From: nisha_at_ncbs.res.in
Date: Thu Jun 01 2006 - 02:22:21 CDT
Hi
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-
ERROR! FAILED TO RECOGNIZE CMAP
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
Nisha
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