It’s my first attempt at explicit solvent CpHMD. In summary, my objective is to predict whether structural changes of a protein-ligand complex brought about by changes in pH result in the release of the ligand. I intend to perform simulations at pHs 5, 6 and 7.
As a starting point, I’m using the same md.in files described in
http://jswails.wikidot.com/explicit-solvent-constant-ph-md <
http://jswails.wikidot.com/explicit-solvent-constant-ph-md>
I’ve successfully generated protein_solv.cpin which I then used in heating and equilibrating the system using the following input commands:
(heat) $PMEMD -O -i heat.in -c subA.min.rst -p subA_solv.modO.prmtop -ref subA.min.rst -cpin subA_solv.cpin -o subA.heat.out -r subA.heat.rst -x subA.heat.nc
(equilibration) $PMEMD -O -i equil.in -p subA_solv.modO.prmtop -c subA.heat.rst -cpin subA_solv.cpin -o subA.equil.out -cpout subA.equil.cpout -r subA.equil.rst -x subA.equil.nc -cprestrt subA.equil.cpin
In the equilibration step, I obtained the equil.out, equil.cpout, equil.rst, and equil.nc but NOT the expected equil.cpin
I’d be grateful for any suggestions regarding this problem(?)
Regards
George
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Received on Sat Sep 02 2017 - 10:30:03 PDT
