-equal no. of snapshots: 5 != scalar(-8730.1822 -8780.8066 -8779.8121)

The number of values in the <PREFIX>_<com|rec|lig>.all.out files are not consistent. One of the files contains data for more snapshots than another, e.g. for the complex data for 15 snapshots are available whereas for the receptor only data for 10 snapshots are available. This can be the case if one calculation was not successully ended and another calculation is started without deleting the <PREFIX>_<com|rec|lig>.all.out files before. Delete all <PREFIX>_<com|rec|lig>.all.out files and run a new analysis, or remove those entries from the <PREFIX>_<com|rec|lig>.all.out files which were created in the previous, unsuccessful calculation and then conduct a statistical analysis with mm_pbsa_statistics.pl.


=>> Print output (decomp) to $output
$output not opened
e.g.: =>> Print output (decomp) to mysystem_statistics.out
         mysystem_statistics.out not opened

The output file in which the results of the statistical analysis shall be stored (<PREFIX>_statistics.out) could not be opened for writing. Please ensure that the writing permissions are correctly set, so that the specified file can be created.


=>> Print output (decomp) to $output
Missing values for $calc $var
e.g.: =>> Print output (decomp) to mysystem_statistics.out
         Missing values for MM BGAS

Values for at least one of the enegetic components, e.g. the backbone internal energy (BGAS) from the molecular mechanics calculation (MM), are missing. This error can have different causes, but it always means that values that shall be printed to the output file are not available. Check the format of the residue specification in the @DECOMP section of the MM-PB/SA input file and in the <PREFIX>_statistics.in file.


Wrong no of molecular species
e.g.: Wrong no of molecular species

Data for less than three molecular species available for the calculation of the delta energies. Data for complex, receptor, and ligand must exist, when delta values, i.e. E_delta = E_complex - E_receptor - E_ligand, shall be calculated.


Missing values for $calc $var
e.g.: Missing values for MM BGAS

Values for at least one enegetic component needed for statistical analysis, e.g. the backbone internal energy (BGAS) value from the molecular mechanics calculation (MM), are missing. This error can have different causes, but it always means that values that are required for the statistical analysis are not available. If you are running a decomposition analysis, check the correct format of the residue specification in the @DECOMP section of the MM-PB/SA input file and in the <PREFIX>_statistics.in file. Furthermore ensure that the extracted coordinate files contain no water molecules unintendedly. Another possible source of error can be a wrong specification of snapshot numbers. E.g. if you try to calculate energies for snapshots 200 to 300, but snapshots with corresponding numbers do not exist under PATH, the molecular mechanics energies for these snapshots cannot be calculated. In this case the "=>> Calculating energy / entropy contributions" section of the console output is empty, since the energy is not computed. Please ensure that snapshots with the name <PREFIX>_<com|rec|lig>.crd.<number> with numbers in the specified range exist in the PATH folder.


No data for " . "$i" . "+0 $calc $var $j
e.g.: No data for 0+0 MM BOND 0

This error often occurs if the MM-PB/SA analysis is run in a folder in which old data from a previous run of mm_pbsa.pl exist. Please delete all old files, especially all <PREFIX>_<com|rec|lig>.all.out files, and then re-start the analysis.


No data for " . "$i" . "+1 $calc $var $j
e.g.: No data for 0+1 MM BOND 3

This error often occurs if the MM-PB/SA calculation is carried out in a folder in which old data from a previous run of mm_pbsa.pl exist. Please delete all old files, especially all <PREFIX>_<com|rec|lig>.all.out files, and then re-start the analysis.


No data for " . "$i" . "+2 $calc $var $j
e.g.: No data for 0+2 MM BOND 3

This error often occurs if the MM-PB/SA calculation is carried out in a folder in which old data from a previous run of mm_pbsa.pl exist. Please delete all old files, especially all <PREFIX>_<com|rec|lig>.all.out files, and then re-start the analysis.


Error while mapping for $j: $maprec $maplig
e.g.: Error while mapping for 206: -1 -1

Mapping of residues in the decomposition analysis was not successful. Please ensure that the residue definitions in the @DECOMP section of the MM-PB/SA input file and / or in the <PREFIX>_statistics.in file are correct. An example of a decomposition analysis can be found under $AMBERHOME/src/mm_pbsa/Examples/05_MMPBSA_Decomp_Residue.


