[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
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
I am now going to attempt running some examples.
Thanks again for your help!
Kelly
________________________________
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
--
==========================================
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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