[gmx-users] additional bond description (isopeptide bond) between two chains

Justin Lemkul jalemkul at vt.edu
Tue Feb 12 14:09:16 CET 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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