[gmx-users] Parameters for neutral phosho-amino acids

Michael McGovern mpmcgovern at wisc.edu
Mon Oct 26 20:12:43 CET 2009

Hi everyone.  I'm doing some simulations of a phosphorylated peptide.  Right now, I'm using the amber force field with some parameters that were obtained for charged phosphorylated amino acids in a paper I found.  Now I want to simulate uncharged phosphate groups, but the paper only gave parameters for -1 and -2 charge states.  I'm stuck on this.  I'm only missing two bond parameters.  They are the OH-P-OH angle and the HO-OH-P-OH dihedral, where the atom type names are shown below:
   O2 (-)   | |R-P-OH-HO   | |  O2
(-1 charge)
   O2   | |R-P-OH-HO    |   OH    |   HO(neutral)
Is there some way of getting these parameters?  Once that is done, I still would need to assign charges.  Does anyone have any idea what the best way forward would be?  I would prefer to stay in the amber force field, but if that's not possible I'm open to others.
Thanks for your time!

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