Antechamber is a set of auxiliary programs for molecular mechanic (MM) studies. This software package is devoted to solve the following problems during the MM calculations: (1) recognizing the atom type; (2) recognizing bond type; (2) judging the atomic equivalence; (3) generating residue topology file; (4) finding missing force field parameters and supplying reasonable and similar substitutes. As an accessory module in the AmberTools package, antechamber can generate input automatically for most organic molecules in a database. The algorithms behind these manipulations may be useful outside the Amber family of programs as well.

In the following, we list the usage of the programs in the antechamber package (circa 2007; for more recent information see the AmberTools Manual; for the latest information execute the program with the -h option). As to algorithms beyond those programs, please refer to our paper submitted to Journal of Chemical Information and Computer Science. At the bottom of this page, we provide an example ( TP) to demonstrate how to use antechamber programs to generate prep and frcmod files to be read by LEaP. More examples and tutorials are available in other pages. We also have a trouble-shooting page, where there are some tips on how to use antechamber programs efficiently and properly.

Programs in Antechamber

Am1bcc reads in an ac file to assign atom types and bond types according to AM1-BCC definitions (ATOMTYPE_BCC.DEF in $AMBERHOME/dat/antechamber). This program first calls atomtype and bondtype to do atom type and bond type perception and then does Bond Charge Correction (BCCPARM.DAT in $AMBERHOME/dat/antechamber). There are five options of "-j" flag. If there is some problem with the assignments, you may manually revise them and run am1bcc with "-j" set to 0, which means no assignment to be performed. Bear in mind that am1bcc dose not run mopac to get AM1-Mulliken charges itself, which is required according to AM1-BCC scheme. you can generate AM1-Mulliken charge using antechamber.


Usage: am1bcc -i input_file_name in ac format 
              -o output_file_name 
              -f output_file_format(pdb or ac, optional, default is ac)
              -p bcc_parm_file_name (optional))
              -j atom and bond type judge option, default is 0)
                 0: No judgement
                 1: Atom type
                 2: Full bond type
                 3: Partial bond type
                 4: Atom and full bond type
                 5: Atom and partial bond type

#! /bin/csh -fv
set mols = /bin/ls *.mol2
foreach mol ($mols)
set mol_dir = $mol:r
antechamber -i $mol_dir.mol2 -fi mol2 -fo ac -o $ -c mul
am1bcc -i $ -f ac -o $ -j 5

The above script finds all the files with extension of "mol2" in the current directory. For each file, antechamber is run to get Mulliken charges. Then am1bcc is carried out to assign AM1-BCC charges.

The antechamber program itself is the main program of Antechamber package. In most of cases, one should use this program instead of a series of separated programs to do molecular format conversion, atom type assignment and charge generation etc. However, in some special cases, for instance, to generate an amino-acid-like residue topology file (prep input file), you may need run a set of programs (atomtype, bondtype, am1bcc, prepgen etc) to reach your aim. Sometimes program failure happens, you may check the intermediate files (in capital letters) to find the problem and correct them. Then you need to run a series of programs to achieve your purpose.


Usage: antechamber -i   input file name
                   -fi  input file format
                   -o   output file name
                   -fo  output file format
                   -c   charge method
                   -cf  charge filename
                   -nc  net molecular charge (int)
                   -a   additional file name
                   -fa  additional file format
                   -ao  additional file operation
                        crd : only read in coordinate
                        crg: only read in charge
                        name  : only read in atom name
                        type  : only read in atom type
                        bond  : only read in bond type 
                   -m   multiplicity (2S+1), default is 1
                   -rn  residue name, if not available in the input file, default is MOL
                   -rf  residue toplogy file name in prep input file, default is molecule.res
                   -mp  mopac program name, default is
                   -mk  mopac keyword in a pair of quotation mark
                   -gk  gaussian keyword in a pair of quotation mark
                   -at  atom type, can be gaff, amber, bcc and sybyl, default is gaff
                   -du  check atom name duplications, can be yes(y) or no(n), default is no
                   -j   atom type and bond type prediction index, default is 4 
                        0    : no assignment
                        1    : atom type 
                        2    : full  bond types 
                        3    : part  bond types 
                        4    : atom and full bond type 
                        5    : atom and part bond type 
                   -s   status information can be 0 (brief), 1 (the default) and 2 (verbose)
                   -pf  remove the intermediate files: can be yes (y) and no (n), default is no
                   -i -o -fi and -fo must be appear in command lines and the others are optional

