AMBER Archive (2004)

Subject: Re: AMBER: Test Calculation of atomic charges (RESP) for RNA bases

From: FyD (
Date: Mon Sep 13 2004 - 16:59:11 CDT

Dear Vlad,

> Thank you very much for your advices and answers. Just a few remarks:
> RN-6r column in my previous email means that only one molecule was used
> with 6 reorientations. And indeed I got convergence (~0.02) between
> those charges and the ones calculated with multi-RN fit. Second,
> regarding what Francois I am not going to mix reproducible
> charges and non-reproducible charges. I meant that I will calculate that
> charges by a multi-RN fit using both the new nucleotides and the old ones.

Ok, sorry I did not understand this part.

> I generally agree that if one can properly explain MD behaviour with
> a aset of charges they should be ok....but what i am actually wondering
> is .. if I dont plan to run MD calculations with these analogues but I
> am just interested in having them parameterized.
> One last question: Are the differences observed especially on the
> atoms of the RG residue acceptable ???

I am a little surprised by the differences you got between RG and Multi-RN for
the N1 atom for instance i. e. diff = 0.12. My guess is that such differences do
not originate ONLY from an orientation difference (although you never know).
Indeed, as I told you the max diff. induced by molecular orientation diff. we
found was .07, and .04 was a difference often observed. So something else might
be responsible of such a higher difference.

- In R.E.D. we use Opt=Tight in the geometry optimization to 'force' the
accuracy of the target minimum. I think it is always possible that the minima
you got might be different from the ones calculated in 1994-1995... As said
Piotr, at that time it was more difficult to get a nucleotide optimized.

A good example of this problem is the methyl rotamers closed to a carbonyl which
are responsible of quite strange charge diff. Did you try to compare the charges
of methyl rotamers of NMA ? The minima present almost the same energy but the
RESP charges are really different...

- The orientation of DMP can induce tricky results. See
The question is: which CH3O group is defined as the number X or the number Y in
the inter-molecular restraints ? This is ambigous.

There are so much parameters that it is difficult to say, the most random being
that everybody is human and that errors can be very easily done in particular
in tables of numbers and/or RESP inputs... It is also a reason why we decided
to wrote R.E.D. to provide an automatic/rigorous way to derive RESP and ESP
charges to limit the potential number of errors.

I hope this helps, regards, Francois

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