I agree, if you meant by "restraint=20" that the force constant is 20, you
should expect to see much less than 1A movement if the restraints were
applied correctly. This is a very strong restraint.
On Mon, Jan 13, 2020, 5:35 AM Dr. Anselm Horn <anselm.horn.fau.de> wrote:
> Hi Debarati,
>
> another possibility to monitor the movements of the ligand within its
> binding pocket with a single variable is to rms-fit the trajetory to the
> initial receptor structure and then calculate the rmsd value of the
> ligand without fitting/superimposition. Thus, you obtain an rmsd vs.
> time plot describing the flexibility of the ligand with respect to its
> initial structure with respect to the protein environment.
>
> However, since you imposed harmonic restraints upon your ligand, you
> probably won't see large movements.
>
> Hope that helps.
>
> Regards,
>
> Anselm
>
>
> On 01/11/2020 04:21 PM, Debarati DasGupta wrote:
> > Dear users,
> > I have a naive question regarding tracking my ligand position as the
> trajectory progresses (5ns of equilibration); I have a weak ligand tethered
> to a binding pocket of a receptor and have applied restraint=20 throughout
> the minimization and equilibration steps so that it does not move out of
> the pocket.
> > But I was wondering would I be able to use cpptraj (any action commands)
> to track how much the ligand actually moves throughout my 5ns of NPT
> equilibration.
> > Is there a way to do it?
> >
> > I can write a distance script and try to find the distance of the ligand
> to the center of the binding pocket per frame (using cpptraj distance
> command), but I thought there may be another way to do it?
> >
> > Thanks
> > Debarati
> >
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>
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Received on Mon Jan 13 2020 - 02:30:02 PST
