From: Chang, Christopher (Christopher_Chang_at_nrel.gov)
Date: Mon Aug 08 2005 - 18:48:33 CDT

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