[gmx-users] SO3- force field

[Justin A. Lemkul]

Lucio Ricardo Montero Valenzuela wrote:
> 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.

But be aware that PRODRG charges and charge groups often require modification, 
or at the very least, validation.

And use the PRODRG 2.5 (beta) server with Gromos96 - PRODRG is for ffgmx, which 
is long since deprecated.

-Justin

> Best regards
>     Lucio Montero
> Mensaje citado por Jin Hee <chemgirl at hanmail.net>:
> 
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>> Dear all,
>>  
>> 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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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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