AMBER Archive (2007)

Subject: Re: AMBER: cyclohexane and decalin on amber

From: Jones de Andrade (johannesrs_at_gmail.com)
Date: Mon Oct 01 2007 - 00:46:44 CDT

Hi François.

Thanks a lot for thelinks and reference. I guess they will be helpfull.

Can I make one question? Well, unfortunatelly I could not yet get access to
the reference you sent me (will have to get in touch with the author for
this specific one). But, from what I could get from its abstract, it was not
fairly easy to reproduce the eectrostatic potencial around a simple molecule
like cyclohexane with only simple atomic point charges.

I wonder what would lead to such a difficult on simple alcanes for that.
Specially considering the "trick" used of placing extra punctual charges in
midle of the hidrogens. I would not in a first instance expect such problems
on such simple molecules. Could you please give me any indication of what
sort of molecule "characteristic" or "property" would lead to such problems?
I still wandering what would be a good reason for that, even considering
some kind of "polarizability effect" that first came to my mind, but I'm
absolutelly unsure on this.

Thanks a lot in advance for all help! ;)

Sincerally yours,

Jones

On 9/30/07, FyD <fyd_at_q4md-forcefieldtools.org> wrote:
>
> 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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