AMBER Archive (2009)

Subject: Re: [AMBER] Ligand covalent bonds appear to be broken

From: moitrayee_at_mbu.iisc.ernet.in
Date: Fri Oct 30 2009 - 08:43:25 CDT

Thanks a lot.

Best Regards,
Moitrayee

> 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.
>
> Good luck!
> Jason
>
> 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
>> guess.
>>
>> --Tom
>>
>> 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
>> following
>> > two methods:
>> >
>> > 1. I convert my crds to pdbs using ptraj. The script for it using the
>> following
>> > 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
>> which
>> > 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
>> ligand
>> > 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
>> error.
>> > 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
> 352-392-4032
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