                             List of the File Formats  

                file format type  abbre. index | file format type abbre. index
                Antechamber        ac       1  | Sybyl Mol2         mol2    2 
                PDB                pdb      3  | Modified PDB       mpdb    4 
                AMBER PREP (int)   prepi    5  | AMBER PREP (car)   prepc   6 
                Gaussian Z-Matrix  gzmat    7  | Gaussian Cartesian gcrt    8 
                Mopac Internal     mopint   9  | Mopac Cartesian    mopcrt 10 
                Gaussian Output    gout    11  | Mopac Output       mopout 12 
                Alchemy            alc     13  | CSD                csd    14 
                MDL                mdl     15  | Hyper              hin    16 
                AMBER Restart      rst     17 

                AMBER restart file can only be read in as additional file

                             List of the Charge Methods  

                charge method     abbre.  index | charge method      abbre. index
                RESP               resp     1  |  AM1-BCC            bcc     2
                CM2                cm2      3  |  ESP (Kollman)      esp     4
                Mulliken           mul      5  |  Gasteiger          gas     6
                Read in Charge     rc       7  |  Write out charge   wc      8

antechamber -i g98.out -fi gout -o sustiva_resp.prep -fo prepi -c resp
antechamber -i g98.out -fi gout -o sustiva_bcc.prep -fo prepi -c bcc
antechamber -i g98.out -fi gout -o sustiva_gas.prep -fo prepi -c gas
antechamber -i g98.out -fi gout -o sustiva_cm2.prep -fo prepi -c cm2
antechamber -i g98.out -fi gout -o -fo ac
antechamber -i -fi ac -o sustiva.mpdb -fo mpdb
antechamber -i -fi ac -o sustiva.mol2 -fo mol2
antechamber -i sustiva.mol2 -fi mol2 -o sustiva.gzmat -fo gzmat
antechamber -i -fi ac -o -fo ac -c gas

The usage of antechamber is very flexible. Sometimes you may need run it several times to achieve your aim. For example, a prep input file requires all the atom names to be unique. However, the version of antechamber in amber7 does not check atom name duplication at all(in this version, duplication is checked in default), you may run antechamber twice to get rid off atom name duplication. First, you may convert your file to a gaussian input file (gcrt or gzmat) or mopac input file (mopcrt, mopint), then convert it back.


Atomtype reads in an ac file and assign atom types. We have prepared four atom type definition files in $AMBERHOME/dat/antechamber, which are ATOMTYPE_AMBER.DEF (amber), ATOMTYPE_GFF.DEF (general amber force field), ATOMTYPE_BCC.DEF (AM1-BCC) and ATOMTYPE_GAS.DEF (gasteiger). You choose these file by "-p" flag. You may revise these file or write your own atom type definition files (read in by "-d" flag) according the rules. The details on defining atom types is in ATOMTYPE_GFF.DEF.

Usage: atomtype -i input_file
                -o output_file (ac)
                -f file_format(ac (the default) or mol2)
                -p amber or gaff or bcc or gas, it is suppressed by "-d" option
                -d atom_type_definition_file, optional


atomtype -i -o -p amber

This command assigns atom types for using AMBER atom type definition file.

Bondtype is a new program since amber8. It is a cpp program that reads in an ac or mol2 file and assign bond types (single (1), double (2), triple (3), aromatic single (7), aromatic double (8), delocalized (9) and conjugated (6)). In first place, bondtype reads in a parameter file (APS.DAT in $AMBERHOME/dat/antechamber) to select a set of valence states with the lowest penalty scores. Then a iterative function is applied to assign bond types for each valence state in a increasing order of penalty scores. The program halts if the bond type assignment is successful. Details please refer to our antechamber paper .


Usage: bondtype -i input file name 
                -o output file name 
                -f file format (ac or mol2)
                -j judge bond type level option, default is part
                   full  full judgement
                   part  partial judgement, only do reassignment according
                         to known bond type information in the input file

bondtype -i -o -f ac -j full
bondtype -i sustiva.mol2 -o -f mol2 -j part

These commands read in an ac or mol2 files and output an ac file with atom type information in BOND fields.


Crdgrow reads an incomplete pdb file (at least three atoms in the file) and a prep input file, and then generate a complete pdb file. It can be used to do residue mutation. For example, if you want to change one protein residue to another one, you may just keep the mainchain atoms in a pdb file and read in the prep input file of the residue you wanted, crdgrow will generate the coordinates of the missing atoms.

