[gmx-users] About Bond in Topology

vidhya sankar scvsankar_agr at yahoo.com
Sat Sep 22 08:23:13 CEST 2012

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

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