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
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.
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.
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.
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.
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.
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.
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.
The Sander output file that should have been created in the previous MM-PB/SA calculation could not be opened.
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.
The Sander output file that should have been created in the previous MM-PB/SA calculation could not be opened.
The pqr file from which radii and charges shall be read (RADIOPT=2) could not be linked.
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.
The iAPBS output file that should have been created in the previous MM-PB/SA calculation could not be opened.
The iAPBS output file that should have been created in the previous MM-PB/SA calculation could not be opened.
The execution of Delphi is not running properly.
The delphi output file that should have been created in the previous MM-PB/SA calculation could not be opened.
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.
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.
Nmode calculation not running properly. Have a look into the <nmode_out_file> for the error message created by nmode.
The nmode output file that should have been created in the previous NMODE calculation could not be 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.
PDB file that shall be used for the creation of a corresponding PQR file could not be 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.
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.
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.
Temporary PDB file that should have been created with ambpdb before could not be opened.
PDB file that shall be read for centering the system could not be opened.
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.
Provided coordinate file could not be opened for checking atom number consistency between coordinate and topology file.
Provided topology file could not be opened for checking atom number consistency between coordinate and topology file.
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.
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.
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.
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.
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).
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.
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.
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.
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.
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>.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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>.
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.
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.
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.
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.
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.
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.
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.
The directory you specified as PATH in the MM-PB/SA input file does not exist.
Either the COMPT keyword is missing in the provided MM-PB/SA input file or the specified
complex topology file does not exist.
Either the RECPT keyword is missing in the provided MM-PB/SA input file or the specified
receptor topology file does not exist.
Either the LIGPT keyword is missing in the provided MM-PB/SA input file
or the specified ligand topology file does not exist.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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).
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.
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.
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.
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.
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.
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: 238–250.
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
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.
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).
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.
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.
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.
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.
Input parameters in the MM-PB/SA input file; are not correct.
If ISTRNG > 0.0, REFE should be set to 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.
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>
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.
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.
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.
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.
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
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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+)'],
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.
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.
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.
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.
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> ...
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.
Internal error of the procedure: An error that usually should not appear and has not been reported so far.
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).
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.
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.
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).
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.
The environment variable AMBERHOME was not correctly set. Please consult the AMBER Users' Manual on how to
set this variable.
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.
The nmode input file could not be created. Please ensure that you have writing permissions in the
folder in which the analysis is conducted.
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.
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.
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.
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.
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.
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
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
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
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
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
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
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
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
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.
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.
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.