No data for " . "$i" . "+1 $calc $var $maprec
e.g.: No data for 0+1 MM BGAS 3842

At least one of the enegetic values needed for statistical analysis, e.g. a backbone internal energy (BGAS) value from the molecular mechanics calculation (MM), is missing. This error can have different causes, but it always means that a value that is required for the statistical analysis is not available. One possible reason can be that the residue assignment for the decomposition analysis is not correct. Please ensure that the residues are correctly specified in the @DECOMP section of the MM-PB/SA input file and / or in the <PREFIX>_statistics.in file.


No data for " . "$i" . "+2 $calc $var $maplig
e.g.: No data for 0+2 MM BGAS 3842

At least one of the enegetic values needed for statistical analysis, e.g. a backbone internal energy (BGAS) value from the molecular mechanics calculation (MM), is missing. This error can have different causes, but it always means that a value that is required for the statistical analysis is not available. One possible reason can be that the residue assignment for the decomposition analysis is not correct. Please ensure that the residues are correctly specified in the @DECOMP section of the MM-PB/SA input file and / or in the <PREFIX>_statistics.in file.


Missing values for $calc $var
e.g.: Missing values for MM BGAS

Values for at least one enegetic component needed for statistical analysis, e.g. the backbone internal energy (BGAS) values from the molecular mechanics calculation (MM), are missing. This error can have different causes, but it always means that values that are required for the statistical analysis are not available.


=>> Treat special parameters
No surf specification given in treat_special
e.g.: No surf specification given in treat_special

Internal error of the procedure: The surface area data required for the calculation of the nonpolar solvation free energy contribution could not be found. This error has not been reported on the AMBER mailing list yet.


=>> Treat special parameters
No entr specification given in treat_special
e.g.: No entr specification given in treat_special

Internal error of the procedure: The entropy data required for the calculation of the entropic energy contribution could not be found. This error has not been reported on the AMBER mailing list yet.


=>> Treat special parameters
No rule found for $calc $var
e.g.: No rule found for MM BGAS

Although special treatment of data was requested, no rule for data handling could be found. This error has not been reported on the AMBER mailing list yet.


=>> Calc missing parameters
No entries for $tocalc" . "_" . "$tovar existing
e.g.: No entries for MM_GAS existing

Values for the respective energy component, e.g. the internal energy (GAS) from the molecular mechanics (MM) calculation, are missing. Because of this the calculation of missing parameters had to be aborted.


=>> Calc missing parameters
No value for "last" available
e.g.: No value for "last" available

Internal error of the procedure: The last value that shall be considered in the calculation of missing values could not be identified. This error has not been reported on the AMBER mailing list yet.


=>> Reading files
Reading $file
$file not opened
e.g.: Reading mysystem_com.all.out
        mysystem_com.all.out not opened

One of the <PREFIX>_<com|rec|lig>.all.out files could not be opened for reading. If you run a stand-alone statistical analysis, please ensure that the required <PREFIX>_<com|rec|lig>.all.out files exist in the folder in which the calculation shall be conducted. Another source of error could be too restrictive permissions for the respective files.


WARNING: Missing <property> for <mm-pbsa_energy_type> in <snapshot_nr> -> Taken from <previous_snapshot_nr>
e.g.: WARNING: Missing PB for PB in 2 -> Taken from 1

This message warns you that the statistics script (mm_pbsa_statistics.pm) could not find a specific property <property> that is needed for calculating one of the MM-PB/SA energy types <mm-pbsa_energy_type> specified in the mm_pbsa.in file for the snapshot with the number <snapshot_nr>. In this case this property is copied from a previous snapshot with the number <previous_snapshot_nr>. You should try to find out why this specific value is missing. There are a couple of reasons why there could be a missing property. (1) The Poisson Boltzmann solver will sometimes fail for small molecules. In this case the PB property is missing for those snapshots. This issue can be solved by increasing the fillratio variable in the mm_pbsa_createinput.pm script from 2 to 4. For consistency this should be done for all snapshots. (2) The statistics script (mm_pbsa_statistics.pm) may be looking for properties that are just not there because they were not calculated. Check the *.all.out and the other *.out files that are evaluated during the statistics and why certain values are not there. You might find values for ELRAELE, EPB and PBNONPOL missing. These properties are only calculated for a hybrid solvation scheme in MM-PB/SA (with IVCAP > 0 in the mm_pbsa.in file). In regular MM-PB/SA without this hybrid solvation scheme these properties are not calculated. However, if the adequate patch is not applied the statistics will be looking for these properties in the *.all.out file, find nothing, and cause the issue. There was a patch for AMBER 10 and it will be included in AMBER 11 that the statistics script (mm_pbsa_statistics.pm) will only be looking for these properties if actually the hybrid model was used. What kind of calculation is performed now depends on the header in the *.all.out file. The keyword PB indicates the "traditional" MM-PB/SA while PBHyb indicates MM-PB/SA using the hybrid solvation scheme. If you don't have the patch at hand, you can also just modify your mm_pbsa_statistics.pm script in the $PB section of the $VARREG hash table (see below). If the first index for these three properties is set to 0, they wont be looked after during statistics.

