[gmx-users] SO3- force field

[Lucio Ricardo Montero Valenzuela]

Hello,
You may try to separate the sulphate from the PDB file, to run pdb2gmx without
it, ant run the PRODRG program to calculate the topology file for the sulphate
(and also its structure in gromacs format). Then you can merge your topology
and structure files for the sulphate with the respective files for the system
without sulphate. The procedure is detailed on tutorials available in the web
for gromacs 3.2 and 4.
Best regards
    Lucio Montero
Mensaje citado por Jin Hee <chemgirl at hanmail.net>:

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> Dear all,
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> I want to run SO3- form that is oxidation of cys in protein  (SH --> SO3-).
> When I used pdb2gmx, SO3-'s atom type didn't define.
> Please, does anyone have experince with SO3- and can point me to reasonable
> parameter.
>  
> thanks for any comment
> Jin Hee
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> [ÇѸÞÀÏ Express]¸ÞÀϸñ·Ï°ú ¹Ì¸®º¸±â¸¦ µ¿½Ã¿¡!
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Lucio Ricardo Montero Valenzuela
Instituto de Biotecnologia, UNAM
Departamento de Biologia Molecular de Plantas
Av. Universidad 2001, Col. Chamilpa
Cuernavaca 62210
Mexico

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