Normal mode analysis from VMD

[Atulsingh17]

I have installed PRODY. When I am running Normal mode wizard from VMD it show error message as following.

Traceback (most recent call last):
File "/usr/local/bin/prody", line 6, in
from pkg_resources import load_entry_point
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 3088, in
@_call_aside
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 3072, in _call_aside
f(*args, **kwargs)
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 3101, in _initialize_master_working_set
working_set = WorkingSet._build_master()
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 574, in _build_master
ws.require(requires)
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 892, in require
needed = self.resolve(parse_requirements(requirements))
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 778, in resolve
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'ProDy==2.0.1' distribution was not found and is required by the application
Traceback (most recent call last):
File "/usr/local/bin/prody", line 6, in
from pkg_resources import load_entry_point
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 3088, in
@_call_aside
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 3072, in _call_aside
f(args, **kwargs)
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 3101, in _initialize_master_working_set
working_set = WorkingSet._build_master()
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 574, in _build_master
ws.require(requires)
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 892, in require
needed = self.resolve(parse_requirements(requirements))
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 778, in resolve
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'ProDy==2.0.1' distribution was not found and is required by the application
while executing
"exec $::NMWiz::pybin $::NMWiz::prody anm --quiet -s $selstr {}$args "$pdbfn""
(procedure "::NMWiz::prodySubmitANMjob" line 42)
invoked from within
"::NMWiz::prodySubmitANMjob"
(procedure "::NMWiz::prodySubmitJob" line 22)
invoked from within
"::NMWiz::prodySubmitJob"
invoked from within
".nmwizprody.submitFrame.prodySubmit invoke"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w invoke]"
(procedure "tk::ButtonUp" line 22)
invoked from within
"tk::ButtonUp .nmwizprody.submitFrame.prodySubmit"
(command bound to event).

Any suggestions would be appreciated.

THANKS

[jamesmkrieger]

How did you install ProDy?

[Atulsingh17]

I installed it manually by using the source code downloaded from this link.

https://pypi.org/project/ProDy/#files

[jamesmkrieger]

You downloaded those files and then did what?

[jamesmkrieger]

Why didn't you just use pip install prody?

[Atulsingh17]

Well I was having problem with pip which may be due different python version.
And I used these commands for installation.

tar -xzf ProDy-x.y.z.tar.gz
cd ProDy-x.y.z
python2.7 setup.py build
python2.7 setup.py install

[jamesmkrieger]

ok

Have you checked whether you got the prody executables in your installation directory? You probably need to use build_ext too

[jamesmkrieger]

We usually recommend using anaconda to handle pip and all the other environment things so you may want to consider that.

[Atulsingh17]

Yes I get that because previuosly when I installed PRODY in my system it was working fine with VMD. But I had to format it due some ubuntu repository problem and reinstalled. This time I am getting this problem.
I am going to try and fix python version problem and then retry with pip.

Thanks for your help.

[jamesmkrieger]

I'm not sure I've really helped yet but you're welcome anyway

[Atulsingh17]

Ok
I have no idea about what build_ext will do.
So I think It would be better for me to correct that pip problem and then retry.

[jamesmkrieger]

We usually use build_ext. It should build the c extensions I think. We use it for development install (see http://prody.csb.pitt.edu/manual/devel/develop.html)

[Atulsingh17]

Ok I will check this too and update.
I also checked that executable are in the installation directory (/usr/local/bin/prody).
Do think this issue might be related with python.

[jamesmkrieger]

Great that the executables are there. I don't really know what the problem is then.

It sounds like something to do with VMD not finding them. Is /usr/local/bin in your PATH?

[Atulsingh17]

Yes /usr/local/bin is in PATH.

[jamesmkrieger]

Did you make sure that your prody python module is also in your PYTHONPATH?

[jamesmkrieger]

Any luck yet? Otherwise, we could arrange a video call to look at it.

[Atulsingh17]

Actually I am out of my institute due to family issues so I am not able to look into it. Will contact you once I reach the institute.
I appreciate your time and concern.
Thanks.

[jamesmkrieger]

Ok, no worries. Hope everything is as ok as it can be