VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Aug 14 2007 - 11:31:49 CDT

On Tue, 14 Aug 2007, Audrey Salazar wrote:

AS> Hello,
AS> I am a first year grad student new to VMD. I would like to be able to
AS> make images and movies in VMD 1.8.6. As MSMS is required by VMD to
AS> make movies (according to page 1 of the VMD Images and Movies

hello,
not correct. you need MSMS only if you want to use the MSMS
representation (and not e.g. SURF which is shipped with VMD).

AS> tutorial), I installed MSMS. I tested the MSMS separately as suggested
AS> by http://mgltools.scripps.edu/downloads (the page after this one,
AS> doesn't want to load, but I clicked on the Unix/Linux i86 link) and
AS> the output from MSMS is correct. This suggests that this program is
AS> working as it should.
AS>
AS> As I have previously built VMD from source code, I decided to do that
AS> again. I followed the following instructions (from README file for
AS> VMD 1.8.6):
AS>
AS> For quick installation of the binary distribution for Unix do the following:
AS> 1) Uncompress and untar the distribution into a working directory.
AS> In this working directory, there are several subdirectories such
AS> as bin, src, doc, data, as well as this README and a configure script.
AS> Change to this working directory after the unpacking is complete.
AS>
AS> 2) Edit the file 'configure'; change the values for
AS> the $install_library_dir and $install_bin_dir to a directory in
AS> which vmd data files and executables should be installed, be sure
AS> that you installing into a clean target directory and not overwriting
AS> an existing version of VMD (which would otherwise give problems):
AS>
AS> $install_bin_dir is the location of the startup script 'vmd'.
AS> It should be located in the path of users interested in running VMD.
AS>
AS> $install_library_dir is the location of all other VMD files.
AS> This included the binary and helper scripts. It should not be
AS> in the path.
AS>
AS> 3) A Makefile must be generated based on these configuration variables
AS> by running "./configure".
AS>
AS> When I typed ./configure, I get the following oiutput:
AS>
AS> perl: warning: Setting locale failed.
AS> perl: warning: Please check that your locale settings:
AS> LANGUAGE = (unset),
AS> LC_ALL = (unset),
AS> LANG = "english"
AS> are supported and installed on your system.
AS> perl: warning: Falling back to the standard locale ("C").
AS> using configure.options: LINUX OPENGL FLTK TK ACTC IMD SPACEBALL
AS> LIBTACHYON VRPN NETCDF TCL PYTHON PTHREADS NUMPY SILENT
AS>
AS> ** From the last line, I am gathering that the config script did not
AS> find MSMS. Am I correct in my assumption?

no. the configure script is not the typical autoconf/automake configure
that that scans your system for installed components and properties,
but just a perl script that compiles a Makefile from templates based
on options that you provide on the command line. this looks like you
are actually using a binary distribution of VMD and not the sources.

regardless, support for MSMS is always compiled in, regardless of
whether you have it installed or not.

AS> ** How can I make sure that VMD is configured to work with MSMS? Do I
AS> need to edit the configure.options file to include MSMS?

nothing. just compile(?)/install it.

cheers,
   axel.
AS>
AS> Thank you in advance.
AS>
AS> Audrey Salazar
AS> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.