What steps will reproduce the problem?
1. Installing pmx @ mac
2.
3.

What is the expected output? What do you see instead?
running install
running build
running build_py
creating build
creating build/lib.macosx-10.9-intel-2.7
creating build/lib.macosx-10.9-intel-2.7/pmx
copying pmx/__init__.py -> build/lib.macosx-10.9-intel-2.7/pmx
copying pmx/atom.py -> build/lib.macosx-10.9-intel-2.7/pmx
copying pmx/atomselection.py -> build/lib.macosx-10.9-intel-2.7/pmx
copying pmx/builder.py -> build/lib.macosx-10.9-intel-2.7/pmx
copying pmx/chain.py -> build/lib.macosx-10.9-intel-2.7/pmx
copying pmx/cpp.py -> build/lib.macosx-10.9-intel-2.7/pmx
copying pmx/ffparser.py -> build/lib.macosx-10.9-intel-2.7/pmx
copying pmx/forcefield.py -> build/lib.macosx-10.9-intel-2.7/pmx
copying pmx/forcefield2.py -> build/lib.macosx-10.9-intel-2.7/pmx
copying pmx/futil.py -> build/lib.macosx-10.9-intel-2.7/pmx
copying pmx/geometry.py -> build/lib.macosx-10.9-intel-2.7/pmx
copying pmx/histogram.py -> build/lib.macosx-10.9-intel-2.7/pmx
copying pmx/library.py -> build/lib.macosx-10.9-intel-2.7/pmx
copying pmx/model.py -> build/lib.macosx-10.9-intel-2.7/pmx
copying pmx/molecule.py -> build/lib.macosx-10.9-intel-2.7/pmx
copying pmx/mutdb.py -> build/lib.macosx-10.9-intel-2.7/pmx
copying pmx/ndx.py -> build/lib.macosx-10.9-intel-2.7/pmx
copying pmx/odict.py -> build/lib.macosx-10.9-intel-2.7/pmx
copying pmx/options.py -> build/lib.macosx-10.9-intel-2.7/pmx
copying pmx/parser.py -> build/lib.macosx-10.9-intel-2.7/pmx
copying pmx/rotamer.py -> build/lib.macosx-10.9-intel-2.7/pmx
copying pmx/tCNC.py -> build/lib.macosx-10.9-intel-2.7/pmx
copying pmx/xtc.py -> build/lib.macosx-10.9-intel-2.7/pmx
running build_ext
building 'pmx/_pmx' extension
creating build/temp.macosx-10.9-intel-2.7
creating build/temp.macosx-10.9-intel-2.7/src
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os 
-pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE 
-DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g 
-fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch x86_64 -arch i386 
-pipe -Isrc 
-I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c 
src/Geometry.c -o build/temp.macosx-10.9-intel-2.7/src/Geometry.o
clang: error: unknown argument: '-mno-fused-madd' 
[-Wunused-command-line-argument-hard-error-in-future]
clang: note: this will be a hard error (cannot be downgraded to a warning) in 
the future

What version of the product are you using? On what operating system?
MacOs 10.9.2, 3.1 GHz Intel Core i7
8 GB 1600 MHz DDR3

Please provide any additional information below.

Although I have installed all needed packages I couldm't Install pmx 

Original issue reported on code.google.com by [email protected] on 13 Mar 2014 at 3:52

Hi,

could you add a comment how to install pmx as user? I always forget how to do 
that. And new users will surely run into that. The way that is documented needs 
root privileges:

python setup.py install


Neither --help shows how to change the installation directory nor it is obvious 
how to change it from looking into the code. 

Along that: is the following actually required? It shows up after --help:

python setup.py build

Thanks
Soren

Original issue reported on code.google.com by [email protected] on 18 Feb 2015 at 7:06

Hi

You recommend to make a global installation of the packages. I would recommend against this in general (as it might mess with the distribution package manager) and since most users who install this package won't have sudo rights. Installing only for the current user with python setup.py install --user is better. It will also work for normal users.

best Max

Hi
when issuing sudo python setup.py install command, I am facing following error that python.h is not found. Any help will be appreciated.