Usage: crdgrow -i input file name 
               -o output file name 
               -p prepin file name
               -f prepin file format: prepi (the default) or prepc


crdgrow -i ref.pdb -o new.pdb -p sustiva_int.prep

This command reads in ref.pdb (only four atoms) and prep input file sustiva_int.prep, then generates the coordinates of the missing atoms and writes out a pdb file (new.pdb).

Database is new program since amber8, it reads in a multiple record files (such as sdf or mol2) and each record is cut out and be processed with commands defined in a definition file. The keywords of how to cut record is also defined in the definition file.


Usage: database -i database file 
                -d definition file 

database -i -d define.dat

This command reads a nci database in sdf file and a definition file. For each record, commands defined in define.dat are run sequentially.

Delphigen reads in an ac file and generate the charge and radius file for delphi calculations.


Usage: delphigen -i input file name (ac)
                 -c charge file name 
                 -r radius file name 
                 -m modified pdb file name (optional)
                 -p radius parameter file name (optional)


delphigen -i -r sustiva.radius -c sustiva.crg -m sustiva.mpdb

This command reads in and generate the radius file sustiva.radius (the default radius definition file - RADIUS.DAT is in $ACROOT/dat) and the charge file sustiva.crg. A mpdb file (pdb file with radius and charge record) is generated.

Espgen reads in a gaussian (92,94,98,03) output file and extract the electrostatic potential information and output a esp file to be read by resp program.


Usage: espgen -i   input_file_name 
              -o   output_file_name 

espgen -i sustiva_g98.out -o sustiva.esp

The above command reads in sustiva_g98.out and write out sustiva.esp, which can be used by resp program.


Please select:
1. calculate the bond length parameter: A-B
2. calculate the bond angle parameter: A-B-C
3. exit


Parmcal is an interactive program to calculate the bond length and bond angle parameters, according to rules outlined in the gaff paper.

Parmchk reads in an ac file or a prep input file or a mol2 file as well as a force field file (gaff.dat in $AMBERHOME/dat/leap/parm). It writes out an additional force field file (frcmod file) with the missing parameters. Each atom type has one or several corresponding atom types for which force field parameters are exchangeable (ATCOR.DAT in $AMBERHOME/dat/leap/parm). Be careful to those problem parameters marked by "ATTN, need revision".


Usage: parmchk -i input
               -o frcmod
               -f format (prepi, prepc, ac ,mol2) 
               -p ff parmfile
               -c atom type corresponding file, default is ATCOR.DAT
               -w print out parameters that matching improper dihedral parameters
                  that contain 'X' in the force field parameter file, can be 'Y' (yes)
                  or 'N' (no), default is 'Y'

parmchk -i sustiva.prep -f prepi -o frcmod

This command reads in sustiva.prep and find the missing force field parameters listed in frcmod. The "-w" flag is recommended to set to "Y" (the default) for the current version of tleap and xleap.

Prepgen generates the prep input file from an ac file. The output file format can be prepi (internal coordinate prep) and prepc (Cartesian coordinate prep). It is recommended to use internal coordinates if the atomic sequence is not a concerned issue. In default, the program automatically generates one of the longest paths as the mainchain; however, you may also specify a mainchain yourself in the mainchain file. In this file, you can also specify which atoms to be deleted, and whether to do charge correction or not. A mainchain file is necessary to generate amino-acid-like residues, which are characterized as having one head atom and one tail atom to be connected to other residues. Sample mainchain files are in $AMBERHOME/dat/antechamber. There is a tutorial on how to generate an amino-acid-like residue.


Usage: prepgen -i  input_file (ac) 
               -o  output_file 
               -f  format (car or int, default: int)
               -m  mainchain_file 
               -rn residue_name (default: MOL)
               -rf residue_file_name (default: molecule.res)
                   -f -m -rn -rf are optional


prepgen -i -o sustiva_int.prep -f int -rn SUS -rf SUS.res
prepgen -i -o sustiva_car.prep -f car -rn SUS -rf SUS.res
prepgen -i -o sustiva_int_main.prep -f int -rn SUS -rf SUS.res -m mainchain_sus.dat
prepgen -i -o ala_cm2_int_main.prep -f int -rn ALA -rf ala.res -m mainchain_ala.dat

The above commands generate different kinds of prep input files with or without specifying a mainchain file.

Respgen generates the input files for two-stage resp fitting. The current version only support single molecule fitting. Atom equivalence is recognized automatically.


