getting pkas for residues #2

noeliaferruz · 2016-03-24T14:17:36Z

Hello guys,

I am not sure how to use the propka implementation. Following the tutorial I tried:

system = Molecule('4xv1_prep.pdb')
pkas = pka(system , pH=6.5 )
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
NameError: name 'pka' is not defined

So then I tried:

from htmd.molecule.pka import pka as pka
>>> pkas = pka(system, pH=6.5 )


During handling of the above exception, another exception occurred:

T
NameError: Failed to execute PropKa

I am using the pfizer version: You are on the latest HTMD version (0.1.32).

Any help is appreciated.

The text was updated successfully, but these errors were encountered:

mj-harvey · 2016-03-24T21:36:46Z

You probably need to get the propka Fonda package updated.
On 24 Mar 2016 15:20, "Noelia Ferruz" notifications@github.com wrote:

Hello guys,

I am not sure how to use the propka implementation. Following the tutorial
I tried:

system = Molecule('4xv1_prep.pdb')
pkas = pka(system , pH=6.5 )
Traceback (most recent call last):
File "", line 1, in
NameError: name 'pka' is not defined

So then I tried:
from htmd.molecule.pka import pka as pka

pkas = pka(system, pH=6.5 )
Traceback (most recent call last):
File
"/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/python3/anaconda3-2.3.0/bin/propka31",
line 9, in
load_entry_point('PROPKA==3.1', 'console_scripts', 'propka31')()
File
"/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/python3/anaconda3-2.3.0/lib/python3.4/site-packages/PROPKA-3.1-py3.4.egg/propka/run.py",
line 13, in main
File
"/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/python3/anaconda3-2.3.0/lib/python3.4/site-packages/PROPKA-3.1-py3.4.egg/propka/molecular_container.py",
line 54, in init
File
"/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/python3/anaconda3-2.3.0/lib/python3.4/site-packages/PROPKA-3.1-py3.4.egg/propka/molecular_container.py",
line 109, in extract_groups
File
"/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/python3/anaconda3-2.3.0/lib/python3.4/site-packages/PROPKA-3.1-py3.4.egg/propka/conformation_container.py",
line 40, in extract_groups
File
"/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/python3/anaconda3-2.3.0/lib/python3.4/site-packages/PROPKA-3.1-py3.4.egg/propka/conformation_container.py",
line 145, in setup_and_add_group
File
"/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/python3/anaconda3-2.3.0/lib/python3.4/site-packages/PROPKA-3.1-py3.4.egg/propka/conformation_container.py",
line 154, in init_group
File
"/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/python3/anaconda3-2.3.0/lib/python3.4/site-packages/PROPKA-3.1-py3.4.egg/propka/group.py",
line 355, in setup
File
"/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/python3/anaconda3-2.3.0/lib/python3.4/site-packages/PROPKA-3.1-py3.4.egg/propka/group.py",
line 738, in setup_atoms
IndexError: list index out of range
Traceback (most recent call last):
File
"/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/python3/anaconda3-2.3.0/lib/python3.4/site-packages/htmd/molecule/pka.py",
line 53, in pka
op = check_output( [ propka, fn, "-o" , str(pH) ] )
File
"/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/python3/anaconda3-2.3.0/lib/python3.4/subprocess.py",
line 620, in check_output
raise CalledProcessError(retcode, process.args, output=output)
subprocess.CalledProcessError: Command
'['/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/python3/anaconda3-2.3.0/bin/propka31',
'/tmp/tmpb9n7fo8c.pdb', '-o', '6.5']' returned non-zero exit status 1

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "", line 1, in
File
"/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/python3/anaconda3-2.3.0/lib/python3.4/site-packages/htmd/molecule/pka.py",
line 56, in pka
raise NameError("Failed to execute PropKa")
NameError: Failed to execute PropKa

I am using the pfizer version: You are on the latest HTMD version (0.1.32).

Any help is appreciated.

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#2

giadefa · 2016-04-02T06:26:24Z

i can replicate the error

tonigi · 2016-04-11T16:13:22Z

For now please use the proteinPreparation with returnDetails=True, you'll get pkas . Eventually there will be a separate function.

giadefa · 2016-04-21T14:29:43Z

@tonigi what's the status?

tonigi · 2016-04-21T15:05:13Z

committed a prototype stand-alone function but propka seems to require proper atom name alignments.

stefdoerr · 2016-04-21T15:19:24Z

I fixed the atom name alignments. I am going to push it now

On Thu, Apr 21, 2016 at 5:05 PM, Toni G notifications@github.com wrote:

committed a prototype stand-alone function but propka seems to needs
proper atom name alignments

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#2 (comment)

stefdoerr · 2016-04-21T15:22:13Z

Done. Now you can pull and test the atom name alignments.

