VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 14 2007 - 12:23:16 CDT

Hi,
  Do you have MSMS installed as "msms" and in a directory that's in
your command search path? VMD finds MSMS using your command shell's
search path. If you can run it by invoking 'msms' at the command line,
then VMD should be able to find it. The error messages you got from
Perl look pretty harmless, since the configure script ran properly.
You just need to continue with the 'cd src; make install' steps as
described in the documentation, in order to complete the install.
Reinstalling VMD will have no bearing on whether or not it fins MSMS
however, just so you know... It will find MSMS by the command search
path, or if you manually set the environment variable MSMSSERVER to
the fully qualified pathname of the executable.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 14, 2007 at 11:07:38AM -0500, Audrey Salazar wrote:
> Hello,
> I am a first year grad student new to VMD. I would like to be able to
> make images and movies in VMD 1.8.6. As MSMS is required by VMD to
> make movies (according to page 1 of the VMD Images and Movies
> tutorial), I installed MSMS. I tested the MSMS separately as suggested
> by http://mgltools.scripps.edu/downloads (the page after this one,
> doesn't want to load, but I clicked on the Unix/Linux i86 link) and
> the output from MSMS is correct. This suggests that this program is
> working as it should.
>
> As I have previously built VMD from source code, I decided to do that
> again. I followed the following instructions (from README file for
> VMD 1.8.6):
>
> For quick installation of the binary distribution for Unix do the following:
> 1) Uncompress and untar the distribution into a working directory.
> In this working directory, there are several subdirectories such
> as bin, src, doc, data, as well as this README and a configure script.
> Change to this working directory after the unpacking is complete.
>
> 2) Edit the file 'configure'; change the values for
> the $install_library_dir and $install_bin_dir to a directory in
> which vmd data files and executables should be installed, be sure
> that you installing into a clean target directory and not overwriting
> an existing version of VMD (which would otherwise give problems):
>
> $install_bin_dir is the location of the startup script 'vmd'.
> It should be located in the path of users interested in running VMD.
>
> $install_library_dir is the location of all other VMD files.
> This included the binary and helper scripts. It should not be
> in the path.
>
> 3) A Makefile must be generated based on these configuration variables
> by running "./configure".
>
> When I typed ./configure, I get the following oiutput:
>
> perl: warning: Setting locale failed.
> perl: warning: Please check that your locale settings:
> LANGUAGE = (unset),
> LC_ALL = (unset),
> LANG = "english"
> are supported and installed on your system.
> perl: warning: Falling back to the standard locale ("C").
> using configure.options: LINUX OPENGL FLTK TK ACTC IMD SPACEBALL
> LIBTACHYON VRPN NETCDF TCL PYTHON PTHREADS NUMPY SILENT
>
> ** From the last line, I am gathering that the config script did not
> find MSMS. Am I correct in my assumption?
>
>
> ** How can I make sure that VMD is configured to work with MSMS? Do I
> need to edit the configure.options file to include MSMS?
>
> Thank you in advance.
>
> Audrey Salazar
> --
> Audrey L. Salazar
> Amaral Research Group
> Dept. of Chemical and Biological Engineering Phone: 847.491.2188
> Northwestern University
> Evanston, IL USA 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078