Dear APBS users,
I have an extremely naive question.
I generated the PQR file of a protein via Gromacs and took advantage of the APBS Pymol plugin to calculate and visualize its electrostatic surface (clicking the "color by potential on sol. acc. surf.", as suggested in http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-pymol).
The surface is completely positively charged, also in correspondence to acidic residues. This is due to the fact that the electrostatic potential is an overall property, and the negative charges of glutamate and aspartate residues (localized on their gamma and beta carboxyl groups, respectively) are not enough to compensate for the positive electrostatic potential generated by the rest of the protein -- is this right?
Thank you very much in advance.
Dulbecco Telethon Institute c/o DIBIT Scientific Institute
Biomolecular NMR Laboratory, Basilica 3A2
Via Olgettina 58, 20132 Milano (Italy)
Tel : 0039-0226434922
Fax : 0039-0226434153
Email : email@example.com; firstname.lastname@example.org
Site : https://sites.google.com/site/dimspil82/