VMD-L Mailing List

From: Brian Radak (brian.radak_at_gmail.com)
Date: Thu Apr 12 2018 - 12:23:35 CDT

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> 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
>
> --
> Stefano GUGLIELMO PhD
> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
> 10125 Turin, ITALY
> ph. +39 (0)11 6707178
>
>