VMD-L Mailing List

From: Chang, Christopher (Christopher_Chang_at_nrel.gov)
Date: Tue Aug 09 2005 - 14:15:03 CDT

Justin,

   You're a godsend. Thanks a lot, that works great!

Cheers,

Chris

> -----Original Message-----
> From: Justin Gullingsrud [mailto:justinrocks_at_gmail.com]
> Sent: Tuesday, August 09, 2005 12:30 PM
> To: Chang, Christopher
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Atom renumbering in DCD file
>
>
> Sure, catdcd can do this. Use the "-i" option and give it the atoms
> you want to appear in the new dcd file. The list of atoms is
> zero-based, and atoms can appear in any order, as many times as you
> like.
>
> http://www.ks.uiuc.edu/Development/MDTools/catdcd/
>
> Cheers,
> Justin
>
> On 8/8/05, Chang, Christopher <Christopher_Chang_at_nrel.gov> wrote:
> > Hi,
> >
> > I am trying to analyze a NAMD dynamics trajectory of a
> protein-protein complex using CHARMM. The particular analysis
> method can't use two unconnected molecules as input, but each
> member's dynamics can be analyzed separately and the results
> added together. Unfortunately, atom numbers are retained
> during an "animate write" operation, so once atoms are
> extracted from the complex DCD file, there is a mismatch in
> atom numbers between any PSF file CHARMM builds (always
> starts at 1)and the NAMD trajectory.
> > Is there a way to offset the atom numbers in a DCD file?
> For example, if protein 2 starts at atom 3000, can it be
> extracted such that this atom becomes number 1 in a new DCD
> file, 3001 becomes 2, etc.? Even better, can certain atom
> selections be assigned ranges of numbers?
> >
> > Thanks,
> >
> > Chris
> >
> > Christopher H. Chang, Ph.D.
> > Research Associate
> > National Renewable Energy Laboratory
> > 1617 Cole Blvd., Mail Stop 1608
> > Golden, CO 80401
> > Phone (303) 275-3751
> > Fax (303) 275-4007
> >
> >
> >
>
>
> --
> The spirit of Plato dies hard. We have been unable to escape the
> philosophical tradition that what we can see and measure in the world
> is merely the superficial and imperfect representation of an
> underlying reality.
> -- S.J. Gould, "The Mismeasure of Man"
>