[PyMOL] apbs plugin in pymol

Dear All,

I am having a small problem using the apbs plugin in pymol on my pdb  
(I am using fink installed pymol and apbs versions on Mac OSX 10.4.8).

When I try to run apbs I received the following message:

"Unable to assign parameters for 100 atoms in the selection  
unassigned. Please either remove these unassigned atoms and re- 
start ..."

In principle, I think I understand the problem is that pdb2pqr cannot  
assign charges to certain atoms, in my case posttranslationally  
modified cysteine residues.

My question would be what the best way to fare with those atoms is.  
Since the modification introduces an acidic patch, if possible I  
would like to leave the atoms in (rather than remove them) when  
calculating surface charge representation, as this could be informative.

So perhaps my question boils down to what the optimal way to manually  
assign reasonable charges (in the pqr-file) for this oxidised  
cysteine (sulfinic acid; O-S=O) is.

I also noticed that I get the same error message with residues where  
side-chain atoms have been removed (such as surface lysines), while  
leaving the original residue name. But then I suppose there is no way  
around this.

Thank you very much in advance for any comments!

Best regards,

Florian
--------------------------------------------
Florian Schmitzberger
Medical Biochemistry and Biophysics
Karolinska Institute
Scheeles vaeg 2
SE-171 77 Stockholm, Sweden
Tel: +46-8-524-86875