From: Saumik Sen (
Date: Thu Oct 15 2015 - 03:49:50 CDT

Dear Sir,

I was trying to generate a psf file for my protein pdb file using vmd
automatic psf builder. In result I was able to get the psf file but without
the pdb waters. For my protein, the intra-crystal waters play a very
crucial role in its properties.

Is there anyway to keep the pdb intra-crystal water molecules intact while
generating the psf file with hydrogen atoms added to it. I hope my question
is clear to you.

Thank you in advance,

With Regards,
Saumik Sen
IIT Bombay