AMBER Archive (2007)

Subject: Re: AMBER: cyclohexane and decalin on amber

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Sun Sep 30 2007 - 02:20:29 CDT

Quoting Jones de Andrade <johannesrs_at_gmail.com>:

> I'm having some problems in order to proper simulate some decalin and
> cyclohexane derivatives with amber force field.
>
> Does anybody knows about any reference where somebody performed simulations
> with those systems? I'm having some problems with both densities and
> intermolecular energies, but I'm not quite sure if it's source is on
> simulation parameters choosen, a limitation on the basic models themselves
> or in the derivations I've done.

You might look in R.E.DD.B. http://q4md-forcefieldtools.org/REDDB/
Cyclohexane is in differents projects obtained with 1 or 2 conformations

Use the Download tool:
use for "-- Molecule name" Cyclohexane, you get three projects.

I am sure you can follow a similar strategy for decaline(s).

However, please read the "Cyclohexane" abstract carefully and look at
the RRMS value !
Read also the following publication:
http://www3.interscience.wiley.com/cgi-bin/abstract/109583172/ABSTRACT?CRETRY=1&SRETRY=0

Other publications on similar topics are available @ the Bibliography
section of R.E.DD.B.

regards, Francois

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