[gmx-users] query regarding atom type
sonali11dhindwal at yahoo.co.in
Sat Mar 27 19:03:03 CET 2010
Thanks a lot for your mail.
I hope it will help me.
--- On Sat, 27/3/10, durmaz at zib.de <durmaz at zib.de> wrote:
From: durmaz at zib.de <durmaz at zib.de>
Subject: Re: [gmx-users] query regarding atom type
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Saturday, 27 March, 2010, 8:56 PM
i'm doing simulation of protein-ligand systems since a few weeks and i've
been starting with a nice tutorial for acpypi (python script)
in order to create topology-files for several (42) ligands in an automized
way. works very fine so far.
changes, that i've applied to the tutorial: i don't add water at the
pdb2gmx step, but only later at the genbox step. in addition, i add the
include line for the water topology "manually" (script). however, if you
use acpypi, you should remove the coordinates/topology (section [
moleculetype ], [ atoms ], [ bonds ], ...) of the protein from the
protein.top (generated by pdb2gmx) and create a own protein.itp file
containing that information, which than needs to be included in the
restriction on acpypi: number of ligand's atoms is limited to about 200
> Hello All
> I am trying to add ions to my protein, for that I have run this command,,
> [sakshi at localhost ~/sonali]$ grompp -f ions.mdp -c protein_solv.gro -p
> topol.top -o ions.tpr
> and every time I run it, following error is coming
> Fatal error:
> Atomtype OA not found
> I am using OPLSA force field and I have a ligand in my molecule in which
> this atom type is there.
> I have tried to change the atom type after seeing force field's .itp file
> I have also included ligand .itp file in topology file.
> But nothing is working for me.
> Please help
> Thanks in advance
> Sonali Dhindwal
> Your Mail works best with the New Yahoo Optimized IE8. Get it NOW!
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
gmx-users mailing list gmx-users at gromacs.org
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Your Mail works best with the New Yahoo Optimized IE8. Get it NOW! http://downloads.yahoo.com/in/internetexplorer/
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users