On 6/27/12 1:58 PM, Shima Arasteh wrote:
Dear Shounak,
So what's about the FOR residue? I can't eliminate it. I guess if I do as you
suggest, I need to add the FOR to n.tdb and then the procedure would be
different!
You do not need to add FOR to a .tdb entry. These directives are only to modify
protonation states of amines and carboxylates. I believe you tried this before,
and my comment was that such a procedure would not work (and it didn't).
-Justin
Yes, I added the FOR to rtp file on my own.
Sincerely,
Shima
----- Original Message -----
From: shounakb <[email protected]>
To: [email protected]
Cc:
Sent: Wednesday, June 27, 2012 10:22 PM
Subject: [gmx-users] Re: pdb2gmx error
Shima, I use gromacs-4.5.4. Without the FOR residue, my gmx.ff/aminoacids.rtp
file works fine for the sequence you originally specified. (pdb2gmx executes
without any errors)
I guess you added the FOR cap's topology yourself?
Justin, could this be an issue?
Sincerely,
Shounak
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--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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