From: Justin Gullingsrud (justinrocks_at_gmail.com)
Date: Tue Aug 09 2005 - 13:30:08 CDT

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"