[gmx-users] Protein Drug simulation Parameters

tasneem kausar tasneemkausar12 at gmail.com
Mon Sep 26 10:43:29 CEST 2016

Dear All

I have performed MD simulation of protein and drug crystal structure. I
have generated drug  itp file from PRODRG server and corrected the charges
of atoms as suggested in Justin's paper J. Chem. Inf. Model. 2010, 50,
I have done 50 ns MD simulation of protein and drug using g43a1 force field
and spc water model. After 15 ns drug molecule comes out of the pocket.
Is this expected during MD simulation. If this occurs what is the reason
behind it.
Should we change any specific parameter for protein drug simulation.

Thanks and Regards

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