[gmx-users] Free Energy calcualtions

[Sai Kumar Ramadugu]

Hi Gromacs Users,
I want to mutate a glutamate in my protein to alanine in presence of a
ligand.
With glutamate, the protein charge is -3. To neutralize the system, I added
3K+ ions.
Now when I mutate GLU to ALA, the charge in state_B will be +1 (protein -2
+ 3K+).

Right now I'm in the charge part of the mutation. Once this is successful,
I will include the VDW mutation too.

I have added the mutation details of Glu to Ala residue in the topology in
[atoms], [bonds], [angles] and [dihedrals] sections.

After I run the grompp command, the result says that my State_B topology
has +1 charge since I am not including mutation of one K+ ion to neutral K+
ion.
How can I mutate 1 particular K+ to K atom and subsequently to a dummy
atom? Since I'm using OPLS force field, we have ions.itp to be used in the
topology file, changing one K+ is making it troublesome for me to implement
in the topology file.
Any suggestions are helpful.

Thanks for your time.

Regards
Sai
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120425/a8a8f0b1/attachment.html>