AMBER Archive (2005)

Subject: Re: AMBER: Leap handling crystallographic waters

From: Furse, Kristina Elisabet (kristina.e.furse_at_vanderbilt.edu)
Date: Tue Nov 22 2005 - 11:13:57 CST

If you want the crystallographic waters to be considered solute and not solvent
for the actual simulation, I think you'll have to rename them--define a new
residue with a name sander does not recognize as solvent. If you don't rename
them, they'll get lumped in with the solvent leap adds.

Kristina

Quoting Andy Purkiss <a.purkiss_at_mail.cryst.bbk.ac.uk>:

> 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_at_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_at_mail.cryst.bbk.ac.uk |
> | Phone 020 7631 6869 (Work) or 0776 490 360 (Mobile) |
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-----------------------------------------------------------------
Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
Email: kristina.e.furse_at_Vanderbilt.Edu
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