[Chimera-users] PDB column overlap --PDB2PQR,APBS

Elaine Meng meng at cgl.ucsf.edu
Wed May 16 16:34:27 PDT 2012

Hi Nikolay,
The figures look pretty nice -- I see you were able to display surfaces!

It is not surprising the ESP results are different, comparing monomer to multimer.  At least both images show some concentration of negative potential in the pore surface, and Coulombic ESP is meant for visualization (identification of more positive and negative regions in a given structure, or differences of surface potential between different but similar structures) rather than for absolute quantitative accuracy. I do agree that in your system, it is better to include the superstructure of multiple subunits in the ESP calculation, if possible, and that it would be really interesting to know if Poisson-Boltzmann ESP shows a similar enhancement of the potential in the superstructure!

My second (chopping data) suggestion was putting the atoms back together in one file before running APBS, so everything would be in one ESP calculation, but it might not work.  

As to whether parts vs. whole affect calculations, I would expect yes for ESP calculations.  For Add Charge on standard residues, no (since the charges for standard residues are just obtained from lookup tables).  For AddH, the results either depend on all atoms open in Chimera at the time (if the "Consider each model in isolation" option is turned off) or all atoms within the same model but not other models (if that option is turned on).
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 16, 2012, at 4:01 PM, Nikolay Igorovich Rodionov wrote:

> Thank you Elaine. I want to visualize the force fields lines through the pore of the helix, I am going to try to isolate the amino acids (and a little extra to be safe) responsible for creating the pore's surface and just create helix based off of that data. I am hoping that the consequent surface charges inside the new pore will reflect the natural surface charge. 
> Since you have mentioned sectioning off by subunits I want to tell you this in case some in the future needs help with a similar issue. Calculation results are significantly different based on how you treat a quandary protein structure, either as individual models or a single molecule. When I work use coulomb's law electrostatic coloring on a helix with individual surface calculations for each subunit I get a large negative potential (-10 eV) in localized regions surround Glu97 and Glu106 of each subunit. On the otherhand, when I combine all of the subunits into a single manageable helix molecule and do one large surface/ESP calculation for all of the atoms combined I get a large negative potential (-10eV) across the entire pore.
> I've attached images. I think that the single molecule approach give more accurate results. What do you think?
> Do you think that this calculation difference extend to other tools as well such as addh?
> Nikolay Rodionov

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