From: Chitrak Gupta (
Date: Thu Oct 15 2015 - 08:14:38 CDT

Hi Saumik,

What code did you use? Did you include the topology file for water along
with the protein topology?


On Thu, Oct 15, 2015 at 4:49 AM, Saumik Sen <> wrote:

> 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