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.
Ref:http://ambermd.org/tutorials/basic/tutorial4b/
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)

Table of Contents

Overview

Tutorial Following

Notice

IP4