Re: AMBER: Test Calculation of atomic charges (RESP) for RNA bases

From: Vlad Cojocaru <>
Date: Mon, 13 Sep 2004 12:10:48 +0200

Dear Piotr and Francois,
   Thank you very much for your advices and answers. Just a few remarks:
RN-6r column in my previous email means that only one molecule was used
with 6 reorientations. And indeed I got convergence (~0.02) between
those charges and the ones calculated with multi-RN fit. Second,
regarding what Francois I am not going to mix reproducible
charges and non-reproducible charges. I meant that I will calculate that
charges by a multi-RN fit using both the new nucleotides and the old ones.
    I generally agree that if one can properly explain MD behaviour with
a aset of charges they should be ok....but what i am actually wondering
is .. if I dont plan to run MD calculations with these analogues but I
am just interested in having them parameterized.
   One last question: Are the differences observed especially on the
atoms of the RG residue acceptable ???
   Thanks again
Best wishes

Piotr Cieplak wrote:

>Hi Vlad
>Yes, you are right there are some discrepancies in the charge fitting
>using the very old (pre 1994) and current RED approach. Previously
>it was quite an effort to run geometry optimization on the whole
>nucleotides now it is much easier to do so.
>Anyway, now we trust more the multi reorientational approach to get charges.
>I don't know what is RN-6r category in your tables but apparently
>one can see some convergence when going from single RN type charge fit
>to RN-6r and Multi-RN approaches. And this would be probably a way to go.
>And charges in AMBER - yes with current technology we can think
>about changing/improving them a little more, but it would also require
>retesting of other properties in MM and most probably adjusting dihedral
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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 Mon Sep 13 2004 - 11:53:00 PDT
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