AMBER Archive (2009)
Subject: Re: [AMBER] Ligand covalent bonds appear to be broken
From: Jason Swails (jason.swails_at_gmail.com)
Date: Fri Oct 30 2009 - 08:11:03 CDT
Tom is correct. You can make sure that the bonding information is "correct"
by first loading the amber topology file and loading the PDBs as frames in
that molecule. This is especially evident when you save an average pdb
structure from ptraj (it can appear as though everything is bonded with
everything else nearby). VMD will then use the prmtop file for tha
atom/bond information and use the PDBs solely for their coordinates.
On Fri, Oct 30, 2009 at 7:53 AM, Tom Joseph <ttjoseph_at_gmail.com> wrote:
> If I'm not mistaken, ptraj doesn't write bond information to PDBs. So
> VMD has to guess where the bonds are based on atom names and distances
> between atoms. In some cases bonds in your ligand exceed the canonical
> bond lengths, so VMD doesn't draw the bond. The prmtop files, on the
> other hand, have explicit bond information so VMD doesn't have to
> 2009/10/30 <moitrayee_at_mbu.iisc.ernet.in>:
> > Dear Amber Users,
> > I am facing a problem when visualizing my simulations with VMD. I am
> > two methods:
> > 1. I convert my crds to pdbs using ptraj. The script for it using the
> > actions:
> > rms first out rms @CA
> > center @CA
> > image
> > strip :WAT
> > go
> > When I load this pdbs to VMD using animatepdbs.tcl script (available at
> VMD site
> > to load multiple pdbs), everything seems allright except my ligand, in
> > some covalent bonds appear to be broken for the line or bond
> representation of
> > the ligand. However, using VDW sphere representation, I can see the whole
> > intact.
> > 2. I use another method for visualization. I directly load my
> trajectories to
> > VMD using the parameter files and crds. In this case, I find no such
> > Everything is perfectly fine in all representation types.
> > Is this some visualisation effect ? Please help me with your valuable
> > suggestions/comments.
> > Thanks a lot in advance.
> > Best Regards,
> > Moitrayee
> > --
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Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
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