Comments (18)
You probably need to get the propka Fonda package updated.
On 24 Mar 2016 15:20, "Noelia Ferruz" [email protected] 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 definedSo then I tried:
from htmd.molecule.pka import pka as pkapkas = 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 1During 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 PropKaI am using the pfizer version: You are on the latest HTMD version (0.1.32).
Any help is appreciated.
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#2
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i can replicate the error
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For now please use the proteinPreparation with returnDetails=True
, you'll get pkas . Eventually there will be a separate function.
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@tonigi what's the status?
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committed a prototype stand-alone function but propka seems to require proper atom name alignments.
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I fixed the atom name alignments. I am going to push it now
On Thu, Apr 21, 2016 at 5:05 PM, Toni G [email protected] wrote:
committed a prototype stand-alone function but propka seems to needs
proper atom name alignments—
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#2 (comment)
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Done. Now you can pull and test the atom name alignments.
On Thu, Apr 21, 2016 at 5:19 PM, Stefan Doerr [email protected] 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 [email protected] wrote:
committed a prototype stand-alone function but propka seems to needs
proper atom name alignments—
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#2 (comment)
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Atom name alignments solved in multiscalelab/htmd#20
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Should work as soon as 7bf7b04 is merged.
from htmd.
So, @tonigi, we should test this or since you merged it, it is already well tested?
from htmd.
Reasonably tested. I'd close the issue and open new ones if specific cases arise.
from htmd.
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.
from htmd.
i can't close issues here
from htmd.
i will close it after she tests it.
from htmd.
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
from htmd.
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.
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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
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solved
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