[AMBER] Tracking ligand position throughout equilibration stages

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Sat, 11 Jan 2020 15:21:37 +0000

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?


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Received on Sat Jan 11 2020 - 07:30:01 PST
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