[gmx-users] Re: About Bond breaking and usage of constraints

Justin Lemkul jalemkul at vt.edu
Wed Sep 12 19:45:35 CEST 2012

On 9/12/12 1:34 PM, vidhya sankar wrote:
> Dear justin ,
>                          Thank you fro your Reply
>                       I am doing MD for  Cyclic poly Peptide With ARG as
> N-termina and PRO as C-terminal .  I have run pdb2gmx it is oak.  . I have
> solvated and added ions successfully
> But when i Run the Energy Minimization The Bond between  N atom of  ARG and C
> atom of PRO is broken .
> What  Should i Do To keep this Bond Through entire EM and MD ?    Can i Use
> Constraints option in topology file
>   if i need to use  Constraints option What is the  Syntax  ?  Also The Bond is
> not constructed between N atom and C atom of terminal ARG and PRO residues in
> Topology

Then you already have your answer.  Bonds do not break or form during MD. 
pdb2gmx does not produce cyclic polypeptide topologies unless you have made 
appropriate modifications.  As you are observing, there is no such bond and you 
need to add it (and any other resulting bonded parameters like angles, 
dihedrals, and impropers) yourself.



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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