From: Saumik Sen (
Date: Thu Oct 15 2015 - 08:41:39 CDT

Dear Chitrak,

As I mentioned in my previous mail that I am using automatic psf builder in
VMD in my windows machine. It probably only
included top_all27_prot_lipid_na.inp file (since unfortunately full path is
not visible) for proteins. And I don't see any topology file for water in
the folder under VMD where all the topology files are stored. I am using
VMD 1.9.1 version.

I am waiting for your valuable suggestions.


With Regards,

On Thu, Oct 15, 2015 at 6:44 PM, Chitrak Gupta <> wrote:

> Hi Saumik,
> What code did you use? Did you include the topology file for water along
> with the protein topology?
> Best,
> Chitrak.
> 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