AMBER Archive (2005)

Subject: Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends

From: FyD (fyd_at_u-picardie.fr)
Date: Wed Jun 22 2005 - 16:56:30 CDT

> I was checking out the RESP charges of some of the RNA residues: RC, RC5
> and RC3, for example. The net charge of RC is -1, while the net charge of
> RC5 and RC3 are -0.3081 and -0.6919, respectively.

& RC5 + RC3 = -1

> When I compare RC with
> RC3, only O3' and H3T charges are different. When I compare RC with RC5,
> only O5' and H5T are different. I was wondering how the charges are
> defined in 5' and 3' ends.

See Cieplak et al. J. Comput. Chem 1995, 16, 1357-1377

> Are they defined in a way such that the 3'
> residues are going to have -0.6919 net charge while 5' residues are going
> to have -0.3081 net charge? I will use this information to create my own
> 3' and 5' end for some non-standard residues. Thanks in advance.

Please read the corresponding paper.

Regards, Francois 

-- 
  F.-Y. Dupradeau
DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
The Scripps Research Institute, La Jolla, CA, USA
       --
http://www.u-picardie.fr/labo/lbpd/FyD.htm
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