Water molecules have charges and nonzero dipole and quadrupole moments so the fact that they are changing the electrostatic potential is not surprising. In fact, you are observing the polarization of explicit molecules that continuum models attempt to capture through the local dielectric coefficient values.
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From: email@example.com [firstname.lastname@example.org]
Sent: Friday, May 17, 2013 06:47 PM Pacific Standard Time
Subject: [apbs-users] electrostatic potential calculations
I have calculated or rather generated electrostatic potential map for a protein using pdb2pqr and APBS in PYMOL. But the problem is, in presence and in absence of water molecules (present with pdb file), the scenario is coming different. The positive regions, in presence of water molecules, show negative in absence of water molecules. I got some clue, recently, saying the presence of explicit water molecules may affect the surrounding by changing the charge environment (hydrogen bonding effect). But the charges of all the atoms of protein, generated by pdb2pqr, are same, irrespective of presence or absence of water molecules.
Can anybody suggest further why this type of discrepancy is coming from this calculations?
Thanks and regards,