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!
Medical Biochemistry and Biophysics
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