Usage: respgen -i inputfile (ac)
               -o output file 
               -f format (resp1 or resp2) 
                  resp1 - first stage resp fitting 
                  resp2 - second stage resp fitting


respgen -i -o sustiva.respin1 -f resp1
respgen -i -o sustiva.respin2 -f resp2
resp -O -i sustiva.respin1 -o sustiva.respout1 -e sustiva.esp -t qout_stage1
resp -O -i sustiva.respin1 -o sustiva.respout1 -e sustiva.esp -q qout_stage1 -t qout_stage2
antechamber -i -fi ac -o -fo ac -c rc -cf qout_stage2

The above commands first generate the input files (sustiva.respin1 and sustiva.respin2) for resp fitting, then do two-stage resp fitting and finally use antechamber to read in the resp charges and write out an ac

An Example - TP

The most common use of the antechamber program suite is to prepare input files for LEaP automatically. The starting point can be any file format supported by antechamber (pdb, mol2, sd etc.) People may use database program or write his/her own scripts to run antechamber programs sequentially. automates the process of developing a charge model, assigning atom types, and partially automates the process of developing parameters for the various combinations of atom types found in the molecule.

The following are some commands may be appeared in the scripts

1. antechamber -fi mol2 -fo prepi -i input.mol2 -o output.prepi -c bcc -j 4 -at gaff
2. parmchk -i output.prepi -o output.frcmod -f prepi

The first command can be replaced with several separated ones

a. antechamber -fi mol2 -fo ac -i input.mol2 -o -c mul
b. am1bcc -i -f ac -o -j 4
c. atomtype -i -o -f ac -p gaff
d. prepgen -i -o output.prepi -f car

Suppose you have a PDB file called tp.pdb (thiophenol) shown below.

ATOM      1  CG  TP      1      -1.959   0.102   0.795  1.00  0.00
ATOM      2  CD1 TP      1      -1.249   0.602  -0.303  1.00  0.00
ATOM      3  CD2 TP      1      -2.071   0.865   1.963  1.00  0.00
ATOM      4  CE1 TP      1      -0.646   1.863  -0.234  1.00  0.00
ATOM      5  C6  TP      1      -1.472   2.129   2.031  1.00  0.00
ATOM      6  CZ  TP      1      -0.759   2.627   0.934  1.00  0.00
ATOM      7  HE2 TP      1      -1.558   2.719   2.931  1.00  0.00
ATOM      8  S15 TP      1      -2.782   0.365   3.060  1.00  0.00
ATOM      9  H19 TP      1      -3.541   0.979   3.274  1.00  0.00
ATOM     10  H29 TP      1      -0.787  -0.043  -0.938  1.00  0.00
ATOM     11  H30 TP      1       0.373   2.045  -0.784  1.00  0.00
ATOM     12  H31 TP      1      -0.092   3.578   0.781  1.00  0.00
ATOM     13  H32 TP      1      -2.379  -0.916   0.901  1.00  0.00

(This file may be found at $AMBERHOME/test/antechamber/tp/tp.pdb). The the basic command to create a "prepin" file for LEaP is just:

antechamber -i tp.pdb -fi pdb -o tp.prepin -fo prepi -c bcc -j 4 -at gaff

This command says that the input format is pdb, output format is prepin, and the AM1-BCC charge is to be assigned, the atom type is gaff. The output file- tp.prepin is listed as below. file tp.prepin.

    0    0    2

This is a remark line
TP     INT  0
   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
   4  CG    ca    M    3   2   1     1.540   111.208   180.000  -0.11890
   5  H32   ha    E    4   3   2     1.106    67.689    -5.945   0.14320
   6  CD1   ca    M    4   3   2     1.400   120.476   114.483  -0.11330
   7  H29   ha    E    6   4   3     1.016   119.603  -105.804   0.13490
   8  CE1   ca    M    6   4   3     1.399   120.112   103.689  -0.13730
   9  H30   ha    E    8   6   4     1.172   119.429   145.095   0.13350
  10  CZ    ca    M    8   6   4     1.400   119.867    -0.280  -0.11270
  11  H31   ha    E   10   8   6     1.172   106.739   174.651   0.13280
  12  C6    ca    M   10   8   6     1.400   120.043     0.105  -0.14510
  13  HE2   ha    E   12  10   8     1.080   119.962   179.978   0.13060
  14  CD2   ca    M   12  10   8     1.400   120.059     0.129   0.01730
  15  S15   sh    M   14  12  10     1.400   120.111   179.881  -0.25610
  16  H19   hs    E   15  14  12     0.999   109.520    59.997   0.19080

  CD2   CG

  CD2  CD1   CG  H32
   CG  CE1  CD1  H29
  CD1   CZ  CE1  H30
   C6  CE1   CZ  H31
  CD2   CZ   C6  HE2
   C6   CG  CD2  S15


If the "-at" flag is set to "amber", the AMBER atom type is assigned.

