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amber:gaff
Table of Contents
Overview
- This page is showing how to build a topology files for IP4 in amber.
- What is GAFF:
- AMBER force field ,GAFF for short.
- GAFF is compatible with the AMBER force field and it has parameters for almost all the organic molecules made of C, N, O, H, S, P, F, Cl, Br and I
- And the Ambertools antechamber, parmchk can be helped to generate *frcmod files which is needed for the generation of both the topology and the coordinate files.
- Old version:http://ambermd.org/antechamber/example.html
Tutorial Following
- add H
reduce sustiva.pdb > sustiva_h.pdb
- convert RESU_NAME: from EFZ INTO SUS,output is sustiva_new.pdb,also,number H atoms to let them part of your residue
python convert.py
convert.py: #!/usr/bin/python from pdblib.base import * prot=Mol('./sustiva_h.pdb') for res in getreses(prot): res.name='SUS' prot.renumber(1,1) prot.write('sustiva_new.pdb')
- caculate charges using AM1-BCC models
antechamber -i sustiva_new.pdb -fi pdb -o sustiva.mol2 -fo mol2 -c bcc -s 2
- Check missing bonds
parmchk -i sustiva.mol2 -f mol2 -o sustiva.frcmod
- add missing
tleap -f leap.in
leap.in: source leaprc.ff99SB source leaprc.gaff SUS = loadmol2 sustiva.mol2 check SUS loadamberparams sustiva.frcmod saveoff SUS sus.lib saveamberparm SUS sustiva.prmtop sustiva.inpcrd quit
- Usage:
tleap -f leap2.in
leap2.in: source leaprc.ff99SB source leaprc.protein.ff14SB source leaprc.gaff loadamberparams /home/panying/work/MDdock_jiangp/analysis/1.2_IP4par_incr/test/sustiva.frcmod loadoff /home/panying/work/MDdock_jiangp/analysis/1.2_IP4par_incr/test/sus.lib complex = loadpdb 1FKO_trunc_sus.pdb saveamberparm complex 1FKO_sus.prmtop 1FKO_sus.inpcrd savepdb complex 1FKO_sus.pdb quit
Notice
- please notice that after adding H atoms by using “reduce”,change atom number of them!
IP4
- ref:
- /home/panying/work/MDdock_jiangp/analysis/1.2_IP4par_incr/try_1st_IP4(blue)
amber/gaff.txt · Last modified: 2017/07/05 14:44 by 127.0.0.1
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