Re: Some water molecules are missing in psf

From: Giacomo Fiorin (
Date: Fri Nov 03 2017 - 08:49:48 CDT

There is a limit in the PDB format on the residue number. You should see
that many water residue numbers are duplicated, by use of different segment


On Thu, Nov 2, 2017 at 6:33 PM, Amali Guruge <> wrote:

> Dear All,
> I want to simulate a system which contains nearly 96000 water molecules
> and 700 PEG molecules. I modeled the system and I got top and parm files
> from ParaChem. When I tried go generate psf file, it generates a pdb with
> only 9999 water molecules. What could be the reason for this? Appreciate,
> if anyone can help me.
> Thank you.

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD

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