[gmx-users] About Presence of Bond In Topology

[Peter C. Lai]

Molecular visualization programs determine bonds through distance
measurements. Especially since .gro files do not contain connectivity
information. The topology is where the bond infomration is stored.
So check there...

On 2012-09-22 12:33:31PM +0800, vidhya sankar wrote:
> 
> 
> Dear Justin Thank you for your Reply
> 
> After pdb2gmx When i Visualize the resultant .gro file  of  my cyclic peptide in VMD 
> 
> I have Observed the Bond Between  Nitrogen atom (N ) of First residue and Carbon atom (C) of Last residue   I have not observed The same bond when I open and Visualize in Chimera .  Then How Could i Confirm Whether the bond is present or Not?
> 
> Thanks in Advance
> 
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Peter C. Lai			| University of Alabama-Birmingham
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