[gmx-users] Protonation and solvation software

Justin A. Lemkul jalemkul at vt.edu
Thu Dec 3 12:58:56 CET 2009

Lucio Ricardo Montero Valenzuela wrote:
> What is the best software for protonating and for solvating pdb files for doing
> Molecular Dynamics with GROMACS?.

The Gromacs tools themselves - pdb2gmx allows you to select protonation states 
and add back any necessary hydrogen atoms when generating the topology, and 
genbox does solvation.


>    Best regards.
>         Lucio.
> Lucio Ricardo Montero Valenzuela
> Instituto de Biotecnologia, UNAM
> Departamento de Biologia Molecular de Plantas
> Av. Universidad 2001, Col. Chamilpa
> Cuernavaca 62210
> Mexico
> ----------------------------------------------------------------
> Este mensaje fue enviado desde el servidor Webmail del Instituto de Biotecnologia.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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