Dear AMBER list,
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. 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. 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.
Best,
--
Ilyas Yildirim
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- Department of Chemisty - -
- University of Rochester - -
- Hutchison Hall, # B10 - -
- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
- http://www.pas.rochester.edu/~yildirim/ -
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Received on Tue Jun 21 2005 - 03:53:00 PDT
