unable to calculate surface potential at different pH values of whole capsid

[waynebow94]

Hello everyone,

I'm new to the party and have some issues regarding calculating my surface potential and hope to find a solution for my problem.

I try to calculate the surface potential at different pH values with the following arguments for the pdb2pqr command line in APBS tools 2.1 in Pymol (e.g. pH 2): --with-ph=2.0 --ph-calc-method=propka

When I want to show the surface potential only the asymmetric unit is calculated at pH 2.0 and the other parts the protein container surface seem to be calculated at pH 7.0 - so at standard pH value. Why is only a part calculated at pH 2.0 and the other residues at standard? What do I have to change? I created the capsid through generating symmetry mates and saved it in one PDB file as one object. Also if i want to use the web server, only the asymmetric unit is calculated for the given pH value.

Thanks a lot in advance and stay healthy.

[sobolevnrm]

Hello –

Can you please provide information about the PDB file you’re attempting to analyze?

Thank you,

Nathan

From: waynebow94 [email protected] Sent: Friday, March 27, 2020 06:15 To: Electrostatics/apbs-pdb2pqr [email protected] Cc: Subscribed [email protected] Subject: [Electrostatics/apbs-pdb2pqr] unable to calculate surface potential at different pH values of whole capsid (#538)

Hello everyone,

I'm new to the party and have some issues regarding calculating my surface potential and hope to find a solution for my problem.

I try to calculate the surface potential at different pH values with the following arguments for the pdb2pqr command line in APBS tools 2.1 in Pymol (e.g. pH 2): --with-ph=2.0 --ph-calc-method=propka

When I want to show the surface potential only the asymmetric unit is calculated at pH 2.0 and the other parts the protein container surface seem to be calculated at pH 7.0 - so at standard pH value. Why is only a part calculated at pH 2.0 and the other residues at standard? What do I have to change? I created the capsid through generating symmetry mates and saved it in one PDB file as one object. Also if i want to use the web server, only the asymmetric unit is calculated for the given pH value.

Thanks a lot in advance and stay healthy.

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[waynebow94]

Hello Nathan!

I'm looking at 3DKT.

All the best.

[speleo3]

I tried processing 3DKT with options --with-ph=2.0 --ph-calc-method=propka like you said. One problem (after working around some others) is that propka will run out of chain identifiers. In my fork of pdb2pqr I increased the number of possible chains to 96. However, the assembly of 3DKT has 120 chains. It would be possible to process it after combining some of the chains.

I tried uploading a PDB file with combined chains to the new pdb2pqr server but it failed with 413 Request Entity Too Large (size is 11MB).

Upload to the old server worked but failed with dG out of range (error disguised as "local variable 'pH_opt' referenced before assignment", see this possible fix)

[sobolevnrm]

Thanks, Thomas!

I also wanted to confirm that Wayne was using the biological assembly ( https://files.rcsb.org/download/3DKT.pdb1.gz, which would need to be uploaded) rather than the asymmetric unit (the default option for 3DKT).

Thanks again,

Nathan

On Fri, Apr 3, 2020 at 5:54 AM Thomas Holder [email protected] wrote:

I tried processing 3DKT with options --with-ph=2.0 --ph-calc-method=propka like you said. One problem (after working around some others) is that propka will run out of chain identifiers. In my fork of pdb2pqr https://github.com/speleo3/apbs-pdb2pqr/commits/pymol I increased the number of possible chains to 96. However, the assembly of 3DKT has 120 chains. It would be possible to process it after combining some of the chains.

I tried uploading a PDB file with combined chains to the new pdb2pqr server http://apbs-rest-test.westus2.cloudapp.azure.com/pdb2pqr but it failed with 413 Request Entity Too Large (size is 11MB).

Upload to the old server worked but is still running http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/querystatus.cgi?jobid=15859176012&calctype=pdb2pqr .

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[waynebow94]

Dear all,

thanks for the input!

First I tried with the asymmetric unit, now I want to use the biological assembly. How do I proceed now? I didn't really get it, sorry. If I want to upload the biological assembly I rename it to e.g. 3dkt_ba.pdb and upload it. If I want to visualize the surface potential afterwards in Pymol, I still only see the asymmetric unit and its surface potential. I lose the informations about other states or the other parts of the capsid can't visualize them.

Thanks for the patience for me as a newbie and greetings!

[sobolevnrm]

Hi Wayne --

The biological assembly is very large; it may be too big for the default settings on the new PDB2PQR server. Were you able to successfully run it there?

Thanks,

Nathan

On Wed, Apr 15, 2020 at 2:40 AM waynebow94 [email protected] wrote:

Dear all,

thanks for the input!

First I tried with the asymmetric unit, now I want to use the biological assembly. How do I proceed now? I didn't really get it, sorry. If I want to upload the biological assembly I rename it to e.g. 3dkt_ba.pdb and upload it. If I want to visualize the surface potential afterwards in Pymol, I still only see the asymmetric unit and its surface potential. I lose the informations about other states or the other parts of the capsid can't visualize them.

Thanks for the patience for me as a newbie and greetings!

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[sobolevnrm]

Oops. That check-in should have been assigned to another issue. Sorry for confusion.

[waynebow94]

Hey Nathan,

unfortunately not. :(

All the best.