AMBER Archive (2004)

Subject: Re: AMBER: contributed parameters

From: FyD (fyd_at_u-picardie.fr)
Date: Fri Feb 20 2004 - 18:05:48 CST

Hi-,

> If I were to reproduce the results in table VI page 1368 applying the
> summary page 1367,

First, you will NOT be able to reproduce the published values... It is why we
developped RED. With RED you can control the orientation of your minimized
molecule and thus the charges are reproducible... We found that for a same
minimum, RESP charge differences up to ~ .045 e for an atomic charge can be
observed if the molecular orientation is 'controled' (or better to say 'not'-
controlled ;-) by the ab-initio software (Gaussian or GAMESS)...

> 1) Do I apply the intermolecular restraint for phosphate-joints to
> each nucleoside (G,C,A,T) and at the same time (in the first stage)
> the
> intermolecular sugar equivalencing restrain (except C1' and H1') is
> applied to the four nucleosides?

Well, I think it is clear in the Cieplak et al JCC paper, in the Summary page
1367. The listing of all the restraints is available this section: 5 different
types of restraints in the 1st RESP stage and only methyl and methylene groups
are re-fit in the second stage... This means you need 5 molecular electrostatic
potential (4 nucleosides and the DMP)...

> 2) If the approach in 1) is correct, would adding modified nucleotides
> on
> top of four regular nucleosides (G,C,A,T) and using the similar
> strategy work

Ouf!!! It means huge computer time because you have to get ab-initio data for
the 4 'normal' nucleoside minima... My understanding is that the goal of the JCC
paper was to develop charges for the REGULAR nucleotides. In your case, why not
simply using different conformations of your unusual nucleoside (you have to use
inter-conformational restraints; you can see examples in the RED manual where we
used multi-orientation fit; orientation and conformation are treated in the same
way in the RESP input...) with DMP (with inter-molecular restraints between DMP
and the different conformations used).

or why not using the Spector et al strategy as I alread told you ?

> - I mean if I should still expect similar charges for the four bases
> and their C1' and H1' atoms as generated in 1)?

We applied Cieplak et al. strategy using ONLY different conformations of an
unusual nucleoside (with DMP also) and the C1' and H1' charges were very similar
that those reported in the JCC paper for the 4 regular DNA nucleosides...

> Is that how you applied your unusual nucleotide?

Unusual means to me not the regular 4 DNA nucleosides...

Regards, Francois

F.-Y. Dupradeau
 --
The Scripps Research Institute, San Diego, CA
Faculte de Pharmacie, UPJV, Amiens, France
 --
http://www.u-picardie.fr/labo/lbpd/fyd.htm
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