Re: [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3 water model

From: Karla Galdamez <>
Date: Mon, 21 May 2018 18:54:49 -0700


I hope you are well! I am trying to activate a VMD window to reformat a
restart.rst file, would anyone share how to bring forth the VMD window from
the command line?

Thank you!

On Mon, May 21, 2018 at 11:24 AM, Sadegh Faramarzi Ganjabad <> wrote:

> Hello,
> I have converted CHARMM inputs to AMBER inputs. Not sure why but there are
> extra bonds between two hydrogen atoms in the water molecules in the
> original CHARMM files. When I try to run the AMBER inputs it complains
> about those extra bonds. Here is the error I get
> Hydrogen atom 23639 appears to have multiple bonds to atoms 23638 and
> 23640 which is illegal for SHAKEH.
> Is there a way to fix the error? I cannot manually remove all extra bonds
> from the original CHARMM inputs, so I was thinking of a way to have AMBER
> ignore them.
> Thanks,
> Sadegh Faramarzi,
> Research Assistant
> West Virginia University, Department of Chemistry
> _______________________________________________
> AMBER mailing list

Karla M. Galdamez, Ph.D
Research Fellow
Chemistry and Biochemistry Department
AMBER mailing list
Received on Mon May 21 2018 - 19:00:02 PDT
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