[gmx-users] How to fix miising atoms in a pdb file?

[Tsjerk Wassenaar]

Hi,

If you install modeller, you can also use this simple python script to fix
side chains:

###########

#!/usr/bin/env python

import sys
import modeller
import modeller.scripts

env = modeller.environ()
env.io.atom_files_directory = ['../atom_files']
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')

modeller.scripts.complete_pdb(env,sys.argv[1]).write(sys.stdout)

##########

Use as

./fix.py in.pdb > fixed.pdb


Hope it helps,

Tsjerk

On Wed, Jan 13, 2016 at 8:26 AM, Simone Bolognini <simo.bolognini at gmail.com>
wrote:

> For what I know, if you open the pdb file with SPDBV il will automatically
> fix the missing atoms. Then you should only take care of saving the new
> structure in a new pdb and you're done!
>
> Simone
> Il 13/gen/2016 08:13, "Seera Suryanarayana" <palusoori at gmail.com> ha
> scritto:
>
> > Dear gromacs users,
> >
> > I have one pdb file which does not have one atom and I need to be fixed
> > that atom in the pdb to run MD simulations. Kindly suggest me to how to
> fix
> > it. Can I mutate the residue of my interest with the same residue by
> using
> > pymol or SPDBV to fix the missing atoms?
> >
> > Thanks in Advance
> > Surya
> > Graduate student
> > India.
> > --
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-- 
Tsjerk A. Wassenaar, Ph.D.