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AMBER Archive (2005)Subject: Re: AMBER: RED and Multi-Orientation
From: FyD (fyd_at_u-picardie.fr)
Quoting Raviprasad Aduri <rpaduri_at_chem.wayne.edu>:
> I am working on deriving partial charges for modified RNA bases. I am using
We found with Piotr that deriving RESP charges for RNA nuclosides/tides is
> To my surprise the charge values are not consistent when I am going from
A .05 charge difference (induced by a mol. orientation) is very common.
It is why multi-orientation RESP/ESP fit has been implemented in R.E.D.
> I am actually taking the resp inputs produced by the RED and putting the
0.1182, OK
Yes, this part is now automatically handled in R.E.D.-III, we still have to
> I am using the "espot" file produced by the RED as my esp input file.
OK
> I am attaching both the Pseudouridine and N2-methyl Guanine data in the
I would 1st try to understand the charge orientation dependence using a simple
> 2. What is the minimum number of orientations we need to obtain reasonably
Reproducibility of RESP/ESP charges is achieved _because_ the molecular
Once again see the FAQ-I http://www.u-picardie.fr/labo/lbpd/RED/FAQ-I.htm
> 3. Why do we equivalence the polar hydrogens in the first stage fitting and
This is the way developped by the Kollman's group in 1993-1995.
Regards, Francois
-- • F.-Y. Dupradeau • DMAG EA 3901 & Faculte de Pharmacie, Amiens, France •••• http://www.u-picardie.fr/labo/lbpd/FyD.htm ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
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