I am trying to set up a simulation of a protein with the MARTINI
force field.
Two of the histidines in the protein are judged to be protonated and
thus charged. This histidine is not described in the MARTINI force
field as far as I can tell?
No there is no parameters for charged histidines.
I thought I could modify my way out of it by simply changing one of
the SP1 beads to an SQd bead,
That is probably the best you can do. There are no partitioning data
for it so
you are on your own there! Be sure not to have overestimated
interactions.
and go with the same bonded interactions as for a regular histidine,
it is reasonable.
but my problem is that I can find no
parameters for non-bonded interaction with a charged ring bead.
Well in the file:
http://md.chem.rug.nl/cgmartini/images/parameters/martini_v2.1.itp
there are non-bonded parameters for SQd!
Does anyone have a solution to my problem?
Regards
Lea
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