[gmx-users] MARTINI protonated histidine

Lea Thøgersen lea at birc.au.dk
Mon May 10 16:00:23 CEST 2010

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?

I thought I could modify my way out of it by simply changing one of  
the SP1 beads to an SQd bead, and go with the same bonded interactions  
as for a regular histidine, but my problem is that I can find no  
parameters for non-bonded interaction with a charged ring bead.

Does anyone have a solution to my problem?


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