Generating psf files for non-proteins

From: Scott, Greg (
Date: Thu Apr 08 2004 - 13:08:21 CDT

I am new to NAMD and was hoping to use it to look at some smaller, non-protein systems. I have tried to use psfgen to build a psf file from a pdb file that I have generated by using steps similar to those posted in the tutorials for converting protein pdb files to psf files, but have not had any success. I have also tried to build a psf file manually, but have apparently not done that correctly either. Is it possible that my pdb file is not in the right format since I don't have any residue names? I assume that psfgen should be able to handle small systems, but I have been unable to get it to work properly. If anyone can point me in the right direction on how to generate psf files for small, non-protein molecules, I would greatly appreciate the help.
Thank you,
Greg Scott

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