AMBER Archive (2005)

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

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Mon Jun 20 2005 - 20:51:11 CDT

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
  ---------------------------------------------------------------
  - 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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