[gmx-users] How to calculate the free energy difference of solvation for a Tyr-Phe mutation!
leafyoung81-group at yahoo.com
Tue Jun 27 14:08:36 CEST 2006
700AA is too much a dinosaur for MD. Perhaps you can focus on the chain
which contains that mutation.
Also, for solvation energy, you may check GBSA model available in AMBER
Mikko Hellgren wrote:
> Hi all,
> I would like to get some advice on how to calculate the free energy
> difference of solvation between two proteins, a native (about 700AA)
> and one with a single mutation of a Tyr to Phe.
> The Tyr residue is located in the exterior of the protein structure
> and involved in two hydrogen bonds from the hydroxyl group to two
> other residues in the protein.
> From CD spectra we know that the spectra is unchanged by this mutation
> and this indicate a conserved secondary structure. The structure of
> the native protein is known but not for the mutant - can one from
> these background data get support that there is only minor changes in
> the structure between the native and the mutant and that these
> changes could be modeled well with a "long" MD simulation?
> Could the Linear response theory be used for calculation of the free
> energy difference of solvation for the single mutation or do I have to
> do something a bit more fancy? Or could one perhaps use experimental
> data for solvation free energy differences between amino
> acids?....Anyhow I would like to get a suggestion on how this can be
> I would also be great-full for any suggestions of a suitable MD
> tutorial or review article on the subject.
> Thanks for any advice or comments on these not so specific questions -
> sry about that!
> Mikko Hellgren - Graduate Student
> mikko.hellgren at ki.se
> One cannot avoid making mistakes if one tries to produce a set of
> words, or of mathematical formulae, to describe nature. Nature is more
> complicated than language or mathematics. Nevertheless, one must do
> one's best to produce a set of symbols which are not to discordant
> with the facts.
> J.B.S. Haldane, preface to "What is Life?", Lindsay Drummond, 1949
> gmx-users mailing list gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
More information about the gromacs.org_gmx-users