Comparing electrostatics in APBS using .dx file

[Dermot Mallon]

Hello all,

I have a protein that is bound to a peptide of ~8 amino acids. I have used modeller to simulate the same protein bond to different 8 aa peptides.

I can calculate the solvent accessible electrostatics for this.

I wonder now like to compare them. i.e. determine the difference in the electrostatics of each.

In order to (try to) do this, I have taken both PDB files, created PQR files using PDB2PQR. I've  loaded these in ABPS (with identical grid properties) which creates a .dx file. I understand that this contains the electrostatic potential for all points within the grid. I've written a python script that takes one value away from the respective value in the second file. This creates a third file with 'net' electrostatics. 

In PyMol, I load one of the PDB files and to it I apply the new .dx file through the APBS plugin. 

I would expect the whole surface of the protein to be roughly 0 and then the altered peptide area to be different to a variable degree depending on the exact differences in aa sequence.

I get something that appears roughly what I expected but with quite a lot of 'non-zero' electrostatics in areas that should be the same between molecules. I wonder if this approach is reasonable, or if anyone can suggest an alternative?  

Many thanks for your help and any suggests would be grateful received!

Dermot

[Baker, Nathan]

Hello --

What surface definition and source of potential data did you use? I prefer the solvent-accessible surface for most applications.

That being said, your positive potential values are relatively small so it seems they do match your expectation for an approximately neutral surface potential.

Thanks,

--
Nathan Baker
Pacific Northwest National Laboratory
Phone: +1-509-375-3997
http://nabaker.me

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[dhmallon]

Hi Nathan,

Thanks for your reply.

This is the apbs input file as created by PDB2PQR:

read
    mol pqr /home/dermot/Desktop/EBVr.pqr
end
elec 
    mg-auto
    dime 161 161 193
    cglen 107.0000 102.0000 130.0000
    fglen 83.0000 80.0000 97.0000
    cgcent mol 1
    fgcent mol 1
    mol 1
    lpbe
    bcfl sdh
    pdie 2.0000
    sdie 78.5400
    srfm smol
    chgm spl2
    sdens 10.00
    srad 1.40
    swin 0.30
    temp 298.15
    calcenergy total
    calcforce no
    write pot dx pot
end
elec 
    mg-auto
    dime 161 161 193
    cglen 107.0000 102.0000 130.0000
    fglen 83.0000 80.0000 97.0000
    cgcent mol 1
    fgcent mol 1
    mol 1
    lpbe
    bcfl sdh
    pdie 2.0000
    sdie 2.0000
    srfm smol
    chgm spl2
    sdens 10.00
    srad 1.40
    swin 0.30
    temp 298.15
    calcenergy total
    calcforce no
end
print elecEnergy 2 - 1 end
quit

I was very much looking to use the solvent accessible surface, which is what I assumed I was doing based on putting in an srad of 1.4. I also tried 2.8 and 4.2 although that did not change the appearance when visualising in PyMOL - do I need to state which surface definition I am using?

thanks for your help.

Dermot

On Wednesday, 27 February 2013 18:32:01 UTC, Baker, Nathan wrote:

Hello --

What surface definition and source of potential data did you use?  I prefer the solvent-accessible surface for most applications.

That being said, your positive potential values are relatively small so it seems they do match your expectation for an approximately neutral surface potential.

Thanks,

--
Nathan Baker
Pacific Northwest National Laboratory
Phone: +1-509-375-3997
http://nabaker.me

[Baker, Nathan]

Hello --

Sorry for the confusion. I meant which surface are you visualizing in PyMOL — you can choose between the molecular and solvent-accessible surface. However, I still think that the potential range is small enough to be considered roughly neutral.

Thanks,

--
Nathan Baker
Pacific Northwest National Laboratory
Phone: +1-509-375-3997
http://nabaker.me

From: Dermot Mallon <dhma...@gmail.com<javascript:><mailto:dhma...@gmail.com<javascript:>>>
Date: Tuesday, February 26, 2013 7:35 AM
To: APBS-USERS mailing list <apbs-...@googlegroups.com<javascript:><mailto:apbs-...@googlegroups.com<javascript:>>>
Subject: [apbs-users] Comparing electrostatics in APBS using .dx file

Hello all,

I have a protein that is bound to a peptide of ~8 amino acids. I have used modeller to simulate the same protein bond to different 8 aa peptides.

I can calculate the solvent accessible electrostatics for this.

I wonder now like to compare them. i.e. determine the difference in the electrostatics of each.

In order to (try to) do this, I have taken both PDB files, created PQR files using PDB2PQR. I've loaded these in ABPS (with identical grid properties) which creates a .dx file. I understand that this contains the electrostatic potential for all points within the grid. I've written a python script that takes one value away from the respective value in the second file. This creates a third file with 'net' electrostatics.

In PyMol, I load one of the PDB files and to it I apply the new .dx file through the APBS plugin.

I would expect the whole surface of the protein to be roughly 0 and then the altered peptide area to be different to a variable degree depending on the exact differences in aa sequence.

I get something that appears roughly what I expected but with quite a lot of 'non-zero' electrostatics in areas that should be the same between molecules. I wonder if this approach is reasonable, or if anyone can suggest an alternative?

Many thanks for your help and any suggests would be grateful received!

Dermot

------------------------------------------------------------------------------
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[dhmallon]

This was visualization problem when using PyMol.

I fixed this by using the command

alter all,vdw=vdw+1.4

show surface

Nathan, many thanks for your help.

Dermot

On Wednesday, 27 February 2013 18:32:01 UTC, Baker, Nathan wrote:

Hello --

What surface definition and source of potential data did you use?  I prefer the solvent-accessible surface for most applications.

That being said, your positive potential values are relatively small so it seems they do match your expectation for an approximately neutral surface potential.

Thanks,

--
Nathan Baker
Pacific Northwest National Laboratory
Phone: +1-509-375-3997
http://nabaker.me