VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Apr 12 2018 - 14:57:32 CDT

+1 for using a different representation. VDW is awesome, and usually you just don't show your waters. :)

-Josh

On 2018-04-12 12:14:31-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:

This is a well-known artifact due to the fact that many simulation packages (but not NAMD, oddly enough) flag rigid water molecules by putting a bond between the hydrogen atoms inside the topology. I don't believe there is any automated solution to the problem other than to: 1) infer connectivity by some method other than the topology (e.g. a PDB) , 2) manually remove the bond, or 3) use a different representation.

HTH,
BKR

On Thu, Apr 12, 2018 at 10:03 AM, Stefano Guglielmo <stefano.guglielmo_at_unito.it<mailto:stefano.guglielmo_at_unito.it>> wrote:
Dear vmd users,
I'm not sure whether this is an issue for vmd list: but I generated a hydrated system with amber force field (AmberTools16), but when visualizing the system in VMD water molecules appear as triangles, as if there were also a bond between the two hydrogen atoms.
Does anyone has an idea about the reason?

Thanks
Stefano 

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Stefano GUGLIELMO PhD
Assistant Professor of Medicinal Chemistry
Department of Drug Science and Technology
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