From: Chitrak Gupta (
Date: Thu Oct 15 2015 - 09:32:29 CDT

Hi Saumik,

I don't usually use the autopsf (maybe someone else on the thread could
comment more on that). But a quick look at it tells me that you probably
need to add the water topology file along with the default file that you
mentioned. I think you can download the latest CHARMM topology files from
this website

However, do note that the latest files will be CHARMM36 whereas the one you
have mentioned is CHARMM27. I don't know if it is a good idea to mix (i.e.
use protein topologies from CHARMM27 and water topology from CHARMM36). You
might want to use the latest, CHARMM36 version for everything.


On Thu, Oct 15, 2015 at 9:41 AM, Saumik Sen <> wrote:

> 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.
> Thanks,
> With Regards,
> Saumik
> 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