jinzhezenggroup/computational-chemistry-agent-skills/antechamber

Name: antechamber
Author: jinzhezenggroup

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jinzhezenggroup/computational-chemistry-agent-skills
molecular-dynamics/antechamber/SKILL.md
Updated 16 Sep 2026
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A command-line tool in AmberTools for preparing small molecules or non-standard residues within GAFF/AMBER-compatible chemical space for molecular mechanics simulations, by automating atom/bond typing, charge generation or import, and force-field–compatible input generation. USE WHEN you are working in AMBER, dealing with molecules not covered by standard force fields, and already have a structure that can be processed (e.g., pdb, mol2, ac, gout). Typical use cases include parameterizing ligands or modified residues (assigning atom/bond types, generating or reading partial charges), converting structures from upstream tools into mol2/prepi formats, and preparing topology-ready inputs for downstream tools such as LEaP. DO NOT USE for standard residues, metal complexes, inorganic systems, or when no valid molecular structure is available (e.g., only SMILES).

Install

npx vskill@latest install jinzhezenggroup/computational-chemistry-agent-skills/antechamber

SKILL.md

antechamber

antechamber is a command-line tool for parameterizing small organic molecules or non-standard residues for molecular mechanics simulations.

Quick Start

Run antechamber:

bash

antechamber [-i INPUT_FILE] [-fi INPUT_FORMAT] [-o OUTPUT_FILE] [-fo OUTPUT_FORMAT] [options]

Command Line Usage

text

Usage: antechamber -i     input file name
                   -fi    input file format
                   -o     output file name
                   -fo    output file format
                   -c     charge method
                   -cf    charge file name
                   -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
                          radius: only read in radius
                          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, overrides input file, default is MOL
                   -rf    residue topology file name in prep input file,
                          default is molecule.res
                   -ch    check file name for gaussian, default is 'molecule'
                   -ek    mopac or sqm keyword, inside quotes; overwrites previous ones
                   -gk    gaussian job keyword, inside quotes, is ignored when both -gopt and -gsp are used
                   -gopt  gaussian job keyword for optimization, inside quotes
                   -gsp   gaussian job keyword for single point calculation, inside quotes
                   -gm    gaussian memory keyword, inside quotes, such as "%mem=1000MB"
                   -gn    gaussian number of processors keyword, inside quotes, such as "%nproc=8"
                   -gdsk  gaussian maximum disk usage keyword, inside quotes, such as "%maxdisk=50GB"
                   -gv    add keyword to generate gesp file (for Gaussian 09 only)
                          1    : yes
                          0    : no, the default
                   -ge    gaussian esp file generated by iop(6/50=1), default is g09.gesp
                   -tor   torsional angle list, inside a pair of quotes, such as "1-2-3-4:0,5-6-7-8"
                          ':1' or ':0' indicates the torsional angle is frozen or not
                   -df    am1-bcc precharge flag, 2 - use sqm(default); 0 - use mopac
                   -at    atom type
                          gaff : the default
                          gaff2: for gaff2 (beta-version)
                          amber: for PARM94/99/99SB
                          bcc  : bcc 
                          abcg2: abcg2 
                          sybyl: sybyl 
                   -du    fix duplicate atom names: yes(y)[default] or no(n)
                   -bk    component/block Id, for ccif
                   -an    adjust atom names: yes(y) or no(n)
                          the default is 'y' for 'mol2' and 'ac' and 'n' for the other formats 
                   -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: 0(brief), 1(default) or 2(verbose)
                   -eq    equalizing atomic charge, default is 1 for '-c resp', '-c bcc', '-c abcg2' and 0 for the other charge methods 
                          0    : no use
                          1    : by atomic paths 
                          2    : by atomic paths and structural information, i.e. E/Z configurations 
                   -pf    remove intermediate files: yes(y) or no(n)[default]
                   -pl    maximum path length to determine equivalence of atomic charges for resp, bcc and abcg2,
                          the smaller the value, the faster the algorithm, default is -1 (use full length),
                          set this parameter to 10 to 30 if your molecule is big (# atoms >= 100)
                   -seq   atomic sequence order changeable: yes(y)[default] or no(n)
                   -dr    acdoctor mode: yes(y)[default] or no(n)

File Formats

File Format Type	Abbreviation	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
Jaguar Cartesian	jcrt	18
Jaguar Z-Matrix	jzmat	19
Jaguar Output	jout	20
Divcon Input	divcrt	21
Divcon Output	divout	22
SQM Input	sqmcrt	23
SQM Output	sqmout	24
Charmm	charmm	25
Gaussian ESP	gesp	26
geostd cif	ccif	27
GAMESS dat	gamess	28
Orca input	orcinp	29
Orca output	orcout	30
pdbqt	pdbqt	31

NOTE: AMBER restart file can only be read in as additional file.

