Make it work on Mac OS X

[ghost]

Dear Tomasz,

this is Andrea Ferrante, immunologist from Alaska. I am trying to run your plugin from PyMol for Mac (OsX 10.7.5) l. I have followed your instructions, and I have PyMOL 1.4.1 and GROMACS 4.5.5 installed as well. I have made sure to have Bash, TkInter, Tix and I have X11. As I open the plugin from PyMol, the following error message shows up, and no graphic interface appears:

Error: 1
<type 'exceptions.IndexError'> Exception in Tk callback
  Function: <function init_function at 0x11066c848> (type: <type
'function'>)
  Args: ()
Traceback (innermost last):
  File
"/Applications/PyMOLX11Hybrid.app/pymol/modules/Pmw/Pmw_1_2/lib/PmwBase.py",
line 1747, in __call__
    return apply(self.func, args)
  File
"/Applications/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/startup/dynamics_pymol_plugin.py",
line 721, in init_function
    gromacs = Gromacs_output()
  File
"/Applications/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/startup/dynamics_pymol_plugin.py",
line 97, in __init__
    while lista_gromacs[force_start_line] != "Select the Force Field:\n":
<type 'exceptions.IndexError'>: list index out of range

Would you be so kind to help me to figure out what is missing? I would really like to run some MD with GROMACS and obviously your plugin would help me a lot. No need to say that I will acknowledge it and refer your paper, should I publish any work done with it.

Thank you in advance for your consideration.

Andrea

[ghost]

Hi Andrea, It looks like plugin has problem with listing GROMACS force fields. Could you check if there is a file ~/.dynamics/test_gromacs.txt and if it is present, paste its content here. Also please paste here result of calling GROMACS from Bash, by command: pdb2gmx Hope we will sort this out. Best regards,

[aferrante]

Hi Tomasz, thank you for your reply

I could not find the file you indicated. Maybe I did not install GROMACS properly? When I call GROMACS from Bash, this is what I get:

       :-)  G  R  O  M  A  C  S  (-:

                      GROwing Monsters And Cloning Shrimps

                            :-)  VERSION 4.5.5  (-:

        Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
      Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, 
        Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, 
           Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, 
                Michael Shirts, Alfons Sijbers, Peter Tieleman,

               Berk Hess, David van der Spoel, and Erik Lindahl.

       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
            Copyright (c) 2001-2010, The GROMACS development team at
        Uppsala University & The Royal Institute of Technology, Sweden.
            check out http://www.gromacs.org for more information.

         This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public License
         as published by the Free Software Foundation; either version 2
             of the License, or (at your option) any later version.

                               :-)  pdb2gmx  (-:

Option     Filename  Type         Description
------------------------------------------------------------
  -f      eiwit.pdb  Input        Structure file: gro g96 pdb tpr etc.
  -o       conf.gro  Output       Structure file: gro g96 pdb etc.
  -p      topol.top  Output       Topology file
  -i      posre.itp  Output       Include file for topology
  -n      clean.ndx  Output, Opt. Index file
  -q      clean.pdb  Output, Opt. Structure file: gro g96 pdb etc.

Option       Type   Value   Description
------------------------------------------------------
-[no]h       bool   no      Print help info and quit
-[no]version bool   no      Print version info and quit
-nice        int    0       Set the nicelevel
-chainsep    enum   id_or_ter  Condition in PDB files when a new chain should
                            be started (adding termini): id_or_ter,
                            id_and_ter, ter, id or interactive
-merge       enum   no      Merge multiple chains into a single
                            [moleculetype]: no, all or interactive
-ff          string select  Force field, interactive by default. Use -h for
                            information.
-water       enum   select  Water model to use: select, none, spc, spce,
                            tip3p, tip4p or tip5p
-[no]inter   bool   no      Set the next 8 options to interactive
-[no]ss      bool   no      Interactive SS bridge selection
-[no]ter     bool   no      Interactive termini selection, instead of charged
                            (default)
-[no]lys     bool   no      Interactive lysine selection, instead of charged
-[no]arg     bool   no      Interactive arginine selection, instead of charged
-[no]asp     bool   no      Interactive aspartic acid selection, instead of
                            charged
-[no]glu     bool   no      Interactive glutamic acid selection, instead of
                            charged
-[no]gln     bool   no      Interactive glutamine selection, instead of
                            neutral
-[no]his     bool   no      Interactive histidine selection, instead of
                            checking H-bonds
-angle       real   135     Minimum hydrogen-donor-acceptor angle for a
                            H-bond (degrees)
-dist        real   0.3     Maximum donor-acceptor distance for a H-bond (nm)
-[no]una     bool   no      Select aromatic rings with united CH atoms on
                            phenylalanine, tryptophane and tyrosine
-[no]ignh    bool   no      Ignore hydrogen atoms that are in the coordinate
                            file
-[no]missing bool   no      Continue when atoms are missing, dangerous
-[no]v       bool   no      Be slightly more verbose in messages
-posrefc     real   1000    Force constant for position restraints
-vsite       enum   none    Convert atoms to virtual sites: none, hydrogens
                            or aromatics
-[no]heavyh  bool   no      Make hydrogen atoms heavy
-[no]deuterate bool no      Change the mass of hydrogens to 2 amu
-[no]chargegrp bool yes     Use charge groups in the .rtp file
-[no]cmap    bool   yes     Use cmap torsions (if enabled in the .rtp file)
-[no]renum   bool   no      Renumber the residues consecutively in the output
-[no]rtpres  bool   no      Use .rtp entry names as residue names

Select the Force Field:
From '/usr/local/gromacs/share/gromacs/top':
 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
 8: CHARMM27 all-atom force field (with CMAP) - version 2.0
 9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
15: [DEPRECATED] Encad all-atom force field, using full solvent charges
16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges
17: [DEPRECATED] Gromacs force field (see manual)
18: [DEPRECATED] Gromacs force field with hydrogens for NMR

Thank you for your support!

Andrea

[ghost]

Thank you for the info. It seems that GROMACS is working from bash, but Python for some reason can not use it. I will try to prepare you some Python tests shortly, which will let us know, what is wrong.

[aferrante]

Thank you Tomasz, much appreciated.

[ghost]

Could you download this file: http://ubuntuone.com/5ZdwrrDVqseFNNb3WIXIuE run it from terminal by command: python mac_test.py and paste here the output?

[ghost]

Closing the issue, as it not reproduce.