Re: Generating psf files for non-proteins

From: Alessandro Pedretti (
Date: Fri Apr 09 2004 - 07:09:52 CDT

You can try to use VEGA 1.5.1 available for free at or the
on-line version at the same URL in order to create a PSF file fixing atomic
charges and assigning the atom types.
Best regards

        Alessandro Pedretti

> Hi,
> 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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