Some parameters missing from phosaa14SB.xml

[rosemary-mantell-cresset]

Hi,

Recently I noticed a few parameters relating to OP that seem to be missing from phosaa14SB.xml.

These are the parameters from parm10.dat that I think might be missing from the XML: NA-P -OP 42.9 102.38 phosphohistidine OP-P -OS 100.0 108.23 OP-P -OS-CA 1 0.0 180.0 -3. phosphotyrosine CR-NA-P -OP 1 0.00 0.0 3. phosphohistidine

The input file frcmod.phosaa14SB is a bit confusing in that it defines a new atom type OP that was already defined in parm10.dat and then exactly duplicates a lot of the parameters for OP from parm10.dat in frcmod.phosaa14SB, except for those few shown above. I have done some testing with residue H1D and I have confirmed (by using tleap to generate a prmtop and then looking at the angleinfo in cpptraj) that angle parameter NA-P-OP defined in parm10.dat is used when generating parameters with AMBER. Looking at the angleinfo for the equivalent prmtop file generated by openmmforcefields (I am using ParmEd to write this file), cpptraj lists a pair of angle parameters for ND1-P-O3P and ND1-P-O2P (corresponding to NA-P-OP) that have both angles and force constants of zero, which does not seem right. Do you think the above parameters should be included in phosaa14SB.xml?

Thank you,

Rosie