[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
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Peter C. Lai | University of Alabama-Birmingham
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