you need to clearly differentiate between energy of the dihedral cosine
series, and energy of the molecule as you rotate the bond. they aren't the
same (because the energy as you rotate has many contributions). the former
can be calculated with some equations and the appropriate parameters, the
latter needs an actual MM calculation as you rotate the bond.
On Sun, Mar 6, 2011 at 5:46 PM, david condon <dec986.gmail.com> wrote:
> Hello All,
>
> I am writing up my manuscript now, and I would like to produce a
> figure comparing modified torsion parameters made by an older, more
> experienced member of my group against standard AMBER parameters.
>
> The files he made are frcmod.parmCHI.LNA and LNA.residues.parmCHI.lib.
> After reading these files, I didn't see anything that would provide
> information about how to display the torsion energy vs. angle
> information.
>
> I have also checked out /programs/amber9/dat/leap and many other
> directories within AMBER without seeing anything pertinent.
>
> How would I go about finding out how to display his modified torsions
> against the standard AMBER torsions?
>
> Thanks for your time,
> -Dave
>
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Received on Sun Mar 06 2011 - 15:30:02 PST
