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 corresponding energy barriers generated by QM
computations, which seem 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 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
looks similar to a QM-generated PES curve.
Thus, I have two questions here (or the paramfit developers could take my
questions as a request)
1) Are there 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, then 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 fit the MM-generated PES curve to
QM-generated PES curve.
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
