[gmx-users] ionomer topolgy

[Justin Lemkul]

On 9/27/13 2:34 PM, Ehsan Sadeghi wrote:
> Hello Gromacs users,
>
> I am the beginner in Gromacs. I want to simulate ionomer in water. I could
> not find a pdb file for my case, and I tried to draw the ionomer in Avogadro
> software and generated the pdb file. However, gmx cannot find my residue
> names. I added my residue name to residuetypes.dat and added the residue in
> aminoacids.rtp in gromos. I does not work and it cannot find my new residue.
> What should I do?
>

Well, there are several Gromos parameter sets; have you modified and then chosen 
the correct one?  In the absence of more detail, it's hard to figure out what's 
gone wrong.

> I also have some question regarding the .rtp file. Do you I need to include [
> bonds] , [angles], [dihedrals] as well? How can I find charge and charge
> groups in the [ atoms] section.
>

You need to at least specify [bonds], from which the angles and dihedrals can be 
generated.  If you have planar groups, you need to specify [impropers] for them.

Parametrization methods vary by force field, but if you're using a Gromos 
parameter set, most of the functional groups should be easily transferable to 
new species.  If you are dealing with something totally new, then you need to 
derive the charges yourself.  Details should be available in the primary 
literature for whatever parameter set you've chosen, as well as publications by 
others.  Prepare to invest some time here; it's not necessarily trivial to 
derive the new values.

-Justin

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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