           "ELRAELE" => [0,0,'ELRAELE = +(-?\d+\.\d+)'], 
           "EPB" => [0,0,'EPB = +(-?\d+\.\d+)'],
           "PBNONPOL" => [0,0,'ENPOLAR = +(\d+\.\d+)'], 

Missing $var for $calc in ($index+$snap_min) (residue ($j+1))
e.g.: Missing TINT for MM in 2 (residue 480)

For one of the residues energy data needed for statistical analysis of decomposition calculation results are missing. Have a close look at the <PREFIX>_<com|rec|lig>.all.out file to find out what values have not been calculated in the MM-PB/SA analysis.


Checking consistency of CALC
Calc mode $must not found
e.g.: Calc mode MM not found

One of the calculation modes that are required for the statistical analysis was not found in the <PREFIX>_<com|rec|lig>.all.out file. This error has not been reported on the AMBER mailing list yet.


Checking consistency of DATA
SURFTEN / SURFOFF values are not consistent across *.all.out files
e.g.: SURFTEN / SURFOFF values are not consistent across *.all.out files

The PB_SURFTEN, PB_SURFOFF and / or GB_SURFTEN, GB_SURFOFF values specified in the header of the <PREFIX>_<com|rec|lig>.all.out files have not the same values assigned in all of the *.all.out files. Compare the SURFTEN and SURFOFF values in the *.all.out files and ensure that they are identical.


=>> Reading input
$input not opened
e.g.: =>> Reading input
        mysystem_statistics.in not opened

The file containing the input information for the statistical analysis could not be opened for reading. Please ensure that a file called <PREFIX>_statistics.in is present in the folder in which the analysis shall be conducted and check that the permissions for the file are set correctly.


=>> Reading input
        $tmp[$i] is not conform with \d+-\d+ or "0"
e.g.: 13,297,298 is not conform with \d+-\d+ or "0"

The format of the <PREFIX>_statistics.in file is not correct. In case of a decomposition analysis, check if you specified the residues that shall be considered in the required format. Residues should be given in the format: <first residue number of interval>-<last residue number of interval> <first residue number of interval>-<last residue number of interval> ...


Error: n must be at least two in calc_moments_of_distr
e.g.: Error: n must be at least two in calc_moments_of_distr

Internal error of the calculation procedure: At least two data points need to be available to be able to conduct averaging of the data. This error message has not occurred on the AMBER mailing list archive yet.


Actually can't be ... ???
e.g.: Actually can't be ... ???

Internal error of the procedure: An error that usually should not appear and has not been reported so far.


No PBCAV, PBDIS, ELRAELE and EPB found, assuming iAPBS calculation.
e.g.: No PBCAV, PBDIS, ELRAELE and EPB found, assuming iAPBS calculation.

Since no data for the energy contributions PBCAV, PBDIS, ELRAELE, and EPB were found in the *.all.out files, it is assumed that the Poisson-Boltzmann equation was solved using iAPBS (a C/C++/Fortran interface to the APBS Poisson-Boltzmann solver).


No skew or curtosis when zero variance in moment

This error message occures when using odd data for statistics in MM-PB/SA. If you have zero variance (i.e. zero second statistical moment) then your standard deviation is zero and calculating the skew (third statistical moment) and curtosis (fourth statistical moment) involves a "divide by zero" which is undefined. The output message is to let you know that the skew and curtosis of the probability distribution are undefined when the variance equals zero. This error message occurs in general if you have 3 or less data points and calculating skew or curtosis makes no sense. In this case it constitutes only a warning and can be ignored. It is also possible that the statistics script (mm_pbsa_statistics.pm) is looking for data that is not provided during the MM-PB/SA calculation. In any case better check your data.


