[gmx-users] Installing Gromacs 4.6.3 using Cygwin

chem grad kelly.summers at usask.ca
Mon Dec 16 22:09:42 CET 2013

Thank you so much for your help!

I think I sorted it out. I configured my environment using the command $PATH=cygdrive/c/Cygwin/usr/local/gromacs/lib:$PATH and now the g_luck command returns a quote and pdb2gmx returns:

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

             Gallium Rubidium Oxygen Manganese Argon Carbon Silicon

                            :-)  VERSION 4.6.4  (-:

        Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
           Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
     Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
        Peter Kasson, Carsten Kutzner, 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) 2001-2012,2013, 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 Lesser General Public License
        as published by the Free Software Foundation; either version 2.1
             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
-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
-[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
-[no]glu     bool   no      Interactive glutamic acid selection, instead of
-[no]gln     bool   no      Interactive glutamine selection, instead of
-[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
-[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

I am now going to attempt running some examples.

Thanks again for your help!
From: Justin Lemkul [via GROMACS] [ml-node+s5086n5013322h50 at n6.nabble.com]
Sent: Friday, December 13, 2013 3:23 PM
To: Summers, Kelly
Subject: Re: Installing Gromacs 4.6.3 using Cygwin

On Fri, Dec 13, 2013 at 3:38 PM, chem grad <[hidden email]<UrlBlockedError.aspx>> wrote:

> Actually... yes, I may have spoken too soon... I can see Gromacs on my
> machine, but I am still struggling to get it to run properly.
> I cannot convince cygwin to source the gromacs files properly (well, at
> least I think that's the problem). When I enter "luck" into the command
> line it returns the "luck: command not found" error message.
"luck" does not exist any more; it is named "g_luck" now.

> Also, both commands I have entered (pdb2gmx and mdrun) have returned the
> following error:
> /usr/local/gromacs/bin/pdb2gmx.exe: error while loading shared libraries:
> cyggmxpreprocess-8.dll: cannot open shared object file: No such file or
> directory
> Maybe I was not as successful as I thought with the install?
Well, the installation succeeded, but now you likely have to configure your
environment to find the libraries.  I honestly have no idea on how to do
that on Windows.  If it were Linux... ;)




Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

[hidden email]<UrlBlockedError.aspx> | (410) 706-7441

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