Starting out with NAMD/VMD

Date: Thu Jun 01 2006 - 02:22:21 CDT


I have just started using NAMD and VMD to run MD on a protein-dna complex
and am running into some basic problems and request your help.

Regarding the topology file, I have used the top_all27_prot_na.rtf file
(as I didn't find top_all27_prot_na.inp file that was suggested to be used
- in the User Guide). However, when I try to generate the psf file using
VMD I get the following error messages-

Aliasing residues ..
Building segments ..
Setting patches ..
Reading residues from pdb file ..
Extracted residues from pdb file ..
Reading coordinates for segments ..
Warning: failed to set coordinates for atoms .. (only for dna - protein
works fine)
Info: guessing coordinates
Warning: poorly guessed coordinates for atoms .. (again, only for dna -
protein works fine)

VMD does generate the psf and pdb files. However, I do not know how to
rectify the errors and would appreciate your help.

With thanks and regards

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