Hi AMBER Users,
I am running umbrella sampling to simulate a reaction that involvoes the
formation of a covalent bond between an electrophilic carbon from a ligand
and SG of an active site cysteine residue. I chose the distance separating
the atoms forming the bond as the reaction coordinate. I have run 33
40-picosecond windows with a 0.1-angstrom change between the windows. The
ligand and the cysteine residue were threated quantum mechanically while
the rest of the protein conventionally.
The bond formed eventually and there was a nice overlap between the
windows. However, when I tried to calculate PMF using WHAM I was getting
the curve upside down; it starts with high value, decreases gradually and
then increases again. The comand I am using for WHAM is:
/wham 1.64 4.94 330 0.1 300 0 meta.dat result.dat
What could be a possible solution for this?
Best Regards,
Mahmood Jasi
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Received on Fri Feb 13 2015 - 05:00:03 PST
