AMBER Archive (2005)

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

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Jun 22 2005 - 17:13:19 CDT

Thanks Francois,

I was reading Cornell's 95 paper, but after sending the email, I realized
that the calculations are explained in detail in Cieplak et al. 95 paper.
Thanks again.

Best,

On Wed, 22 Jun 2005, FyD wrote:

> > 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
>
> 

-- 
  Ilyas Yildirim
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