AMBER Archive (2004)

Subject: Re: AMBER: Differences in RESP charges for G in RG and DG residues

From: FyD (fyd_at_u-picardie.fr)
Date: Sat Sep 04 2004 - 05:12:33 CDT

Dear Vlad,

> The RESP atomic charges on guanine atoms (and the other bases also)
> are different in RG and DG residues. From your experience, are these
> differences significant? I mean, could one use the guanine charges from
> RG into DG residues (or the other way arround) without affecting the MM
> calculations?

Personnally, I prepared unusual nucleotide RESP charges using ONLY B-DNA type
nucleotide for B- and A-DNA simulation...

> I am asking this question because I am wondering if we derive
> charges for base analogues using N-methyl-base (which will obviously be
> different than both in the RG and DG) could these charges be used for
> both R and D residues? Or, we have to derive the charges using the whole
> nucleotide in order to be precise? Obviously the latter will take much
> more time.

I think you wonder the right questions...
I would say you derive the RESP charge using one strategy (using
multiorientation and multiconformation) and you see what you get during the MD.
If it is what you wanted, it is OK otherwise try another method for RESP charge
derivation ;-)

> Another question: was the chi angle ever taken into consideration
> when deriving the RESP charges for the nucleic acids residues, or it is
> assumed that C2'endo pucker means high-anti chi and C3'endo pucker means
> anti chi?.

- If I remember, the chi dihedral is different in a canonical oligonucleotide
B-DNA and when we optimize the nucleoside alone for RESP charge derivation.
This is another problem...

- I think the RESP charges for the whole Cornell et al. database have been
derived based on B-DNA sugar pucker and are used also in A-DNA type
simulation...

> I have done some tests and it seems that the orientation
> sugar-base affects the value of the charges on several base atoms. Also,
> in the original paper (Cieplak & al. 1995) is mentioned that there
> were calculations for the N-methyl bases but this is not detailed. I
> have obtained charges for the N-methyl-G and it would be interested to
> compare them with the original values.

- I would try different RESP charge models (i. e. A- and/or B-nucleoside type;
methyl derivative or with DMP + nucleoside) and see if they effect your MD
simulations...

- Finally, the fact that your unusual base is possibly implied in a strong
hydrogen bond is another source of important charge differences which can
strongly affect your MD simulation...

Regards, Francois
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