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

Justin A. Lemkul jalemkul at vt.edu
Wed Nov 30 23:00:10 CET 2011

Chunxia Gao wrote:
> 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.

I would think you could avoid all these problems by using the pull code for a 
restraint, rather than an intramolecular distance restraint.  The error with a 
net charge of +58 seems to indicate that whatever you're doing to the topology 
is turning on (likely) every charge in the system, rather than just those of 
some small part of it.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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