getting pkas for residues about htmd

[mj-harvey]

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 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]

i can replicate the error

[tonigi]

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

[giadefa]

@tonigi what's the status?

[tonigi]

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

[stefdoerr]

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)

[stefdoerr]

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)

[j3mdamas]

Atom name alignments solved in multiscalelab/htmd#20

[tonigi]

Should work as soon as 7bf7b04 is merged.

[j3mdamas]

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

[tonigi]

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

[j3mdamas]

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]

i can't close issues here

[j3mdamas]

i will close it after she tests it.

[noeliaferruz]

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]

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]

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]

solved