[gmx-users] ionomer topolgy

Ehsan Sadeghi esa38 at sfu.ca
Mon Sep 30 22:58:02 CEST 2013

I was pretty confident that I am modifying the right file. apparently I did not access to the main file; so I asked my supervisor and he provided me with a proper access to the files.

Thanks again Justin.

----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Monday, September 30, 2013 1:45:41 PM
Subject: Re: [gmx-users] ionomer topolgy

On 9/30/13 4:40 PM, Ehsan Sadeghi wrote:
> Many thanks Justin.
> Apparently I was modifying the .rtp file in the wrong location; now the pdb2gmx works and I can start the modelling.

In the future, make sure you're providing accurate answers to the questions 
being asked.  I asked about this at least two or three times and was always 
assured that the modifications were being done properly.  If you want free help, 
you have to make it easy!

> I also have some concern about my pdb file. i generated from my drawing in Avogadro, with some arbitrary bond length and angle. I hope  that I can find the correct bond length and angle with energy minimization; am, I right?

If done in vacuo, probably.



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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