Entry $i $calc $var $index exists -> overwriting
e.g.: Entry 0 PB PB 3 exists -> overwriting

This message is printed when the program reads data from the <PREFIX>_<com|rec|lig> out file for which already data exist in the corresponding data structure. It informs you that the data are overwritten by the new data. One possible cause for this problem is the existence of old output files in the folder in which the calculations are conducted. Please delete all old output files and then re-run the analysis. If this does not help, have a look at the *.all.out files and try to find out which energy contributions cause the problem. Missing energy values and Nan values in the <PREFIX>_<com|rec|lig> files can hint at the origin of the problem.


No values for $tocalc_$tovar existing -> Skipping
e.g.: No values for GB_TGBSUR existing -> Skipping

Values for at least one of the energy components, e.g. the total nonpolar free energy of solvation (TGBSUR) of a GB calculation, is missing. Therefore this energy contribution will be neglected in the statistical analysis. Please note that energy decomposition of the nonpolar solvation energy only works in conjunction with GB and solvent accessible surface area calculation be the ICOSA model. Therefore always set GB == 1 and GBSA == 2 in a decomposition analysis, even if the polar solvation energy shall be calculated with PBSA (PB == 1).


Value for $tocalc_$tovar not mandatory -> Will be omitted
e.g.: Value for PB_PBSOL not mandatory -> Will be omitted

The user is informed that values for the specified energy contribution are not available yet. They will eventually be considered later in the calculation. If values for the respective energy contribution are missing in the <PREFIX>_statistics.out file, have a look at the data in the *all.out files. In case the data for the this energy contribution are missing in the *all.out file, try to find the cause for the problem by setting VERBOSE to 1 in the MM-PB/SA input file and re-running of the calculation.


Can't find environment variable AMBERHOME
e.g.: Can't find environment variable AMBERHOME

The environment variable AMBERHOME was not correctly set. Please consult the AMBER Users' Manual on how to set this variable.


Nmode input
sanmin.<com|rec|lig>.in not opened
e.g.: Nmode input
        sanmin.com.in not opened

The file in which the commands for the minimization conducted before an nmode analysis would be written could not be created. Please ensure that the permissions of the folder in which the analysis is carried out are correctly set.


Nmode input
nmode.<com|rec|lig>.in not opened
Nmode input
        nmode.com.in not opened

The nmode input file could not be created. Please ensure that you have writing permissions in the folder in which the analysis is conducted.


Sander input
sander.<com|rec|lig>.in not opened
e.g.: Sander input
        sander.com.in not opened

Input file for sander calculation that is conducted to determine the molecular mechanics energy and / or the polar solvation energy by the Generalized Born method could not be created. Please ensure that the permissions in the folder in which the analysis is carried out are correctly set.


Delphi input
delphi.prm.$i.$j; not opened
e.g.: Delphi input
        delphi.prm.0.1 not opened

The file in which the parameters for the Delphi calculation would be stored could not be created. Please ensure that you have writing permissions in the folder in which the MM-PB/SA analysis is conducted.


PBSA input
pbsa.<com|rec|lig>.in not opened
e.g.: PBSA input
        pbsa.com.in not opened

The input file for the PBSA program could not be created. Please ensure that the permissions for the folder in which the analysis shall be carried out are correctly set.


iAPBS input
iapbs.in not opened
e.g.: iAPBS input
        iapbs.in not opened

The file in which the parameters for iAPBS (Interface to APBS Poisson-Boltzmann solver) would be stored could not be created. Please ensure that you have writing permissions in the folder in which the analysis shall be conducted.


make_crd input
make_crd.in not opened
e.g.: make_crd input
        make_crd.in not opened

The input file for the make_crd_hg program used for extracting snapshots from trajectories could not be created. Please ensure that the permissions for the folder in which the analysis shall be carried out are correctly set.


make_crd input
Something wrong with MUTANT_ATOM1 definitions
e.g.: make_crd input
        Something wrong with MUTANT_ATOM1 definitions

Definition of the MUTANT_ATOM1 in the @AS (alanine scanning) section of the MM-PB/SA input file is not correct. For an example of a correct specification of the input see $AMBERHOME/src/mm_pbsa/Examples/01_GenerateSnapshots/mm_pbsa.in


make_crd input
Something wrong with MUTANT_ATOM2 definitions
e.g.: make_crd input
        Something wrong with MUTANT_ATOM2 definitions

