Antechamber: Amber to Gromacs Ligand topology
- Mohd Athar
- May 8, 2021
- 1 min read
Antechamber
$AMBERHOME/exe/antechamber -i *.pdb -fi pdb -o *.mol2 -fo mol2 -c bcc -s 2
$AMBERHOME/exe/parmchk -i sustiva.mol2 -f mol2 -o sustiva.frcmod
For amber to gro file
$tleap -f oldff/leaprc.ff99SB
>> source leaprc.gaff
>> SUS = loadmol2 sustiva.mol2
>> check SUS
>> loadamberparams ligand.frcmod
>> saveoff SUS sus.lib
>> saveamberparm SUS sustiva.prmtop sustiva.rst7 ligand.inpcrd
>> quit
------make a script file as script.py----
import parmed as pmd
parm = pmd.load_file('ligand.prmtop', 'ligand.inpcrd')
parm.save('ligand.itp',format='gromacs')
parm.save('ligand.gro')
run as python script.py
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