[AMBER] Ligand is unstable in simulations

From: Midhun K Madhu <midhunk16.iiserb.ac.in>
Date: Mon, 4 Oct 2021 17:40:24 +0530


In my simulations of a lipid-protein system using
Charmm36/Charmm36m forcefield, The ligand is becoming unstable and slowly
coming out of the pocket. Originally, this should be a milliseconds
timescale phenomenon and shouldn't happen within a few hundreds of
nanoseconds, like in my case.

Earlier when I tried accelerated MD (GaMD to be precise), the ligand
completely came out, almost immediately, and that is why I tested the
system using conventional MD. Can someone help me to understand what is
going wrong in the simulations? The system was prepared using CHARMM GUI
and the parameters for the ligand were assigned using the Paramchem server.

With regards,

Ph.D Student
Dept. of Biological Sciences
IISER Bhopal
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Received on Mon Oct 04 2021 - 05:30:03 PDT
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