[gmx-users] Free Energy calcualtions
Sai Kumar Ramadugu
sramadugu at gmail.com
Wed Apr 25 23:05:05 CEST 2012
Hi Gromacs Users,
I want to mutate a glutamate in my protein to alanine in presence of a
With glutamate, the protein charge is -3. To neutralize the system, I added
Now when I mutate GLU to ALA, the charge in state_B will be +1 (protein -2
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+
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.
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