AW: About Bond Deletion

From: Norman Geist (
Date: Thu Apr 11 2013 - 00:57:43 CDT

Hi Vidhya,


I’m not 100% sure, but does a a *.gro file contains bond information? I
think what you see is just a visualization issue when loading structure
files into vmd without bond information, like pdb. In this case, vmd guesses
bonds by distances, to show a better picture of the molecule than just a
atom cloud, this does not change the molecule for real. VMD should also tell
you something like “Determining bonds by distance search” . If you already
have a parameter file for you molecule, loading it solves this. Otherwise
there should be no problem regarding the “wrong bonds” when creating
parameters in vmd (psf).


Mit freundlichen Grüßen


Norman Geist.


Von: [] Im Auftrag
von Vidhya Sankar
Gesendet: Donnerstag, 11. April 2013 05:13
An: Namd List
Betreff: namd-l: About Bond Deletion


Dear Namd User I am beginner of VMD & Namd


I have Constructed My system (CNT wrapped bt Cyclic Petides)

But When I open My .gro file in VMD There is plenty of unusual bond (50
bonds) between Protein and CNT i want To Delete I am Not Able to Pick those
two atom Interactively ( because structure is Shabby) So i Decided To select
and delete those unusually Bonded atoms through Command prompt .it would
be Highly helpful if somebody Help me in Giving commands

I need the Commands

Thanks in Advance


With Regards


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