If you want to restrain a dihedral rotaion, you could use nmr restraints
(nmropt=1) and write an appropriate restraint file to restrain the bond
dihedral (see section 24.1 "Distance, angle and torsional restraints" in
the amber manual).
On Thu, Jul 12, 2018 at 3:19 PM, lucrecia bogado <lucre686.hotmail.com>
wrote:
> Amber List members,
>
> I'm new to Amber handling and I'm trying to solve a problem:
>
> I have been running production MD simulation of enzyme with a ligand by
> Amber14 with ff14sb force field in periodic water box, but amidic bond or
> peptide bond (CO-NH) of the ligand rotates during the dynamics
>
> I would like to know what restrictions should be placed to avoid this
> rotation or where to look for such specifications, because in the user's
> manual they are not very clear.
>
> I would appreciate your help.
>
>
> Thank you,
>
> Lucrecia
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>
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Received on Thu Jul 12 2018 - 16:00:02 PDT
