Re: vmd-l: Re: dcd files generated with catdcd

From: J. Rui Rodrigues (
Date: Fri Apr 30 2004 - 14:02:49 CDT

I usually do this in VMD with the following proc:

proc writeindex {{selection} {filename} {frame 0} } {
  set fileId [open ./$filename.ind w 0640]
  set sel [atomselect top $selection frame $frame]
  puts $fileId "[$sel get index]"
  close $fileId
  $sel writepdb $filename.pdb

where selection is the selection text (e.g, "protein") and filename is the
basename for the index file (.ind) and for a pdb with the selection. In your
case, type ate vmd prompt:

writeindex "protein" your_protein

Rui Rodrigues

Giovanni <> escreveu:

> thanks a lot, but the real problem is when I try to get rid of the water
> using an index file.
> the coordinates of my protein without water are not the same as in the
> original file.
> Maybe there is something wrong in my index file ...
> I generate it using awk and reading the pdb file and I obtain a column
> with the numbers of the atoms that I want in the new dcd.
> --
> ========================================
> Giovanni Bellesia
> Theory and Computation Group
> Department of Chemistry
> University College Dublin
> Belfield, Dublin 4, Ireland
> ========================================

J. Rui Rodrigues
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:37:34 CST