antechamber

Name: antechamber
Author: jinzhezenggroup

113stars23forks

How to install antechamber?

jinzhezenggroup/computational-chemistry-agent-skills/antechamber

$npx -y skills add jinzhezenggroup/computational-chemistry-agent-skills --skill antechamber

Installs into the current project.

Summary

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

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SKILL.md

1	# antechamber
2
3	antechamber is a command-line tool for parameterizing small organic molecules or non-standard residues for molecular mechanics simulations.
4
5	## Quick Start
6
7	Run antechamber:
8
9	```bash
10	antechamber [-i INPUT_FILE] [-fi INPUT_FORMAT] [-o OUTPUT_FILE] [-fo OUTPUT_FORMAT] [options]
11	```
12
13	## Command Line Usage
14
15	```text
16	Usage: antechamber -i input file name
17	-fi input file format
18	-o output file name
19	-fo output file format
20	-c charge method
21	-cf charge file name
22	-nc net molecular charge (int)
23	-a additional file name
24	-fa additional file format
25	-ao additional file operation
26	crd : only read in coordinate
27	crg : only read in charge
28	radius: only read in radius
29	name : only read in atom name
30	type : only read in atom type
31	bond : only read in bond type
32	-m multiplicity (2S+1), default is 1
33	-rn residue name, overrides input file, default is MOL
34	-rf residue topology file name in prep input file,
35	default is molecule.res
36	-ch check file name for gaussian, default is 'molecule'
37	-ek mopac or sqm keyword, inside quotes; overwrites previous ones
38	-gk gaussian job keyword, inside quotes, is ignored when both -gopt and -gsp are used
39	-gopt gaussian job keyword for optimization, inside quotes
40	-gsp gaussian job keyword for single point calculation, inside quotes
41	-gm gaussian memory keyword, inside quotes, such as "%mem=1000MB"
42	-gn gaussian number of processors keyword, inside quotes, such as "%nproc=8"
43	-gdsk gaussian maximum disk usage keyword, inside quotes, such as "%maxdisk=50GB"
44	-gv add keyword to generate gesp file (for Gaussian 09 only)
45	1 : yes
46	0 : no, the default
47	-ge gaussian esp file generated by iop(6/50=1), default is g09.gesp
48	-tor torsional angle list, inside a pair of quotes, such as "1-2-3-4:0,5-6-7-8"
49	':1' or ':0' indicates the torsional angle is frozen or not
50	-df am1-bcc precharge flag, 2 - use sqm(default); 0 - use mopac
51	-at atom type
52	gaff : the default
53	gaff2: for gaff2 (beta-version)
54	amber: for PARM94/99/99SB
55	bcc : bcc
56	abcg2: abcg2
57	sybyl: sybyl
58	-du fix duplicate atom names: yes(y)[default] or no(n)
59	-bk component/block Id, for ccif
60	-an adjust atom names: yes(y) or no(n)
61	the default is 'y' for 'mol2' and 'ac' and 'n' for the other formats
62	-j atom type and bond type prediction index, default is 4
63	0 : no assignment
64	1 : atom type
65	2 : full bond types
66	3 : part bond types
67	4 : atom and full bond type
68	5 : atom and part bond type
69	-s status information: 0(brief), 1(default) or 2(verbose)
70	-eq equalizing atomic charge, default is 1 for '-c resp', '-c bcc', '-c abcg2' and 0 for the ot

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antechamber

113stars23forks

View on GitHub

How to install antechamber?

jinzhezenggroup/computational-chemistry-agent-skills/antechamber

$npx -y skills add jinzhezenggroup/computational-chemistry-agent-skills --skill antechamber

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# antechamber
2
3	antechamber is a command-line tool for parameterizing small organic molecules or non-standard residues for molecular mechanics simulations.
4
5	## Quick Start
6
7	Run antechamber:
8
9	```bash
10	antechamber [-i INPUT_FILE] [-fi INPUT_FORMAT] [-o OUTPUT_FILE] [-fo OUTPUT_FORMAT] [options]
11	```
12
13	## Command Line Usage
14
15	```text
16	Usage: antechamber -i input file name
17	-fi input file format
18	-o output file name
19	-fo output file format
20	-c charge method
21	-cf charge file name
22	-nc net molecular charge (int)
23	-a additional file name
24	-fa additional file format
25	-ao additional file operation
26	crd : only read in coordinate
27	crg : only read in charge
28	radius: only read in radius
29	name : only read in atom name
30	type : only read in atom type
31	bond : only read in bond type
32	-m multiplicity (2S+1), default is 1
33	-rn residue name, overrides input file, default is MOL
34	-rf residue topology file name in prep input file,
35	default is molecule.res
36	-ch check file name for gaussian, default is 'molecule'
37	-ek mopac or sqm keyword, inside quotes; overwrites previous ones
38	-gk gaussian job keyword, inside quotes, is ignored when both -gopt and -gsp are used
39	-gopt gaussian job keyword for optimization, inside quotes
40	-gsp gaussian job keyword for single point calculation, inside quotes
41	-gm gaussian memory keyword, inside quotes, such as "%mem=1000MB"
42	-gn gaussian number of processors keyword, inside quotes, such as "%nproc=8"
43	-gdsk gaussian maximum disk usage keyword, inside quotes, such as "%maxdisk=50GB"
44	-gv add keyword to generate gesp file (for Gaussian 09 only)
45	1 : yes
46	0 : no, the default
47	-ge gaussian esp file generated by iop(6/50=1), default is g09.gesp
48	-tor torsional angle list, inside a pair of quotes, such as "1-2-3-4:0,5-6-7-8"
49	':1' or ':0' indicates the torsional angle is frozen or not
50	-df am1-bcc precharge flag, 2 - use sqm(default); 0 - use mopac
51	-at atom type
52	gaff : the default
53	gaff2: for gaff2 (beta-version)
54	amber: for PARM94/99/99SB
55	bcc : bcc
56	abcg2: abcg2
57	sybyl: sybyl
58	-du fix duplicate atom names: yes(y)[default] or no(n)
59	-bk component/block Id, for ccif
60	-an adjust atom names: yes(y) or no(n)
61	the default is 'y' for 'mol2' and 'ac' and 'n' for the other formats
62	-j atom type and bond type prediction index, default is 4
63	0 : no assignment
64	1 : atom type
65	2 : full bond types
66	3 : part bond types
67	4 : atom and full bond type
68	5 : atom and part bond type
69	-s status information: 0(brief), 1(default) or 2(verbose)
70	-eq equalizing atomic charge, default is 1 for '-c resp', '-c bcc', '-c abcg2' and 0 for the ot

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