As the stderr.txt file says, there seems to be a parsing issue in your submitted structure... for further advice you should ask the pdb2pqr-users mailing list...
Best,
Matias
----- Mensaje original -----
De: "Sadaf Rani" <sadafrani6.gmail.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Sábado, 8 de Junio 2019 9:27:11
Asunto: Re: [AMBER] propka web server
I tried with it but it is giving following error
Status: error
Run time: -1 day, 23:59:59
Current time: Fri Jun 7 10:48:00 2019
------------------------------
There was an error with your query request. This page will not refresh.
- Runtime and debugging information
- Program output (stdout)
<
http://nbcr-222.ucsd.edu/opal-jobs/apppdb2pqr_2.1.11559929544460-482700470/stdout.txt>
- Program errors and warnings (stderr)
<
http://nbcr-222.ucsd.edu/opal-jobs/apppdb2pqr_2.1.11559929544460-482700470/stderr.txt>
If your job has been running for a prolonged period of time and failed with
no reason listed in the standard out or standard error, then the job
probably timed out and was terminated by the system.
I am using it first time can you please suggest me what to do?
thank you in advance
On Fri, Jun 7, 2019 at 6:30 PM Matias Machado <mmachado.pasteur.edu.uy>
wrote:
> What about PDB2PQR server?
>
> http://nbcr-222.ucsd.edu/pdb2pqr
>
> I'm a big fun of it...
>
> Best,
>
> Matías
>
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
> [http://www.sirahff.com]
>
> ----- Mensaje original -----
> De: "Sadaf Rani" <sadafrani6.gmail.com>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> Enviados: Viernes, 7 de Junio 2019 14:17:55
> Asunto: [AMBER] propka web server
>
> Dear Amber users
> I am looking for protonation states of my ligand and for that I want to
> install propka 3.1 as mentioned in the link
> https://github.com/jensengroup/propka-3.1
> but the link propka.ki.ku.dk do not works
> what to do for that?
> Can you please suggest me?
>
> Thanks in advance
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>
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Received on Sat Jun 08 2019 - 14:00:02 PDT
