Re: Three bonds with water in vmd from NAMD DCD

From: Giacomo Fiorin (
Date: Tue Aug 21 2018 - 10:04:42 CDT

It's possible that the solution suggested here is useful to you:

On Tue, Aug 21, 2018 at 10:19 AM Seibold, Steve Allan <>

> Hello,
> I know this has been addressed and that the psf file contains the extra
> bonds between hydrogens in water, but I don't know how to remove the bond
> from the psf file...I also saw an email where a "script" was mentioned to
> remove these bonds but I could not find that script on-line..Could someone
> send me that script? I would greatly appreciate it...
> Thanks, Steve

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

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