[gmx-users] Charge assignment

Michael McGovern mpmcgovern at wisc.edu
Thu May 20 08:39:04 CEST 2010

Hi everyone.
  I'm working on getting parameters for a protein system that has some linker residues in it.  These linkers are nothing too strange, they just have some amine groups.  I can get bonded parameters from the prodrg server.  I know the charge groups are unreliable.  I'm using the 53A6 parameter set, and I read how the charges there were derived.  They specifically did the iteration of parameters manually to give the same charges for the same functional groups.  Does this mean I can take charges from the same functional groups in the rtp files for amino acids and use those charges in my linkers?  If it is necessary to validate, should that be done on the linkers as molecules in their acidic, unlinked form?  Thanks everyone.

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