[Apbs-users] Explicit waters in APBS

[Sandeep S. <ss...@bi...>]

Hi

I have a pdb file of a protein with water molecules buried deep inside
a cavity inaccesible to the bulk solvent.

I want to calculate the electrostatics with explicit buried waters. But
when trying to generate a pqr file using the pdb2pqr program (in tools),
the buried waters are ignored.  I am using TIP3P waters and charmm force
field.

any help ?

Thanks and Regards
Sandeep