igemsoftware/heidelberg_15

Team Heidelberg's new and sharksome software.

iGEM team Heidelberg 2015 software repository

Welcome to our source code repository. It contains our two software tools, MAWS and JAWS, as well as the corresponding manuals. MAWS manual: README_MAWS.md JAWS manual: README_JAWS.md

heidelberg_15's Issues

KeyError: 'POINTERS'

Hi,

When I try to run the maws.py it will first complain that there is a missing identation.
After I fix that it stops at KeyError: 'POINTERS'.

This appears to happen in openmm. Possibly due to issues reading my pdb file.
I am using RCSB identifier: 1BUY.
I tried running it through ambertools pdb4amber, but that did not change the outcome.

The leap.log finishes off with 3x:
WARNING: The unperturbed charge of the unit: 6.000000 is not zero.
FATAL: Atom .R<NALA 1>.A<H 13> does not have a type.

Last line in maws is line 961 in intital
aptamer_top = app.AmberPrmtopFile("%s.prmtop"%Ntide)

Traceback (most recent call last):
File "MAWS.py", line 1216, in
positions_and_Ntides = loop()
File "MAWS.py", line 1109, in loop
pos_Nt_S_task.append(initial(al))
File "MAWS.py", line 961, in initial
aptamer_top = app.AmberPrmtopFile("%s.prmtop"%Ntide)
File "/home/laeb/.pyenv/versions/anaconda2-2.5.0/lib/python2.7/site-packages/simtk/openmm/app/amberprmtopfile.py", line 90, in init
for index in range(prmtop.getNumAtoms()):
File "/home/laeb/.pyenv/versions/anaconda2-2.5.0/lib/python2.7/site-packages/simtk/openmm/app/internal/amber_file_parser.py", line 209, in getNumAtoms
return int(self._getPointerValue('NATOM'))
File "/home/laeb/.pyenv/versions/anaconda2-2.5.0/lib/python2.7/site-packages/simtk/openmm/app/internal/amber_file_parser.py", line 205, in _getPointerValue
return float(self._raw_data['POINTERS'][index])
KeyError: 'POINTERS'

installation error in virtual env.

Hi,

I have to use a virtual env. to use pip. Installation step 4 gives this error for both methods:

$conda install anaconda-launcher
ERROR: The install method you used for conda--probably either pip install conda
or easy_install conda--is not compatible with using conda as an application.
If your intention is to install conda as a standalone application, currently
supported install methods include the Anaconda installer and the miniconda
installer. You can download the miniconda installer from
https://conda.io/miniconda.html.

Linux version 3.10.0-514.6.2.el7.x86_64 ([email protected]) (gcc version 4.8.5 20150623 (Red Hat 4.8.5-11) (GCC) ) #1 SMP Thu Feb 23 03:04:39 UTC 2017

Thanks,

Theo

Preprocessing

I am unable to capture the codes for preprocessing.Help me with a proper codeline .

DCN.prmtop missing

MAWS.py ./ IL6_edited.pdb
['DGN', 'DAN', 'DTN', 'DCN']
Choosing from candidates ...
Constructing Ligand/Aptamer complex ...
Constructing Ligand/Aptamer complex ...
Constructing Ligand/Aptamer complex ...
Constructing Ligand/Aptamer complex ...
Aptamer/Ligand complex constructed.
Loading Aptamer/Ligand complex ...
Aptamer/Ligand complex constructed.
Loading Aptamer/Ligand complex ...
Aptamer/Ligand complex constructed.
Loading Aptamer/Ligand complex ...
Traceback (most recent call last):
File "/home/theoa/qiime-env/env/bin/MAWS.py", line 1212, in
Aptamer/Ligand complex constructed.
Loading Aptamer/Ligand complex ...
positions_and_Ntides = loop()
File "/home/theoa/qiime-env/env/bin/MAWS.py", line 1105, in loop
pos_Nt_S_task = pool.map(initial,alphabet)
File "/usr/lib64/python2.7/multiprocessing/pool.py", line 250, in map
return self.map_async(func, iterable, chunksize).get()
File "/usr/lib64/python2.7/multiprocessing/pool.py", line 554, in get
raise self._value
IOError: [Errno 2] No such file or directory: 'DCN.prmtop'

TabError: inconsistent use of tabs and spaces in indentation

Unable to run the program.
This is the error I am getting

line 414
self.process.sendline("loadamberparams "+_HYBRID)
TabError: inconsistent use of tabs and spaces in indentation

README_MAWS.md needs updates OMNIA install instruction

Section #5 in install states:
"Add new channels where from you will download and install the needed packages with the command conda config --add channels https://conda.binstar.org/omnia"

It should be changed to:
"Add new channels where from you will download and install the needed packages with the command conda install -c omnia omnia"

I am currently installing MAWS and found that step didn't work until I made that change.
Thank you!