AMBER: Re: to Francois

From: Vlad Cojocaru <>
Date: Tue, 14 Sep 2004 13:35:13 +0200

Dear Francois,
    Thanks a lot for all the answers. This discussion is very helpful.
Indeed, the most worrying is the charge on the N1 and C6 atoms of RG.
This charges are -0.4787 and 0.4770 in the amber RG residue. When I
calculated these charges using a C3'endo G nucleotide without any
orientation I got -0.5754 and 0.5691. This is already a quite
significant difference. With 6 reorientations the charges did not change
significantly anymore (-0.5677 and 0.5746). In the multimolecule fit
these charges were again increased to -0.5073 and 0.5921. With the
methyl derivative (+ reorientation) these charges are -0.5532 and
0.5630. Nevertheless from these values there is a big difference between
the amber charge and all the charges that I calculated. It is hard to
believe that all my inputs were wrong, especially that I checked and
rechecked them all the time. I will do now a test calculation also with
the C2'endo nucleotides. I will let you know how this calculation turns
up comparing to the C3'endo.
Thanks again
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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Received on Tue Sep 14 2004 - 12:53:01 PDT
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