Dear Amber community,
I have been currently developing amber parameters for a small molecule.
Rather than using GAFF, i would like to develop parameters using an AMBER
ff.
I have already determined resp charges , bond and angle parameters for the
small molecule. I have also plotted a potential energy curve determined at
the quantum computations level. I now need to optimize my potential curve
by comparing it to non- bonded potentials determined by MM. I used to know
the procedure back in 2007 and I had saved my sander input parameters for
that in my old hard disk. Unfortunately , my hard disk is unreachable and
useless now. I don't have the sander input parameters on top of my head.
Thus, I kind a got stuck here. My question is I just can't remember if I am
supposed to do one-step energy computations for increasing steps of the
torsions under vacuum or in GB implicit solvent MD conditions.
I ll appreciate it much if an amber expert out there could drop the
required sander parameters here.
Best.
Cenk Andac
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Received on Fri Jan 28 2022 - 05:00:02 PST
