From: Nadia Elghobashi-Meinhardt (nelgho_at_gmail.com)
Date: Fri Sep 25 2020 - 02:48:06 CDT
Dear all,
I am trying to use TMD to steer a ligand in a protein
to a binding pocket. The MD runs without any complaints,
but I see nearly no movement of the ligand in the direction of the
binding pocket. In the output, the target RMSD values decrease
linearly, but the actual RMSD values reach a value around 4.5 and
then barely change over the course of the 5ns.
For example:
TMD 3336350 Domain: 0 1.81132 4.49195
TMD 3336360 Domain: 0 1.81131 4.50083
TMD 3336370 Domain: 0 1.8113 4.48549
TMD 3336380 Domain: 0 1.81129 4.48752
TMD 3336390 Domain: 0 1.81128 4.48911
TMD 3336400 Domain: 0 1.81127 4.48904
My TMDfile contains only the coordinates of the ligand
in the binding pocket along with coordinates of about
10 Calpha atoms that define the pocket.
My config file has the following TMD parameters:
TMD on
TMDk 200
TMDFinalRMSD 0
TMDFile target.pdb
TMDFirstStep 0
TMDLastStep 5000000
TMDOutputFreq 10
I have played with TMDk but I see very little change in behavior of the
ligand.
Should I change my biasing selection in the TMDfile?
Thank you in advance for any suggestions.
Nadia
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