AMBER Archive (2009)

Subject: [AMBER] surface binding protein

From: sadaf iqbal (
Date: Sat Oct 31 2009 - 00:28:22 CDT

Hello all,

I am doing simulation of a protein in which substrate is bound to the surface of protein. During MD production run, I have encountered a problem that substrate move away far and far from the binding surface as the simulation proceed. Can anybody help me to tackle this problem associated with the simulation of surface binding substrate/protein complex. I have done simulation with substrate/protein complex in which substrate is in pocket/subsites and never encountered this problem.

Any help in this regard will be highly appreciated.

Sadaf Iqbal

Computational Medicinal Chemistry Unit

Dr. Panjwani Center for Molecular Medicine and Drug Research


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