[gmx-users] About Presence of Bond In Topology

Peter C. Lai pcl at uab.edu
Sat Sep 22 06:39:19 CEST 2012

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
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
pcl at uab.edu			| Birmingham AL 35294-4461
(205) 690-0808			|

More information about the gromacs.org_gmx-users mailing list