Definition of the MUTANT_ATOM2 in the @AS (alanine scanning) section of the MM-PB/SA input file is not correct. For an example of a correct specification of the input see $AMBERHOME/src/mm_pbsa/Examples/01_GenerateSnapshots/mm_pbsa.in


make_crd input
Something wrong with MUTANT_KEEP definitions
e.g.: make_crd input
        Something wrong with MUTANT_KEEP definitions

Definition of MUTANT_KEEP in the @AS (alanine scanning) section of the MM-PB/SA input file is not correct. For an example of a correct specification of the input see $AMBERHOME/src/mm_pbsa/Examples/01_GenerateSnapshots/mm_pbsa.in


make_crd input
Something wrong with MUTANT_REFERENCE definitions
e.g.: make_crd input
        Something wrong with MUTANT_REFERENCE definitions

Definition of the MUTANT_REFERENCE in the @AS (alanine scanning) section of the MM-PB/SA input file is not correct. For an example of a correct specification of the input see $AMBERHOME/src/mm_pbsa/Examples/01_GenerateSnapshots/mm_pbsa.in


make_crd input
Something wrong with LSTART definitions
e.g.: make_crd input
        Something wrong with LSTART definitions

Definition of LSTART (i.e. the first ligand atom in the trajectory entry) provided in the @MAKECRD section of the MM-PB/SA input file is not correct. For an example of a correct specification of the input see $AMBERHOME/src/mm_pbsa/Examples/01_GenerateSnapshots/mm_pbsa.in


make_crd input
Something wrong with LSTOP definitions
e.g.: make_crd input
        Something wrong with LSTOP definitions

Definition of LSTOP (i.e. the last ligand atom in the trajectory entry) provided in the @MAKECRD section of the MM-PB/SA input file is not correct. For an example of a correct specification of the input see $AMBERHOME/src/mm_pbsa/Examples/01_GenerateSnapshots/mm_pbsa.in


make_crd input
Something wrong with RSTART definitions
e.g.: make_crd input
        Something wrong with RSTART definitions

Definition of RSTART (i.e. the first receptor atom in the trajectory entry) provided in the @MAKECRD section of the MM-PB/SA input file is not correct. For an example of a correct specification of the input see $AMBERHOME/src/mm_pbsa/Examples/01_GenerateSnapshots/mm_pbsa.in


make_crd input
Something wrong with RSTOP definitions
e.g.: make_crd input
        Something wrong with RSTOP definitions

Definition of RSTOP (i.e. the last receptor atom in the trajectory entry) provided in the @MAKECRD section of the MM-PB/SA input file is not correct. For an example of a correct specification of the input see $AMBERHOME/src/mm_pbsa/Examples/01_GenerateSnapshots/mm_pbsa.in


Use of uninitialized value in addition
e.g.: Use of uninitialized value in addition (+) at /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1836.

This Perl error message indicates that the addition of a variable cannot be carried out, because that variable is not initialized. This occurs for example if a value cannot be read when calculating MM-PB/SA statistics. Read the log output written by mm_pbsa.pl to the console before the error message thoroughly and check if all energies have been calculated correctly. In addition, if the error occurs while mm_pbsa.pl is calculating the statistics, have a look at the <PREFIX>_<com|rec|lig>.all.out files and check if there are values missing. If this is the case, try to figure out the cause of the problem by re-running the analysis with the VERBOSE option set to 1 in the MM-PB/SA input file. A further source of the error can be the presence of old output files in the folder in which the analysis is conducted. If this is the case, re-run the analysis after deleting all old output files.


Use of uninitialized value in multiplication
e.g.: Use of uninitialized value in multiplication (*) at /usr/local/amber10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.

This Perl error message indicates that the multiplication of a variable cannot be carried out, because that variable is not initialized. This occurs for example if a value cannot be read when calculating MM-PB/SA statistics. Read the log output written by mm_pbsa.pl to the console before the error message thoroughly and check if all energies have been calculated correctly. In addition, if the error occurs while mm_pbsa.pl is calculating the statistics, have a look at the <PREFIX>_<com|rec|lig>.all.out files and check if there are values missing. If this is the case, try to figure out the cause of the problem by re-running the analysis with the VERBOSE option set to 1 in the MM-PB/SA input file. A further source of the error can be the presence of old output files in the folder in which the analysis is conducted. If this is the case, re-run the analysis after deleting all old output files.


USAGE: mm_pbsa.pl <input file>
e.g.: USAGE: mm_pbsa.pl <input file>

Wrong call of the mm_pbsa.pl program. Please specify only the file containg the parameters for the MM-PB/SA analysis after mm_pbsa.pl in the program call.