From: Axel Kohlmeyer (
Date: Thu Apr 10 2008 - 18:19:12 CDT

On Thu, 10 Apr 2008, L. Michel Espinoza-Fonseca wrote:

MEF> Hi all,
MEF> I want to create a new trajectory from a pdb-formatted trajectory
MEF> using VMD. The problem I'm facing is that I'm trying to write the new
MEF> trajectory with one residue having a different name (i.e., THR by
MEF> FOO). I was trying to do the following:
MEF> set all [atomselect top all frame all]
MEF> set res [atomselect top "resid 10" frame all]
MEF> $res set resname FOO
MEF> animate write pdb new_trajectory.pdb $all
MEF> However, every time I run these lines I get the following error: ERROR
MEF> > Invalid molecule id 0
MEF> Do you have any ideas on how to solve this issue?

don't use the "$all" or use "sel $all"
in the animate write. if you're lazy
just write from the GUI...


MEF> Thanks!
MEF> Michel

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.