jinzhezenggroup/antechamber
> 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).
npx skills add https://github.com/jinzhezenggroup/computational-chemistry-agent-skills --skill antechamberantechamber is a command-line tool for parameterizing small organic molecules or non-standard residues for molecular mechanics simulations.
Run antechamber:
antechamber [-i INPUT_FILE] [-fi INPUT_FORMAT] [-o OUTPUT_FILE] [-fo OUTPUT_FORMAT] [options]
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 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 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:
-fi gout), a Gaussian ESP file (-fi gesp) or a GAMESS dat file (-fi gamess) as input.-fi gout) as input.-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.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:
-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.-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.-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.-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.-at is used when the input file does not contain usable atom type information.-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.antechamber -i input.ac -fi ac -o output.mol2 -fo mol2
antechamber -i input.ac -fi ac -o output.mol2 -fo mol2 -a additional.mol2 -fa mol2 -ao crg
antechamber -i input.ac -fi ac -o output.mol2 -fo mol2 -c rc -cf charges.txt
antechamber -i input.ac -fi ac -o output.mol2 -fo mol2 -at amber
antechamber -i input.ac -fi ac -o output.mol2 -fo mol2 -rn LIG
antechamber -i input.pdb -fi pdb -o output.mol2 -fo mol2 -c bcc -nc -1 -at gaff2
antechamber -i input.gout -fi gout -o output.mol2 -fo mol2 -c resp -at gaff2
antechamber -i input.gout -fi gout -o output.mol2 -fo mol2 -c bcc -nc -1 -at gaff2
Take jinzhezenggroup/antechamber from the repository into ~/.claude/skills for personal
use, or into .claude/skills inside a project.
The agent identifies a skill by the name field in its header. Two skills with the
same name cannot sit side by side — one of them will be ignored.