Re: About Bond Deletion

From: Axel Kohlmeyer (
Date: Thu Apr 11 2013 - 00:32:45 CDT

a) this is a VMD question and not a NAMD question. please choose the
mailing list you are posting to properly
b) a .gro file doesn't contain any bond information, so VMD tries to
reconstruct it from heuristics, which - by its very nature - doesn't
always work.
c) those bonds are mostly useless, for doing a proper simulation.
please study the NAMD tutorial to learn how to build a proper topology
for simulations with NAMD
d) VMD commands are - what a surprise - documented in the VMD user's guide.


On Thu, Apr 11, 2013 at 5:12 AM, Vidhya Sankar
<> wrote:
> 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
> S.Vidhyasankar

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

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