Re: [AMBER] Disappearing common atoms in Amber 10 with TI

From: <>
Date: Fri, 17 Jul 2009 09:53:19 +0100


> I want the vc-vh bonds that are c-h bonds to be SHAKEn, do I need to wory
> about make that explicit to Amber or would it understand given the Masses
> of the atoms?

I would explicitly make them C-dummy and H-dummys, CD and HD, but you can
quickly check if they are shaken by testing if the bonds appear in the
bonds_with_hydrogen section of the prmtop file...


Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Fri Jul 17 2009 - 10:07:30 PDT
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