Dear Amber users,
I am working with a phosphonamide. Initially, I was using antechamber
(GAFF) to get parameters for phosphonamide and after creating the
corresponding library I got an unexpected geometry for two angles in
the minimization with explicit solvent (N-P-N, and H-N-P, eg, N-P-N
angle was dropped until ca.83 degrees, and H-N-P angle was dropped until
about 75 degrees ). Then, I was modifying the harmonic constants for
these angles by increasing their values 3 and 5 times and finally I got
a reasonable geometry after minimization.
Currently, I am trying to calculate the harmonic constants for my
special case to implement for GAFF. I was already performing ab initio
calculation at R-HF 6-31G* level for these angles by a systematic
variation of 10 degrees and I am having the corresponding curves
correlating angle variation and energy. My question is how I can scale
these energy barriers to get the harmonic constants for AMBER force
field and reproduce these curves in AMBER?
Any advice in this matter will be highly appreciate.
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Received on Fri Aug 05 2011 - 02:00:02 PDT
