sonali dhindwal wrote:
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 ?
The Dundee PRODRG server produces GROMOS-compatible topologies only. So you
cannot use its output for OPLS (mostly due to the fact that the ligand is
assumed to be united-atom, and OPLS-AA is an all-atom force field). In a
limited number of cases (dealing with molecules that have no hydrophobic groups
and thus no united-atom carbons), you can replace all the atom types with those
found in ffoplsaa.atp.
In the majority of cases, this won't be possible. There are several tools on
the contributed software section of the Gromacs website that can construct
topologies. You can also try using the Gromacs tool x2top, but you may have to
make additions or modifications to the ffoplsaa.n2t file to include all the
functional groups you want.
You should still always validate the results according to the original force
field literature before using them in any simulation.
-Justin
--
Sonali Dhindwal
--- On *Sat, 27/3/10, Justin A. Lemkul /<jalem...@vt.edu>/* wrote:
From: Justin A. Lemkul <jalem...@vt.edu>
Subject: Re: [gmx-users] query regarding atom type
To: "Discussion list for GROMACS users" <gmx-users@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,,
>
> [sak...@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.
-Justin
>
> Please help
> Thanks in advance
>
>
>
> --
> Sonali Dhindwal
>
>
>
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-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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