Dear all,
I meet a problem in understanding how to converge the Charmm FF into
Gromat format for RNA system. In ....../charmm27.ff/ffnabonded.itp
(line 1084-1088), it says:
HN5 ON5 CN7B CN7B 9 180.0 0.0 6
HN5 ON5 CN7B CN7B 9 0.0 3.3472 3
HN5 ON5 CN7B CN7B 9 180.0 0.0 2
HN5 ON5 CN7B CN7B 9 180.0 0.0 1
HN5 ON5 CN7B CN7 9 0.0 1.2552 3
HN5 ON5 CN7B CN7 9 0.0 0.0 1
However, the original Charmm27 FF parameters are given as
(Supporting_info in [Denning, Priyakumar, Nilsson & Macerell Jr., J.
Comput. Chem. 2011, 32, 1929.])
Torsion Vn/2 (c27) Multiplicity Phase
HN5 ON5 CN7B CN7B 0.800 3 0.0
HN5 ON5 CN7B CN7B 0.000 2 0.0
HN5 ON5 CN7B CN7B 0.000 1 0.0
HN5 ON5 CN7B CN7 0.300 3 0.0
HN5 ON5 CN7B CN7 0.000 2 180.0
HN5 ON5 CN7B CN7 0.000 1 0.0
Why there is a term with Multiplicity of 6 for HN5-ON5-CN7B-CN7B in
Gromacs, but not in the original Charmm FF? and similarly a term of
Multiplicity of 2 for HN5-ON5-CN7B-CN7 in the original Charmm FF, but
not in Gromacs? Thanks a lot!
BTW: the Phase terms are also not equal to each other!
best wishes,
Baofu Qiao
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