[gmx-users] query regarding atom type

sonali dhindwal sonali11dhindwal at yahoo.co.in
Sat Mar 27 15:49:27 CET 2010

Hello Sir,
Thanks for your help.
I have generated .itp file for my ligand through dundee server as I was unable to generate it through Gromacs using any force field.
So what changes should I make ?

Sonali Dhindwal

--- On Sat, 27/3/10, Justin A. Lemkul <jalemkul at vt.edu> wrote:

From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] query regarding atom type
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Saturday, 27 March, 2010, 8:14 PM

sonali dhindwal wrote:
> 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 and
> I have also included ligand .itp file in topology file.
> But nothing is working for me.

Then you haven't been changing the right thing(s).  How do you have an OA atom type in the ligand file under OPLS?  What program generated your ligand .itp file?  All OPLS atom types are of the format "opls_XXX," so if you've got anything else, you're dealing with some hybridized, non-functional topology that may in fact be trying to mix force fields.


> Please help
> Thanks in advance
> --
> Sonali Dhindwal
> ------------------------------------------------------------------------
> The INTERNET now has a personality. YOURS! See your Yahoo! Homepage <http://in.rd.yahoo.com/tagline_yyi_1/*http://in.yahoo.com/>.

-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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