solvateBox will leave the crystallographic water molecules in place and
solvate around then. Just load in the pdb file complete with the
crystallographic waters. Solvatebox applies to the unit you are
solvating and it doesn't care whether it is protein or water or both.
On Tue, 2005-11-22 at 14:44 +0100, Vlad Cojocaru wrote:
> Dear Amber users,
> I have a question which might sound trivial but since I am using
> crystallograohic waters in the simulation for the first time, I am
> wondering how does solvateBox or solvateOct in Leap handle the
> crystallographic waters.
> I intend to keep all the crystallographic waters in my simulations
> so I would like to tell Leap that those waters are part of the
> "solute"...
>
> Best
> vlad
> --
>
> Dr. Vlad Cojocaru
> EML Research gGmbH
> Molecular and Cellular Modeling Group
> Villa Bosch
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg
> Germany
> Phone: +49-6221-533266
> Fax: +49-6221-533298
> e-mail: Vlad.Cojocaru.eml-r.villa-bosch.de
> Additional info: my home page
>
--
Cat, n.: Lapwarmer with built-in buzzer.
+---------------------------------------------------------------------+
| Andy Purkiss, School of Crystallography, Birkbeck College, London |
| E-mail a.purkiss.mail.cryst.bbk.ac.uk |
| Phone 020 7631 6869 (Work) or 0776 490 360 (Mobile) |
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Received on Tue Nov 22 2005 - 14:53:00 PST
