psfgen giving wrong structure in the autopdb file

From: Harish Srinivasan (
Date: Thu Apr 06 2017 - 01:37:29 CDT


I am trying to construct a psf file from a given pdb file. I am using an
rtf file for topology of the molecule. After the generating psf file, the
autopdb file generated has a really messed up structure.

I have attached the initial pdb & rtf files and the final generated autopdb
and autopsf files here.

What could be the reason behind this ?

Thank you

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