[gmx-users] Angle deformation of Triphosphate moiety with charge -4 ?..

Alberto Sergio Garay sgaray at fbcb.unl.edu.ar
Tue Jun 5 00:03:53 CEST 2012

Hi all

I'm trying to simulate a UTP (Uridin Tryphosphate) with charge -4:

      O(-)  O(-)  O(-)
      |     |     |
      |     |     |
      O     O     O

I've used the triphosphate  charge parameters published by Oliveira et  
al(1). They used the RESP procedure after calculation of the  
Electrostatic Potential employing Quantum Mecanics calculation with  
6-31(d)* basis sets. In that work they needed to replace the  
triphosphate moiety with charge -3 (which is the one parametrized for  
ATP in the forcefield G43a1) by one with charge -4, like me.

I tried to minimize my UTP molecule in vacuo using that charge set and  
I found that the triphosphate moiety distorted their bending angles  
severely. When I use charge 0 on the triphosphate moiety (during  
minimization) the structure conserved its chemical sense (a tetraedral  
structure). Then I used a charge set similar to that of the  
Triphosphate moiety parametrized in ATP G43a1 and everything went OK.  
So I think that the problem is that the new charge set (-4) has very  
high partial charge on each atom which produce a huge interaction  
between each phosphate moieties.

How can I manage this problem? May be I'm doing something wrong?

[1] A. S. F. Oliveira, A. M. Baptista, and C. M. Soares, J. Phys.  
Chem. B 114, 5486 (2010).

Thank you in advance.


Dr. Sergio Garay
Facultad de Bioquimica y Cs. Biológicas
Universidad Nacional del Litoral
Santa Fe - Argentina
C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221

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