Re: psf-generation.

From: Peter Freddolino (
Date: Fri Aug 01 2008 - 00:06:19 CDT

Hi Soniya,
did you split each chain into a separate pdb file, as in the namd
tutorial? Do any of your chains have duplicated residue IDs? Do you see
any odd console output while running psfgen? There is a limit to the
number of atoms a psf (in the format's current incarnation) can hold,
but I guarantee that you're not reaching it here.

yambem soniya wrote:
> hi,
> I tried to generate a psf of an oligomer which consists of above
> 16,000 atoms.But the result shows only around 3500 atoms? Is there a
> limitation on the number of atoms for which I can generate a psf ?
> Thanks
> -soniya

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