[gmx-users] how to perform a minimization of an isolated drug

[Justin A. Lemkul]

Quoting Sergio de Alencar <sergiodealencar at gmail.com>:

> Dear folks,
>
> I apologize in advance for asking a question which might have been already
> answered by the list.
>
> What I need is to do an energy minimization of an isolated drug using
> GROMACS. I found out from a previous message that it is possibe to do using
> the PRODRG server, but I wonder if it possible to do with GROMACS.
>
> Does anyone know how to do it ?

Just like you would anything else.  Use the coordinates and topology from PRODRG
(beware that the charges are likely unsatisfactory, and ffgmx is deprecated!) as
input into grompp with an appropriate .mdp file for minimization.

-Justin

>
> Thanks a lot
> Sergio
>
> --
> Sérgio de Alencar, M.Sc
> Bioinformatics PhD Student
> Universidade Federal de Minas Gerais, Brazil
>



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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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