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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 AntechamberAm1bcc 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
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
Example
#! /bin/csh -fv
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
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 mopac.sh
-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
----------------------------------------------------------------
Examples
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 sustiva.ac -fo ac antechamber -i sustiva.ac -fi ac -o sustiva.mpdb -fo mpdb antechamber -i sustiva.ac -fi ac -o sustiva.mol2 -fo mol2 antechamber -i sustiva.mol2 -fi mol2 -o sustiva.gzmat -fo gzmat antechamber -i sustiva.ac -fi ac -o sustiva_gas.ac -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. Usage 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
Example
atomtype -i sustiva_resp.ac -o sustiva_resp_amber.ac -p amber This command assigns atom types for sustiva_resp.ac 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
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
Example
bondtype -i sustiva.ac -o sustiva_bondtype.ac -f ac -j full
These commands read in an ac or mol2 files and output an ac file with atom type information in BOND fields. Usage 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
Example
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
Usage: database -i database file
-d definition file
Example
database -i nci.sd -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
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)
Example
delphigen -i sustiva_resp_at.ac -r sustiva.radius -c sustiva.crg -m sustiva.mpdb This command reads in sustiva_resp_at.ac 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
Usage: espgen -i input_file_name
-o output_file_name
Example
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. Usage Please select: 1. calculate the bond length parameter: A-B 2. calculate the bond angle parameter: A-B-C 3. exitExample
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
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'
Example
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
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
Example
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
Usage: respgen -i inputfile (ac)
-o output file
-f format (resp1 or resp2)
resp1 - first stage resp fitting
resp2 - second stage resp fitting
Example
respgen -i sustiva.ac -o sustiva.respin1 -f resp1
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 file-sustiva_resp.ac An Example - TPThe 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
a. antechamber -fi mol2 -fo ac -i input.mol2 -o input.ac -c mul b. am1bcc -i input.ac -f ac -o input.ac -j 4 c. atomtype -i input.ac -o input.ac -f ac -p gaff d. prepgen -i input.ac -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
molecule.res
TP INT 0
CORRECT OMIT DU BEG
0.0000
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
LOOP
CD2 CG
IMPROPER
CD2 CD1 CG H32
CG CE1 CD1 H29
CD1 CZ CE1 H30
C6 CE1 CZ H31
CD2 CZ C6 HE2
C6 CG CD2 S15
DONE
STOP
If the "-at" flag is set to "amber", the AMBER atom type is assigned.
0 0 2
This is a remark line
molecule.res
TP INT 0
CORRECT OMIT DU BEG
0.0000
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
LOOP
CD2 CG
IMPROPER
CD2 CD1 CG H32
CG CE1 CD1 H29
CD1 CZ CE1 H30
C6 CE1 CZ H31
CD2 CZ C6 HE2
C6 CG CD2 S15
DONE
STOP
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 MASS BOND ANGLE DIHE IMPROPER NONBON 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 MASS 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 BOND 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 ANGLE 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 DIHE 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 IMPROPER NONBON 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 MASS BOND CA-SH 255.30 1.772 same as c2-sh ANGLE CA-CA-SH 61.000 125.700 same as c2-c2-sh CA-SH-HS 46.200 95.940 same as c2-sh-hs DIHE CA-CA-SH-HS 1 0.500 180.000 2.000 same as X -c2-sh-X IMPROPER NONBON 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 quit You can read this into LEaP using the following command: tleap -s -f leap.in 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 quit 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
Usage
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
Example
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
Example
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". |