[Chimera-users] APBS electrostatic potential

Elaine Meng meng at cgl.ucsf.edu
Sat Jun 6 08:23:57 PDT 2015


Maybe you wanted to avoid the bumpier appearance of the with-hydrogens molecular surface.

If so, you could consider deleting the hydrogens *after* calculating the APBS potential map (if hydrogens and their charges aren’t needed for anything else you wanted to do), or using the APBS potential map to color the surface of an additional copy of the structure that doesn’t have hydrogens.  In the latter case, just make sure that the map is in the proper spatial relationship to the structure, e.g. the additional copy is superimposed with the copy used to calculate the map, and the map hasn’t been moved relative to the structures.

Elaine

On Jun 5, 2015, at 11:14 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Andrés,
> I would not recommend making any quantitative comparisons between Coulombic and Poisson-Boltzmann potentials: not only are the equations different, but you can easily change the magnitudes by changing the dielectric (e.g. increasing the dielectric constant from 1 to 10 will decrease Coulombic potential magnitudes by a factor of 10). 
> 
> Nevertheless, for visual rendering they should (and in my experience, they do) produce similar qualitative conclusions of which surface regions are more negative or positive.
> 
> We have made the Coulombic calculations very easy to set up, whereas for Poisson-Boltzmann calculations, more preparations of the structure are required.  For example, yes, you do need to add the hydrogens and charges (including on the hydrogens) before running APBS or else you will have a ridiculously negative net charge.  This is because the force field choices in PDB2PQR for adding charges are derived for such all-atom structures,.
> 
> As per the APBS manpage,
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html>
> 
> "A structure should be prepared for APBS calculations by reconstructing missing heavy atoms, adding hydrogens, and assigning atomic charges and radii. These tasks can be done with PDB2PQR alone or in combination with parts of Dock Prep. Atomic charges can be assigned with Add Charge or PDB2PQR, although the latter may be preferred because it includes force fields developed specifically for Poisson-Boltzmann calculations.”
> 
> For additional details on the Chimera PDB2PQR and Coulombic tools:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic.html>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Jun 3, 2015, at 5:45 PM, Felipe Vasquez <anfelvas at gmail.com> wrote:
> 
>> Hi,
>> I am interested on calculating the electrostatic potential of a molecular surface on a protein (specifically visualizing that potential on a previously cavity determined by CASTp). However, althought I did get reasonable results using Coulombic potential, I could not obtain similar results using APBS potential (I obtained a surface too electrostatic, charged negatively and the values have a huge range, not only from -10 to 10 as in the case of Coulombic potential). Should I modify some default values out of the calculation parameters in order to get a similar result to that obtain by Coulombic potential? And it is absolutely indispensable add hydrogens in an APBS estimation?
>> Thanks in advance for your help.
>> Best regards,
>> Andrés Felipe Vásquez J., BSc, MSc.
> 
> 
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