[sudo] password for jmondal:
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/pmx
copying pmx/rotamer.py -> build/lib.linux-x86_64-2.7/pmx
copying pmx/mutdb.py -> build/lib.linux-x86_64-2.7/pmx
copying pmx/histogram.py -> build/lib.linux-x86_64-2.7/pmx
copying pmx/forcefield.py -> build/lib.linux-x86_64-2.7/pmx
copying pmx/options.py -> build/lib.linux-x86_64-2.7/pmx
copying pmx/ffparser.py -> build/lib.linux-x86_64-2.7/pmx
copying pmx/model.py -> build/lib.linux-x86_64-2.7/pmx
copying pmx/geometry.py -> build/lib.linux-x86_64-2.7/pmx
copying pmx/futil.py -> build/lib.linux-x86_64-2.7/pmx
copying pmx/cpp.py -> build/lib.linux-x86_64-2.7/pmx
copying pmx/library.py -> build/lib.linux-x86_64-2.7/pmx
copying pmx/xdrfile.py -> build/lib.linux-x86_64-2.7/pmx
copying pmx/atomselection.py -> build/lib.linux-x86_64-2.7/pmx
copying pmx/init.py -> build/lib.linux-x86_64-2.7/pmx
copying pmx/ndx.py -> build/lib.linux-x86_64-2.7/pmx
copying pmx/chain.py -> build/lib.linux-x86_64-2.7/pmx
copying pmx/builder.py -> build/lib.linux-x86_64-2.7/pmx
copying pmx/molecule.py -> build/lib.linux-x86_64-2.7/pmx
copying pmx/forcefield2.py -> build/lib.linux-x86_64-2.7/pmx
copying pmx/odict.py -> build/lib.linux-x86_64-2.7/pmx
copying pmx/tCNC.py -> build/lib.linux-x86_64-2.7/pmx
copying pmx/parser.py -> build/lib.linux-x86_64-2.7/pmx
copying pmx/atom.py -> build/lib.linux-x86_64-2.7/pmx
copying pmx/xtc.py -> build/lib.linux-x86_64-2.7/pmx
running build_ext
building 'pmx/_pmx' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/src
creating build/temp.linux-x86_64-2.7/src/pmx
x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Isrc/pmx -I/usr/include/python2.7 -c src/pmx/Geometry.c -o build/temp.linux-x86_64-2.7/src/pmx/Geometry.o
In file included from src/pmx/Geometry.h:32:0,
from src/pmx/Geometry.c:31:
src/pmx/pmx.h:32:20: fatal error: Python.h: No such file or directory
#include <Python.h>
^
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

What steps will reproduce the problem?
1. Read XTC file with a periodic box and use get_box()
2. notice that the second column of the matrix is repeated
3. the third column is not displayed at all

What is the expected output? What do you see instead?
box matrix should be properly read

Patch in branch fix-xtc-box at:
https://code.google.com/r/rei4dan-pmx/

Original issue reported on code.google.com by [email protected] on 10 Jan 2014 at 5:24

In random_rotation, uniform random numbers are generated between zero and 360.

I copied part of this code for my project and found that phi should actually be in radians, so that the range should be between 0 and 2pi. Unless something is somehow different on my system.

Hi,
I understand pmx would be under constant development but still it would be helpful for the users if a test dataset eg. tripeptide or trp cage is included in the package with intermediate analysis files.
In addition benchmarks of output free energy parameters would be helpful for users to validate their runs.
Thanks.

Hi, a project of mine involves single-stranded RNA/protein interactions, where we have some experimental / structural information on affinity changes based on single site mutations of the RNA sequence. I'm considering mutational free energy calculations as a complement to help prove our structural models.
I've noted in the code here that while there is no current support in mutate_v2.py to create hybrid topology files, there seems to be an intention of adding the relevant files (via adding mutres_dna.mtp, etc.)

Are there people who do intend to work on this that you know of? Or is this a paused feature?

Pmx installation
Hi dear friends. I try to install Pmx on Ubuntu 20.04 after writing the installation command, below output displayed on terminal. Is Pmx installed?