[Chimera-users] Electrostatic Potential

Elaine Meng meng at cgl.ucsf.edu
Wed Dec 20 11:02:24 PST 2017


Hi Jiri,
I guess you are using PDB2PQR to make input for APBS potential calculations. There is no choice for pKa, only for pH if you use PROPKA, and you just have to decide whether to use the crystallization or reaction pH.  You could certainly use it multiple times for different pH values. 

Re force field, the short answer is I don’t know.  Be aware that the pqr output may not even contain your metal ion, only the protein atoms.  (Just close or hide the original model and look at the pqr model output by PDB2PQR to see what’s in it). As it says in the PDB2PQR help page, residues not in the force field will be omitted from the output.  That is not necessarily bad, just be aware that the potential you get from APBS might be from the protein part only.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html>

The long answer is that it isn’t really a Chimera question but more a general modeling question.  You might read the papers cited for the force fields in the help page (linked above) and/or ask on some modeling forum like ccl.net.  If you ask, you should say what program you are using (e.g. PDB2PQR), the purpose (e.g. electrostatic potential calculation and surface coloring) and what the choices for force field are, to increase your chances of getting any useful reply.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Dec 20, 2017, at 10:16 AM, chemocev marker <jirivitali at gmail.com> wrote:
> 
> Hi
> I am just calculating the Electrostatic Potential, and I wanted to know your opinion which force field is better for metallo proteins.And what is criteria to choose and not to choose the pKA...
> As I am doing the reaction at different pH and what I see in the PDB the proteins are crystallized at different pH then the reaction conditions. Structures are solved at low pH but the reactions are done at high pH.
> best
> Jiri




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