From: Chang, Christopher (
Date: Fri Jun 17 2005 - 15:02:57 CDT

Hi all,

   I am using VMD to process snapshots from a Brownian dynamics run. So, I have a set of input PDB files with filenames A0001.pdb through A0100.pdb generated by the BD program. VMD reads one in at a time, selects a subset of atoms, then writes out a new PDB file with name #.pdb, where "#" ranges from 1 to 100. This is all in the attached BDanimate.tcl script.
   When this script gets to file A0096.pdb (attached, along with A0095.pdb), the strange output in the attached file VMD.strange is generated. For some reason, VMD sees 599 fragments, whereas for the other 99 structures it sees 5 fragments. There is also an "atomselect 99" line, but I would have expected "atomselect 95" at this point, assuming VMD selections number from 0. The output PDB files (attached, for 95.pdb and 96.pdb)seem fine, though.
   Anyone know what's going on?


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

 <<95.pdb>> <<96.pdb>> <<A0095.pdb>> <<A0096.pdb>> <<BDanimate.tcl>> <<VMD.strange>>

  • application/octet-stream attachment: 95.pdb
  • application/octet-stream attachment: 96.pdb
  • application/octet-stream attachment: A0095.pdb
  • application/octet-stream attachment: A0096.pdb