Quoting Sophie Barbe <sbarbe.insa-toulouse.fr>:
> I would like to perform a molecular dynamic of a protein in explicit organic
> solvent: hexan or octan.
> Do you have .lib files for these solvents? could you send them to me ?
> Or otherwise could you explain me how can I generate these files?
If you want to build a box of hexan or octan, you first need to
compute charge values for hexan or octan first, selecting the
conformation you wish to include in the charge derivation procedure.
In R.E.DD.B., you have an example with cyclohexane: See the W-43, W-44
and W-45 R.E.DD.B. projects.
W-43: single conformation RESP fit; chair conf.
W-44: single conformation RESP fit; twist-boat conf.
W-45: Two conformation RESP fit; chair + twist-boat conf.
However, be aware of the warning in the "Project summary" of each project:
Warning: very bad RRMS = 0.98 !
I would strongly suggest you to read the following publication:
http://www3.interscience.wiley.com/cgi-bin/abstract/109583172/ABSTRACT?CRETRY=1&SRETRY=0
See
http://www.u-picardie.fr/labo/lbpd/REDDB/reference more generally.
Once you decided that your set of charge values is correct, you
solvate the molecule of your choice by itself in LEaP and then
equilibrate your box using sander.
See
http://amber.ch.ic.ac.uk/archive/200405/0056.html
regards, Francois
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Received on Sun Jan 28 2007 - 06:07:13 PST
