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

Nikolay Igorovich Rodionov nirodion at syr.edu
Wed May 16 16:01:24 PDT 2012

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

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Wednesday, May 16, 2012 6:46 PM
To: Nikolay Igorovich Rodionov
Cc: chimera-users at cgl.ucsf.edu BB
Subject: Re: [Chimera-users] PDB column overlap --PDB2PQR,APBS

Hi Nikolay,
I don't have an answer about how to make the steps work for huge numbers of atoms (especially given that PDB2PQR and APBS are not our own software -- did you also ask their developers?), but personally I would do Poisson-Boltzmann calculations on a single subunit only, without solvent, since the continuum is meant to model solvent.  The ESP coloring for that subunit could be repeated on the other subunits with the "msc" command Tom Goddard mentioned in an earlier response.

However, if your analysis demands having all the atoms for the whole system for some reason, my only other idea is to chop the data into pieces (write out PDBs for parts, convert to PQR files for those parts, then string together the PQR files into one giant PQR file).  However, I have no idea whether you would have to manually renumber that PQR file, whether APBS would accept such a big PQR file, or if it does, whether it would take forever to run it.
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 2:59 PM, Nikolay Igorovich Rodionov wrote:

> Hi all,
> I am trying do Poisson-Boltzmann calculations through outside software, PDB2PQR and APBS. I am prepare my initial pdb file in chimera using the 'write pdb' method. The final structure is quite large, 737058 atoms, so I am getting overlaps in the data columns after I write the PDB file. This doesn't create a problem for rendering the PDB file but I get parsing errors and other strange occurrences when I try to create a complementary PQR file.  Does anyone know of a work around?
> Here are links to my structures, if you look you will see that a significant portion of  the structure is getting cut off in the PQR. I can't seem to generate more than about 99760 atoms, no matter what I try.
> http://dl.dropbox.com/u/42179401/2TMV.18H.pdb
> http://dl.dropbox.com/u/42179401/2TMV.18Ha.pqr
> Can anyone think of a potential fix? I've experienced this same problem with smaller helix pdb files.
> Thank you,
> Nikolay Rodionov

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