[apbs-users] Problem with Uploading a concatenated PDB trajectory into APBS webserver

[Xingcheng Lin]

Hi,

I tried to use the APBS webserver to upload a trajectory of PDB files with about 40 structures in total. Basically I want to use PROPKA to see the change of pKa prediction of each residue among these structures. The job failed in running.

May I ask if there is anyway to get to this aim with this tool?

Thank you,

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Xingcheng Lin

Graduate Student

Department of Physics and Astronomy
Center for Theoretical Biological Physics

Rice University

[Baker, Nathan]

Hello –

 

I would recommend downloading the command-line version of PDB2PQR – it could be scripted to do this in a Unix type of environment.

Thanks,

 

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Nathan Baker

Laboratory Fellow and Technical Group Manager

Applied Statistics and Computational Modeling Group

Pacific Northwest National Laboratory

+1-509-375-3997

https://www.linkedin.com/in/nathanandrewbaker