    0    0    2

This is a remark line
TP     INT  0
   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
   3  DUMM  DU    M    2   1   0     1.522   111.1        .0      .00000
   4  CG    CA    M    3   2   1     1.540   111.208   180.000  -0.11890
   5  H32   HA    E    4   3   2     1.106    67.689    -5.945   0.14320
   6  CD1   CA    M    4   3   2     1.400   120.476   114.483  -0.11330
   7  H29   HA    E    6   4   3     1.016   119.603  -105.804   0.13490
   8  CE1   CA    M    6   4   3     1.399   120.112   103.689  -0.13730
   9  H30   HA    E    8   6   4     1.172   119.429   145.095   0.13350
  10  CZ    CA    M    8   6   4     1.400   119.867    -0.280  -0.11270
  11  H31   HA    E   10   8   6     1.172   106.739   174.651   0.13280
  12  C6    CA    M   10   8   6     1.400   120.043     0.105  -0.14510
  13  HE2   HA    E   12  10   8     1.080   119.962   179.978   0.13060
  14  CD2   CA    M   12  10   8     1.400   120.059     0.129   0.01730
  15  S15   SH    M   14  12  10     1.400   120.111   179.881  -0.25610
  16  H19   HS    E   15  14  12     0.999   109.520    59.997   0.19080

  CD2   CG

  CD2  CD1   CG  H32
   CG  CE1  CD1  H29
  CD1   CZ  CE1  H30
   C6  CE1   CZ  H31
  CD2   CZ   C6  HE2
   C6   CG  CD2  S15


Then parmchk is performed to find the missing parameters.

parmchk -i tp.prepin -o tp.frcmod -f prepi

For tp.prepin with gaff atom type, all parameters are there and the following is the tp.frcmod file

remark goes here






For tp.prepin with amber atom type, the following is the tp.frcmod file. It is notable that we do not read in parm94 or parm99 force field parameters, therefore, all the parameters of this molecule are missing (atom types in AMBER force fields are capital letters, whereas gaff applies smallcase letters).

remark goes here
CA 12.010        0.360               same as c2 
HA 1.008         0.135               same as hc 
SH 32.060        2.900               same as sh 
HS 1.008         0.135               same as hs 

CA-HA  344.50   1.087       same as c2-hc
CA-CA  479.10   1.387       same as ca-ca
CA-SH  255.40   1.772       same as c2-sh
SH-HS  273.30   1.337       same as hs-sh

CA-CA-HA   50.500     119.700   same as c2-c2-hc
CA-CA-CA   67.200     119.970   same as ca-ca-ca
CA-CA-SH   62.000     125.700   same as c2-c2-sh
CA-SH-HS   46.900      95.940   same as c2-sh-hs

CA-CA-CA-HA   1    6.650       180.000           2.000      same as X -c2-c2-X 
CA-CA-CA-CA   1    3.625       180.000           2.000      same as X -ca-ca-X 
CA-CA-SH-HS   1    0.500       180.000           2.000      same as X -c2-sh-X 
HA-CA-CA-HA   1    6.650       180.000           2.000      same as X -c2-c2-X 
HA-CA-CA-SH   1    6.650       180.000           2.000      same as X -c2-c2-X 
CA-CA-CA-SH   1    6.650       180.000           2.000      same as X -c2-c2-X 


  CA          1.9080  0.0860             same as ca 
  HA          1.4870  0.0157             same as hc 
  SH          2.0000  0.2500             same as sh 
  HS          0.6000  0.0157             same as hs 

If we combine gaff.dat and parm99.dat together ( gaff_parm99m.dat) and run parmchk again, the parameters already in parm99.dat does not show up in tp.frcmod.

parmchk -i tp.prepin -o tp.frcmod -f prepi -p gaff_parm99m.dat

tp.frcmod with the combined force field parameters is listed as the following:

remark goes here

CA-SH  255.30   1.772       same as c2-sh

CA-CA-SH   61.000     125.700   same as c2-c2-sh
CA-SH-HS   46.200      95.940   same as c2-sh-hs

CA-CA-SH-HS   1    0.500       180.000           2.000      same as X -c2-sh-X



It is notable that if missing parameters cannot be reliably estimated, a remark tag of "ATTN: needs revision" is placed at the end of the corresponding lines.

