Re: AMBER: cyclohexane and decalin on amber

From: FyD <>
Date: Mon, 01 Oct 2007 09:20:29 +0200

Quoting Jones de Andrade <>:

> 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.

You get charge values that do not reproduce the MEP computated by QM...

> 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.

We are working on adding extra-points in R.E.D. We might do something
wrong, but, in these alkane cases, and from all our tests the
improvements given by those extra-points are not that impressive, so

Please, consider molecule H-H, the two hydrogens must be equivalent,
the total charge of H2 is zero. This means to me that the charge of
each hydrogen has to be zero... Is it real ?

I do not know really what would be the impact of using such charge
values for alkanes in MD simulation. May be someone in the AMBER
mailing list has an idea ? From what I read, many examples of FF
parameters are developped using those charges for alkanes, and it
looks like that no problem is reported. The best example is the
CT-CT-CT-CT dihedral parameter. Here, either no answer is known, or
this is not a problem...

My feeling is that "being aware of this problem" is already a good
starting point ;-) (to be able to relativize the results obtained in
MD in case of a reviewer would discuss about this point).

Sorry, I did not help a lot. I do not have the answer.
regards, Francois

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Received on Wed Oct 03 2007 - 06:07:15 PDT
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