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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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