AMBER Archive (2004)

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

From: Vlad Cojocaru (
Date: Mon Aug 30 2004 - 10:59:35 CDT

Dear Ambers,
    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
    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.
    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?. 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.
Thank you very much for any answers,
Best wishes

Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
home tel: ++49-551-9963204  

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