[gmx-users] query regarding atom type

[Justin A. Lemkul]

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 /<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.
> 
>     -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

========================================