[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
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?
 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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