[gmx-users] Re: Dear Dr.Van Der Spoel

David van der Spoel spoel at xray.bmc.uu.se
Wed Sep 15 08:24:50 CEST 2010

On 2010-09-14 22.27, mohsen ramezanpour wrote:
> Dear Dr.Van Der Spoel
> I want to calculate binding fre energy between proteins and drugs.
> does Gromacs change protonation state of protein and drug itself when I
> fill my simulating box with solute?
> Or I need to use some server as PROPKA to predict and determine their
> new protonation states in binding,
> and using some server to change their protonation state and at the end
> using gromacs for Molecular dynamics of my binding problem?
> Thanks in advance for your reply
> sincrely yours
> Mohsen
GROMACS does not change the protonation state of proteins - yet. 
Algorithms are being implemented for allowing that, but that will take 
until version 5.0.

Please ask questions on the gmx-users mailing list.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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