Memasang VMD dari File Binary

Salah satu aplikasi kimia yang sering dipakai sebagai viewer dalam komputasi adalah software VMD. 
“VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting”
Untuk memasang VMD dalam Blankon/Ubuntu/Linux perlu dilakukan langkah-langkah berikut:
2.  Masuk ke terminal dengan klik Aplikasi –> Aksesoris –> Terminal atau tekan “Ctrl+Alt+T”
3.  Masuk ke direktori tempat download file VMD
4.  Ekstrak file tersebut dengan ketik: tar -xvf vmd-1.9.bin.LINUX.opengl.tar.gz
5.  Masuk ke folder hasil ekstrak file VMD, ketik cd vmd-1.9
6.  Baca file README dengan ketik: gedit README
     Perhatikan bagian akhir file: Quick Installation Instructions
7.  Perhatikan langkah-langkah instalasi berikut:

Quick Installation Instructions
————————————————-
Detailed instructions for compiling VMD from source code
can be found in the programmer’s guide.

The Windows version of VMD is distributed as a self-extracting
archive, and should be entirely self explanatory. 

The native MacOS X version of VMD is packaged as a disk image and is
extracted by opening the disk image, and dragging the “VMD” application
contained inside into an appropriate directory.

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 andinstall_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'.  </span></div><div style="color: blue; text-align: left;"><span style="font-size: x-small;">     It should be located in the path of users interested in running VMD.</span></div><div style="color: blue; text-align: left;"><span style="font-size: x-small;"></span></div><div style="color: blue; text-align: left;"><span style="font-size: x-small;">    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
    

*** QuickLaTeX cannot compile formula:
install_bin_dir directory is in your path).</span></div><div style="text-align: left;">8.  Baca file "configure", perhatikan bagian awalnya:</div><div style="color: blue;"><span style="font-size: x-small;">#!/usr/bin/env perl</span></div><div style="color: blue;"><span style="font-size: x-small;"># (C) Copyright 1995-2011 The Board of Trustees of the University of Illinois</span></div><div style="color: blue;"><span style="font-size: x-small;">#     All Rights Reserved</span></div><div style="color: blue;"><span style="font-size: x-small;">#</span></div><div style="color: blue;"><span style="font-size: x-small;"># Usage: configure [ optionlist ]   (See full option description down below)</span></div><div style="color: blue;"><span style="font-size: x-small;"># Perl 5.x must be in your path, and /usr/bin/env must exist in order</span></div><div style="color: blue;"><span style="font-size: x-small;"># for this to work correctly.</span></div><div style="color: blue;"><span style="font-size: x-small;"></span></div><div style="color: blue;"><span style="font-size: x-small;">##############################################################################</span></div><div style="color: blue;"><span style="font-size: x-small;"># User modifiable installation parameters, can be overridden by env variables</span></div><div style="color: blue;"><span style="font-size: x-small;">##############################################################################</span></div><div style="color: blue;"><span style="font-size: x-small;"># Name of shell script used to start program; this is the name used by users</span></div><div style="color: blue;"><span style="font-size: x-small;">

*** Error message:
You can't use `macro parameter character #' in math mode.
leading text: ... blue;"><span style="font-size: x-small;">#
You can't use `macro parameter character #' in math mode.
leading text: ... blue;"><span style="font-size: x-small;">#
You can't use `macro parameter character #' in math mode.
leading text: ... blue;"><span style="font-size: x-small;">#
You can't use `macro parameter character #' in math mode.
leading text: ... blue;"><span style="font-size: x-small;">#
You can't use `macro parameter character #' in math mode.
leading text: ... blue;"><span style="font-size: x-small;">#
You can't use `macro parameter character #' in math mode.
leading text: ... blue;"><span style="font-size: x-small;">#
You can't use `macro parameter character #' in math mode.

install_name = “vmd”;


# Directory where VMD startup script is installed, should be in users’ paths.
install_bin_dir="/usr/local/bin";</span></div><div style="color: blue;"><span style="font-size: x-small;"></span></div><div style="color: blue;"><span style="font-size: x-small;"># Directory where VMD files and executables are installed</span></div><div style="color: blue;"><span style="font-size: x-small;">install_library_dir=”/usr/local/lib/install_name";</span></div><div style="color: blue;"><span style="font-size: x-small;"></span></div><div style="color: blue;"><span style="font-size: x-small;"></span></div><div style="color: blue;"><span style="font-size: x-small;"># optionally override hard-coded defaults above with environment variables</span></div><div style="color: blue;"><span style="font-size: x-small;">if (ENV{VMDINSTALLNAME}) {
  install_name =ENV{VMDINSTALLNAME}
}
if (ENV{VMDINSTALLBINDIR}) {</span></div><div style="color: blue;"><span style="font-size: x-small;"> install_bin_dir = ENV{VMDINSTALLBINDIR}</span></div><div style="color: blue;"><span style="font-size: x-small;">}</span></div><div style="color: blue;"><span style="font-size: x-small;">if (ENV{VMDINSTALLLIBRARYDIR}) {
  install_library_dir =ENV{VMDINSTALLLIBRARYDIR}
}

9.  Okay, sekarang masuk ke folder vmd-1.9
10.ketik: ./configure
11. masuk ke folder “src” dengan ketik: cd src
12. ketik: make install
13. Biarkan sampai instalasi selesai
14. untuk menjalankan software VMD ketik: vmd [Enter]
15. Selamat berlatih!

1 Comment

Filed under Kimia, Komputasi, Linux, