[Apbs-users] confused over simple command-line use of apbs

[Paul S. <psh...@sy...>]

I wish to calculate and visualize the electrostatic charge on a small
peptide -- 11 residues in the vicinity of the phospho-acceptor on a  
possible
kinase substrate.  I get stuck at the point where I try to get an  
opendx-format
file out of apbs (required, I think, for pymol).

I am trying to do this all on the command line in order to see, and  
eventually
understand, the transformations that take place at each step.

  1) create a pqr file, and an input file for apbs:
     python ~/s/apps/pdb2pqr/pdb2pqr.py --apbs-input --ff=parse  
eno1.243.253.pdb  eno1.pqr

  2) calculate electrostatic charge on the peptide:
     apbs eno1.in

The only new file created by step 2 is io.mc, which seems to be a  
trace or log file.  Among other
things that confuse me, I can't figure out how to request an opendx  
file.  I must be invoking
apbs incorrectly...

Any advice? Thanks!

  - Paul