RE: Starting out with NAMD/VMD

From: Jacob Poehlsgaard (
Date: Tue Jun 06 2006 - 04:38:53 CDT

Hi Nisha

 I've run into exactly the same problem.
 If I delete the CMAP block from the parameter file, both autopsf and NAMD
runs fine with the combined NA/Protein system. I'm not quite sure if that is
the "correct" way to solve this problem, I feel like somebody who just
yanked out a handful of wires to make my computer work.

> 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 ..

Med venlig hilsen

Jacob Pøhlsgaard

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