[gmx-users] Oleic acid.....topology problem...

[Justin Lemkul]

On 3/28/15 11:33 PM, Kamalesh Roy wrote:
> Dear all,
>
> I am using gromacs latest version in Ubuntu...
> I am trying to simulate oleic acid in a box with some protein.
> Have made the .itp from prodrg server... incorporate the same still not
> recognizing OLA residue.
>

PRODRG parameters always require manual refinement, and the old(er) version of 
the GROMOS force field that it supports will probably have an inadequate 
description of the alkyl chains.  Look into newer parameters, e.g. those derived 
from 53A6.

> I have change the aminoacid.rtp also....
>

You shouldn't.

> Can anybody suggest me the procedure ......
>

You haven't really said what you've done, so it's pointless to guess where the 
problem is.  You haven't even said if there's a specific error that you're 
getting.  If you want free and efficient help, you need to make it easy to 
provide it.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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