From: Elsa F. Sousa Henriques (Henriques_at_fias.uni-frankfurt.de)
Date: Thu May 11 2006 - 02:11:32 CDT
Have you set 'rigidBonds' to all or water? If so, as a simple test, try
to run a few simulation steps with rigidBonds set to none ... it may
just be that psfgen made a poor initial guess of the hydrogen atoms of
your "buried" waters and ShakeH is unable to resolve it.
Hope it helps,
Elsa
Quoting Sergio Anis <sergio.anis_at_verizon.net>:
> hi everybody,
>
> i'm having some problems when i try to add water molecules to my system
>
> i need to add some water molecules inside the protein (in the active
> site), so i put oxygen atoms (classified as OH2, residue TIP3) and
> let the guesscoord to add the H
>
> when i run simulation i receive the error message: 'asymmetric water
> molecule found' and the simulation crash
>
> what does this mean?, and why this doesn't happen when the TIP3 water
> molecules are outside the protein (forming the water box)?
>
> i appreciate any help on this
>
> thanks
>
> sergio
--
Elsa Henriques, Ph.D.
Frankfurt Institute for Advanced Studies Tel: +49 (0)69 798 47502
Max von Laue Str. 1, room 1.215 Fax: +49 (0)69 798 47611
60438 Frankfurt am Main, Germany E-mail:
Henriques_at_fias.uni-frankfurt.de
http://www.fias.uni-frankfurt.de/home/solovyov/MEMBERS/henriques.html
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