On 2/12/13 3:30 AM, durdagis wrote:
Hello all,
I have an isopeptide bond (between Lys site chain and carboxyl terminal of
Gly) in my system and I defined this with specbond.dat and additional
residue types and I edited .rtp files using Amber ff. Although I have this
bond at the beginning (before pdb2gmx), it looks I need to add additional
description for this bond (between two different chains) at the topology
definition. How can I define it? (please see the picture, this is after
energy min.)
Visualization programs detect what they think are bonds by heuristic algorithms.
Whether or not a bond shows up in a visualization program is irrelevant. What
actually matters is whether or not the bond shows up in the topology that
pdb2gmx created. Your approach sounds correct, so you should be fine. Check
the topology to make sure the bond is there, and use simple Gromacs tools like
g_dist to ensure the effect of the bond over the course of a test simulation.
-Justin
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
