Re: [gmx-users] Fwd: electrostatic potential map

Thanks I have little more confusion about the charges assigned to each of the atoms from pdb2pqr. With and without water the charges of all the protein atoms are same! But, then why this type of discrepancy is coming from the potential map? Thanks for giving the apbs mailing list address. I'll pos

Re: [gmx-users] Fwd: electrostatic potential map

Tarak, That's more of a question for the APBS mailing list, but I'll give it my best shot, but I would highly suggest you check out http://www.poissonboltzmann.org/apbs first. APBS is an implicit solvent electrostatics model, and as such you should be careful with what explicit solvent you includ

[gmx-users] Fwd: electrostatic potential map

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