Dear Prof. Case,
Thank you for responding. I think I have found a workaround.
I used the minimized coordinates (to obtain the optimal MM-PES curve in my
previous post) as input in paramfit.
and paramfit determined new dihedral parameters for that.
I have been currently running an MD simulation to test the new parameters.
It has been more 2 usec of simulation
and it appears to reflect our NMR data so far. We'll see how my RNA hairpin
behaves in the long run..
it may be too early to comment in advance but
paramfit seems to be doing its job.
best regards,
Jenk
On Sat, Sep 24, 2022, 4:11 PM David A Case <david.case.rutgers.edu> wrote:
> On Fri, Sep 23, 2022, Cenk Andac via AMBER wrote:
>
> >Is it possible to use the MM-PES and QM-PES energies (shown in the figure
> >above) as inputs (BOTH OF THEM !!) in paramfit and ask paramfit to fit the
> >MM-PES energies to the QM-PES energies??
>
> No. If you wanted a different (hopefully better) MM fit, you would need to
> specify a different functional form to fit.
>
> In the end, the output of paramfit (and other similar codes) is a set of
> force field parameters. Those parameters can be used to your "MM-PES"
> energies, which allows you to make plots like to showed. But the MM-PES
> energies are just for convenience, and can't be used as inputs. The real
> output information lies in the FF parameters you obtain.
>
> ....good luck...dac
>
>
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Received on Fri Sep 30 2022 - 11:30:03 PDT
