Re: [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 
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"  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.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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-- 
Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] How to fix miising atoms in a pdb file?

[Simone Bolognini]

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"  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.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] How to fix miising atoms in a pdb file?

[Seera Suryanarayana]

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.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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