Dear Amber users,
I have been using paramfit to fit PES curves generated by MM and QM.
I had posted my results in the following thread on AMBER Archive.
http://archive.ambermd.org/202209/0065.html
When I implement a single-point PES run by sander, I get energy barriers
much higher than the energy barriers generated by QM computations, which
seems very similar to the energy barriers in a PES curve generated by
paramfit as seen in the first figure in the thread above.
On the other hand, when I carry out a short restrained
minimization (restrained to a dihedral of interest) for the snapshot
coordinates of a trajectory generated by 360 degree rotations (at 5 degree
increments) about a dihedral angle, then I am able to get an MM-generated
PES curve that look s similar to a QM-generated PES curve.
I have two questions here (or the paramfit developers could take questions
as a request)
1) Are any parameter settings in paramfit for a short restrained (to a
dihedral angle of interest) minimization before fitting? For instance; it
would be really helpful if paramfit could restrain a dihedral of interest,
the run a short minimization (like 10 cycles or user-defined cycles) for
snapshots of the structure in a trajectory file, then determine potential
energies and finally the MM-generated PES to QM-generated PES.
2) Is there any option in paramfit to skip the step to generate a PES
curve by paramfit, and rather take sander (or any MM program) generated PES
energies as well QM generated PES energies as inputs and fit them.
best regards,
Cenk Andac,
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Received on Thu Sep 22 2022 - 11:00:03 PDT
