[gmx-users] topology file for thermodynamic integration

[Maik Goette]

Hi

I don't really know, if there is a tutorial.
The way how to use FEP(TI) is written in the manual quite well.
A "short" discription, of what you may want to do is:

Add dummy atoms to your topology file, which resemble the atoms of the
mutated AA.
You can insert the full AA with dummies and use energy group exclusions
or just insert the atoms as dummies, which are not able to be
"converted" from other ones of the original AA.
Then you have to insert the B-values (principles behind that are also in
the manual), in fact Atomtype, Mass and charge of the B-State.

It depends on the FF, what you have to do in the
bonds,pairs,angles,dihedrals section.
If I'm right, OPLS is able to "interpolate" the values by itself, in
others (GMX) you have to manually include the B-values in the topology
file for all atoms, that have a B-value in the atoms section.

Don't forget that, maybe atoms itself don't change, but e.g. their
partial charges . These also need B-values and for that case, their
further parameters have to be changed, too...

Perhaps you should try an ALA->GLY or some other easy perturbation.

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
        mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Hiromichi Tsurui wrote:
> Hi, all of Gromacs users;
> 
> I would like to calculate binding free-energy of protein and peptide, or 
> difference of that between wild type and mutation-containing one. I am 
> going to use thermodynamic integration method. Could anyone let me know 
> a good tutorial ? I want to know especially how to describe topology files.
> 
> Thank you.
> 
> Hiromichi
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.