Dear All,
I am running a simulation of ligand binding in a protein. Ligand is
mostly negatively charged, so as expected it should bind to the positive
region of the protein. To check the possible binding zone, I try to
calculate or rather visualize the electrostatic potential map of a protein
in PYMOL. In this context I am utilizing pdb2pqr and then APBS in PYMOL.
Surprisingly, I see two different types of pictures, in presence and in
absence of water molecules present in the protein pdb file. In presence of
water molecules, some regions in the protein are showing positive while in
absence of water molecules these (same) regions are showing negative
potential. I don't know, exactly, what is the effect of water molecules in
this calculations.
Any short of suggestions would be greatly appreciated. ( I apologize
for posting bit different topic in this mailing list)
Thanks and regards,
Tarak
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