Re: [AMBER] How to add metal ions?

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Wed, 17 Jul 2013 16:09:30 +0200

Hi,

> We want to do some computations about the interaction between the metal
> ion and a small molecular. MD simulation is the first step. But we don?t
> know how to generate initial files just like ?prmtop ?and ?inpcrd? files
> including metal ion and the molecular. How to add the metal ion into the
> small molecular? Could anyone help us or give me some examples about this?

You might be interested in using R.E.D. Server at
q4md-forcefieldtools.org (or better R.E.D. Server Development)

See for instance a project in R.E.DD.B.:
http://q4md-forcefieldtools.org/REDDB/projects/F-88/
http://q4md-forcefieldtools.org/REDDB/projects/F-89/

then, once the force field library is generated you could load it in LEaP:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#1

more generally see tutorials at:
http://q4md-forcefieldtools.org/Tutorial/

regards, Francois



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Received on Wed Jul 17 2013 - 07:30:03 PDT