On Thu, Apr 21, 2016 at 5:19 PM, Stefan Doerr stefan.doerr@upf.edu wrote:

I fixed the atom name alignments. I am going to push it now

On Thu, Apr 21, 2016 at 5:05 PM, Toni G notifications@github.com wrote:

committed a prototype stand-alone function but propka seems to needs
proper atom name alignments

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#2 (comment)

j3mdamas · 2016-04-21T19:41:55Z

Atom name alignments solved in multiscalelab/htmd#20

tonigi · 2016-04-27T17:33:22Z

Should work as soon as 7bf7b04 is merged.

j3mdamas · 2016-04-28T13:17:36Z

So, @tonigi, we should test this or since you merged it, it is already well tested?

tonigi · 2016-04-28T14:00:50Z

Reasonably tested. I'd close the issue and open new ones if specific cases arise.

j3mdamas · 2016-04-28T14:02:07Z

Maybe close it after @noeliaferruz is able to run her case with the new version? Idk when we do a new release, maybe at next dev meeting.

tonigi · 2016-04-28T14:16:12Z

i can't close issues here

j3mdamas · 2016-04-28T14:16:56Z

i will close it after she tests it.

noeliaferruz · 2016-04-28T15:01:44Z

Hi guys!

I open a console using version (1.0.16).
Then replicate the commands I wrote in the first comment and got the same exact error. I guess I should use this feature through ProteinPreparation, right?

Please let me know if I should be using a different version/ commands.

Thanks all,
Noelia

j3mdamas · 2016-04-28T15:05:17Z

Version 1.0.16 does not have the new pKa Toni implemented. You'd have to download the multiscalelab/htmd fork in order to do it. Or wait until we release a new version. Maybe next week.

noeliaferruz · 2016-04-28T16:17:45Z

Hi, I updated my local conda htmd version, and since the versions are the same -compared to the other global conda we have here-, I'll wait until next release.

Thanks

giadefa · 2016-05-10T14:18:46Z

solved

updating fork

giadefa added the bug label Apr 2, 2016

giadefa assigned tonigi Apr 6, 2016

giadefa added this to the v1.1.0 milestone May 10, 2016

giadefa changed the title ~~Protonation~~ getting pkas for residues May 10, 2016

giadefa closed this as completed May 10, 2016

gph82 mentioned this issue Feb 21, 2017

How to choose the TICA lag time? #230

Closed

j3mdamas added a commit that referenced this issue Jul 16, 2017

missing psi4 deps #2 and removing deps of psi4 deps from deps

c1c075a

stefdoerr pushed a commit that referenced this issue Jun 19, 2020

Merge pull request #2 from Acellera/master

0f0b498

updating fork

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getting pkas for residues #2

getting pkas for residues #2

noeliaferruz commented Mar 24, 2016

mj-harvey commented Mar 24, 2016

giadefa commented Apr 2, 2016

tonigi commented Apr 11, 2016

giadefa commented Apr 21, 2016

tonigi commented Apr 21, 2016 •

edited

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stefdoerr commented Apr 21, 2016

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j3mdamas commented Apr 21, 2016

tonigi commented Apr 27, 2016

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tonigi commented Apr 28, 2016

j3mdamas commented Apr 28, 2016

noeliaferruz commented Apr 28, 2016

j3mdamas commented Apr 28, 2016

noeliaferruz commented Apr 28, 2016

giadefa commented May 10, 2016

getting pkas for residues #2

getting pkas for residues #2

Comments

noeliaferruz commented Mar 24, 2016

mj-harvey commented Mar 24, 2016

giadefa commented Apr 2, 2016

tonigi commented Apr 11, 2016

giadefa commented Apr 21, 2016

tonigi commented Apr 21, 2016 • edited Loading

stefdoerr commented Apr 21, 2016

stefdoerr commented Apr 21, 2016

j3mdamas commented Apr 21, 2016

tonigi commented Apr 27, 2016

j3mdamas commented Apr 28, 2016

tonigi commented Apr 28, 2016

j3mdamas commented Apr 28, 2016

tonigi commented Apr 28, 2016

j3mdamas commented Apr 28, 2016

noeliaferruz commented Apr 28, 2016

j3mdamas commented Apr 28, 2016

noeliaferruz commented Apr 28, 2016

giadefa commented May 10, 2016

tonigi commented Apr 21, 2016 •

edited

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