[MMTK] Re: Amber charges for molecules

Konrad Hinsen hinsen@cnrs-orleans.fr
Mon, 28 Jan 2002 19:15:55 +0100


[For technical reasons my following reply to Berit's question never
reached the list. Here it is again.]

Berit Hinnemann <Berit.Hinnemann@fysik.dtu.dk> writes:

> I would like to model molecules like NH3 or CH4, and also formamide and
> N-methylacetamide. I guess for the latter one I could use the partial
> charges from the terminations ACE and NME?

It all depends on how accurate you want to be. Lennard-Jones
parameters can generally be transferred to similar chemical
environments, but partial charges are highly sensitive to the
surrounding atoms and even the configuration. The best solution is
always to fit the partial charges to an electrostatic potential
surface obtained by quantum chemistry, that's also how the original
Amber charges were calculated. MMTK has all you need for fitting, but
you do need the quantum chemistry from somewhere else.

> But more generally: Do you know where I can find the AMBER partial
> charges for NH3 or possibly other small molecules? In an earlier email
> you wrote that you took the group definitions of ACE and NME from the
> Amber parameter and topology files, where did you get them from? I
> looked at the Amber home page, but couldn't find them there.

All the standard Amber parameter and topology files are on the Amber
Web site, that's where I got them from. Some things are a bit hidden
though.

Konrad.
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