[gmx-users] About Bond in Topology

Peter C. Lai pcl at uab.edu
Sat Sep 22 08:30:43 CEST 2012

Also, if you have specified the bond in .top file properly then gromacs
should consider a bond there. Run some MD to see if the bond stays intact...

On 2012-09-22 02:23:13PM +0800, vidhya sankar wrote:
> Thank you Sir. For your repl
> I Would like to construct .top file for Cyclic Peptide .
> My N-terminal residue is ARG  and C-Terminal is  
> PRO .  In pdb There is Bond between N atom of ARG (First residue)  and C atom  of  PRO (Last Residue) When I Generated Topology using pdb2gmx .  But  there is No bond connectivity Between First and Last Atom .Then 
> Manually I have  Edited  .top file and I have defined  the bond Between 
> First Atom  (1) and Last atom (169) . Then I have done EM Successfully .
> My Question Is 
> Will  This  Manual Editing of .top File  create a bond or Not . 
> With Regards
> S.Vidhyasankar
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Peter C. Lai			| University of Alabama-Birmingham
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