Re: Three bonds with water in vmd from NAMD DCD

From: Natalia Ostrowska (
Date: Wed Aug 22 2018 - 04:27:42 CDT

Fix your topology file

2018-08-21 16:17 GMT+02:00 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

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