[gmx-users] Negative arginine?

Steven Spronk spronk at its.caltech.edu
Mon Nov 29 23:00:18 CET 2004

Hello all,

Has anyone ever attempted to perform an MD simulation by mutating an
arginine to a "negative arginine," in other words, making the side chain
of a particular arginine -1 instead of +1?  In principle, all one would
have to do would be to change the charges in the molecular topology file,

If this has been done before, is there some set of charges to place on the
atoms so that the arginine's hydrogen bonding behavior is the least

I know, to be realistic we could simply mutate it to a Glu or Asp, but we
thought that a neutral Arg run and a negative Arg run would be interesting
controls for our "wild-type" run.  Just wondering if there were any
references or if anyone has had similar experiences.


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