On 3/29/15 10:42 PM, Kamalesh Roy wrote:
whenever I am running the pd2gmx it is giving me an error
"OLA not found in residue topology database"
You don't need pdb2gmx. The purpose of pdb2gmx is to generate a topology. The
purpose of PRODRG is to generate a topology (albeit, as I said, likely a
suboptimal one). So if you ran PRODRG you already have a topology and do not
need to process oleic acid via pdb2gmx.
See, for instance,
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
-Justin
On Sun, Mar 29, 2015 at 10:59 PM, Justin Lemkul <jalem...@vt.edu> wrote:
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
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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