Charge Methods

Charge method	Abbreviation	Index
RESP	resp	1
AM1-BCC	bcc	2
CM1	cm1	3
CM2	cm2	4
ESP (Kollman)	esp	5
Mulliken	mul	6
Gasteiger	gas	7
ABCG2	abcg2	8
Read in charge	rc	9
Write out charge	wc	10
Delete Charge	dc	11

NOTE:

RESP charge method requires a Gaussian output file with ESP data (-fi gout), a Gaussian ESP file (-fi gesp) or a GAMESS dat file (-fi gamess) as input.
CM1 and CM2 charge methods require specific interfaces and are not recommended for general use.
ESP (Kollman) charge method requires a Gaussian output file with ESP data (-fi gout) as input.
Gasteiger charge method will ignore the net molecular charge and assign charges based on atom types and connectivity, which may not be suitable for charged molecules.
Read in charge method requires a charge file (-cf CHARGE_FILE) with a whitespace-separated list of floating-point charges, ordered exactly as atoms in the input structure, with no indices, labels, or extra columns.

Parameter Selection Heuristics

Unmentioned options are recommended to be left at their default values unless you have specific needs or understand the implications of changing them. The following heuristics can help guide your choices for the most commonly used options:

Basic IO

-i, -fi, -o, -fo must appear.
-a, -fa, -ao are used when you want to read in additional information from another file and overwrite specific attributes in the input file. WARNING: this can lead to mismatches if the additional file does not correspond to the input file in atom order.
-rn is used when you want to specify a custom residue name in order to increase readability.

Charge Generation

-c is used when the input file does not contain usable atomic charges, including cases where (1) the input file lacks charge information, (2) the existing charges cannot be directly interpreted (e.g., they originate from upstream quantum chemistry calculations where charges are not explicitly mapped one-to-one to atoms or are stored in complex formats), or (3) new charges need to be recalculated using a chosen method.
Typically, -c bcc is recommended for general use. Unless higher accuracy is required or the system is sensitive to charge details, in which case -c resp with a properly prepared Gaussian output file is recommended. The other charge methods are generally not recommended for typical use cases.
-cf is only used when -c rc is specified, otherwise it will be ignored.
-nc is required when charges need to be calculated and the net molecular charge is not zero. It will be ignored if there is no charge calculation.

Calculation Control

-ek is not recommended for general use. If additional mopac or sqm keywords are needed, it is recommended to run mopac or sqm separately.
-gk, -gopt, -gsp, -gm, -gn, -gdsk, -gv, -ge should never be used. If a gaussian job is needed, use external Gaussian instead.

Atom Type Assignment

-at is used when the input file does not contain usable atom type information.
Typically, -at gaff2 is recommended for general use. Unless you are parameterizing a modified residue that must be fully consistent with the standard AMBER force fields, in which case -at amber should be used to ensure compatibility and higher accuracy. The other atom type options are generally not recommended for typical use cases.

Common Examples

Convert antechamber format to Sybyl Mol2

bash

antechamber -i input.ac -fi ac -o output.mol2 -fo mol2

Convert antechamber format to Sybyl Mol2, and use charges from additional file instead

bash

antechamber -i input.ac -fi ac -o output.mol2 -fo mol2 -a additional.mol2 -fa mol2 -ao crg

Convert antechamber format to Sybyl Mol2, and use read in charges

bash

antechamber -i input.ac -fi ac -o output.mol2 -fo mol2 -c rc -cf charges.txt

Convert antechamber format to Sybyl Mol2, and assign AMBER atom types

bash

antechamber -i input.ac -fi ac -o output.mol2 -fo mol2 -at amber

Convert antechamber format to Sybyl Mol2, and rename residue to LIG

bash

antechamber -i input.ac -fi ac -o output.mol2 -fo mol2 -rn LIG

Convert PDB to Sybyl Mol2, use AM1-BCC method to calculate charges with net molecular charge -1 and assign GAFF2 atom types

bash

antechamber -i input.pdb -fi pdb -o output.mol2 -fo mol2 -c bcc -nc -1 -at gaff2

Convert Gaussian output to Sybyl Mol2, use RESP charges method and assign GAFF2 atom types

bash

antechamber -i input.gout -fi gout -o output.mol2 -fo mol2 -c resp -at gaff2

Convert Gaussian output to Sybyl Mol2, but use AM1-BCC method to recalculate charges with net molecular charge -1 and assign GAFF2 atom types

bash

antechamber -i input.gout -fi gout -o output.mol2 -fo mol2 -c bcc -nc -1 -at gaff2

References

antechamber Documentation

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Source

SKILL.md in the repositoryCheckingmolecular-dynamics/antechamber/SKILL.md

Popularity

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Repository forks: 24
7-day trend score: 24

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