From: mohammad agha (
Date: Tue May 08 2012 - 15:32:31 CDT

Dear Gianluca, Thank you very much from your help, but I don't know how do I change the configure file and when I type ./configure , I see these: linux_at_linux-P41T-D3:~/vmd-1.8.6$ ./configure ./configure: line 13: =: command not found ./configure: line 16: =/usr/local/bin: No such file or directory ./configure: line 19: =/usr/local/lib/: No such file or directory ./configure: line 23: syntax error near unexpected token `{' ./configure: line 23: `if ($ENV{VMDINSTALLNAME}) {' Please help me. Best Regards Sara ________________________________ From: Gianluca Interlandi <> To: Wang Yi <> Cc: mohammad agha <>; "" <> Sent: Tuesday, May 8, 2012 8:53 PM Subject: Re: vmd-l: flashing the VMD Sara, My guess is that VMD is not correctly installed. You should read the instructions in the README file. You need to edit the file "configure" and modify "$install_bin_dir" "$install_library_dir" to point to the directory where these are installed, then you have to run "./configure", cd to the src directory and run "make install". It's better if you delete the VMD installation and start over following the instructions: 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".   4) After configuration is complete, cd to the src directory,     and type "make install".  This will install VMD in the two     directories listed above.  Note that running "make install"     twice will print error messages because you are attempting to     overwrite some read-only files.  Similarly, if you have incorrectly     specified the target installation directories or attempt to overwrite     an existing VMD installation, you will get error messages.   5) When installed, type 'vmd' to start (make sure the     $install_bin_dir directory is in your path). Gianluca > > > > On 2012-5-8, at ??6:18, mohammad agha wrote: > >      Dear Dr. Kohlmeyer > I did what you said and After "vmd -dispdev text", was typed: > /usr/local/lib/vmd/vmd_LINUX: Command not found. > May I ask you to help me, Please? > > Best Regards > Sara > > > > ----------------------------------------------------- Gianluca Interlandi, PhD                     +1 (206) 685 4435            Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. -----------------------------------------------------