[Chimera-users] APBS electrostatic potential

Felipe Vasquez anfelvas at gmail.com
Wed Jun 3 17:45:29 PDT 2015


I am interested on calculating the electrostatic potential of a molecular
surface on a protein (specifically visualizing that potential on a
previously cavity determined by CASTp). However, althought I did get
reasonable results using Coulombic potential, I could not obtain similar
results using APBS potential (I obtained a surface too electrostatic,
charged negatively and the values have a huge range, not only from -10 to
10 as in the case of Coulombic potential). Should I modify some default
values out of the calculation parameters in order to get a similar result
to that obtain by Coulombic potential? And it is absolutely indispensable
add hydrogens in an APBS estimation?

Thanks in advance for your help.

Best regards,

*Andrés Felipe Vásquez J., BSc, MSc.*
Grupo de Fisiología Molecular
Subdirección de Investigación Científica y Tecnológica
Dirección de Investigación en Salud Pública
Instituto Nacional de Salud
Avenida calle 26 No. 51-20 - Zona 6 CAN
+57 (1) 2207700 ext. 1419
Bogotá, D.C., Colombia
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