At last, we may load prepin and frcmod files as well as other files (such as pdb file of a protein etc) to LEaP, add count ions and water and generate topology files for sander and other AMBER programs.

The following is an example of LEaP script:

source leaprc.gaff
mods = loadAmberParams frcmod
loadAmberPrep tp.prepin
saveAmberParm TP prmtop prmcrd

You can read this into LEaP using the following command:

tleap -s -f

Suppose I (I.prepin, I.frcmod are prep input and frcmod files of I) is a inhibitor of protein P and C.pdb is the pdb file of the complex. you may apply the following LEaP script to generate topology file (C.prmtop) for the complex.

LoadAmberPrep I.prepin			//load prep input file 
LoadAmberParams I.frcmod		//load additional force field
LoadAmberParams parm99.dat		//load parm99 force field
LoadAmberParams gaff.dat		//load gaff force field
sys = loadpdb C.pdb			//load pdb file
Addions sys Cl- 0			//add count ions, suppose add Cl- to neutralize the system
solvatebox sys WATBOX216 sys 10.0	//add solvent molecules, suppose add a box water
saveAmberParm sys C.prmtop C.prmcrd

For more examples, please go to the tutorial page

Translate performs translation or rotation or least-squared fitting on a file in either pdb, ac or mol2 format. There are five "command" modes, which are

  • center
    Move an atom (specified by -a1) or the geometric center of the molecule to the Cartesian coordinate orgin.
  • translate
    Translate the molecule; the X-vector, Y-vector and Z-vector are specified by -vx, -vy, -vz, respectively.
  • rotate1
    Rotate the molecule by an amount (in degrees, specified by -d) along the axis defined by two atoms (specified by -a1 and -a2).
  • rotate2
    Rotate the molecule by an amount (in degrees, specified by -d) along the axis defined by two points (specified by ((-x1, -y1, -z1) and (-x2, -y2, -z2)).
  • match
    Do a least-squares fit, wth the reference molecule being read in with "-r" flag.


 translate -i  input file name (pdb, ac or mol2)
           -o  output file name
           -r  reference file name
           -f  file format
           -c  command (center, translate, rotate1, rotate2, match)
               center:     need -a1;
               translate:  need -vx, -vy and -vz;
               rotate1:    need -a1, -a2 and -d;
               rotate2:    need -x1, -y1, -z1, -x2, -y2, -z2 and -d;
               match:      need -r;
           -d  degree to be rotated
           -vx x vector
           -vy y vector
           -vz z vector
           -a1 id of atom 1 (0 = coordinate center)
           -a2 id of atom 2
           -x1 coord x for point 1
           -y1 coord y for point 1
           -z1 coord z for point 1
           -x2 coord x for point 2
           -y2 coord y for point 2
           -z2 coord z for point 2

translate -i nad.mol2 -f mol2 -o nad_trans.mol2 -c center -a1 0
translate -i nad.mol2 -f mol2 -o nad_match.mol2 -c match -r nad_ref.mol2
translate -i nad.mol2 -f mol2 -o nad_rotate.mol2 -c rotate2 -x1 0.0 -y1 0.0 -z1 0.0 -x2 1.0 -y2 0.0 -z2 0.0 -d 90.0

The first command translates the coordinate center of the molecule to the origin; the second command performs least-squares fitting using nad_ref.mol2 as the referential molecule; the last command rotates the molecule 90 degrees about the X-axis.

Top2mol2 reads in an AMBER topology file and a crd or rst file to produce a mol2 file that contains bond type information (one should be cautious with the bond types assigned by the program, especially for organic molecules). It is usful if one wants to quick check the sander minimized structure or the latest MD structure in rst format. Usage

Usage: top2mol2 -p  topology file name
                -c  rst or crd file name
                -o  output file name)
                -ac atom type corresponding file (optional)
                -bc bond type corresponding file (optional)
                -at atom type: sybyl (the default) or amber, optional
                -bt bond type: sybyl (the default) or amber (all set to 1), optional
                -wt keep water flag: 1 (including water) or 0 (removing water, the default), optional

translate -p dna.prmtop -c dna.prmcrd -o dna.mol2
translate -p dna.prmtop -c dna.prmcrd -o dna_wat.mol2 -wt 1

The first command produces a mol2 file by extracting the molecular topology and coordinate information in dna.prmtop and dna.prmcrd, respectively. The water molecules were excluded in default; the second command produces a mol2 file that includes water molecules by setting the "wt" flag to "1".

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