Hello Saikat,
I worked in a system containing a small molecule with a phosphate moiety,
and used GAFF as force field.
I experienced problems with some of its H overlapping O atoms, but
fortunately, it's a well know issue, solved by changing just some LJ
parameters of O, as reported in this paper: J. Chem. Theory Comput., 2012,
8 (11), pp 4405–4412 DOI: 10.1021/ct300613v (
https://pubs.acs.org/doi/full/10.1021/ct300613v?src=recsys).
I don't know your system, but maybe you can use GAFF, or another amber
force-field and use those adaptations.
Best Regards
Em seg, 27 de ago de 2018 às 12:10, Saikat Pal <saikatpaliitg.yahoo.com>
escreveu:
> Dear all,Are there any forcefield present of bioorganic polyphosphate in
> AMBER.
>
> Thanks and Regards,
> Saikat Pal
>
>
>
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>
--
Alechania Misturini
Mestranda em Físico-Química
Bacharel e Licenciada em Química
Grupo de Estrutura Eletrônica Molecular –〈
GE
⎜
EM
〉
*Departamento de Química – CFM*
*Universidade Federal de Santa Catarina – Brasil*
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Received on Mon Aug 27 2018 - 09:00:02 PDT
