[gmx-users] free energy calculation " State B has non-zero total charge: 5.800000e+01 "

Chunxia Gao chunxia.gao at chem.gu.se
Wed Nov 30 22:09:32 CET 2011

Dear gmx users:

I am using the free energy to calculate the ligand binding affinity to protein, during the decouple process, I need to put some restraint between the protein and the ligand, e.g. distance restraint.

But distance restraint is only for intramolecular, so I need to make a hybrid [moleculetype] section that includes the protein and the ligand, which means the ligand sort of  becoming a residue of the protein. In this case, I do not know how to put my ligand in the couple-moltype? or I need to manually put all these state B for the ligand? 

Anyway, so I manually put all these B-state parameters for the ligand, as I turned the B state charge to zero, when I did the grompp, it showed up a note:  State B has non-zero total charge: 5.800000e+01. so what does it mean? What can I do for this?

Will be really appreciated for answering back.


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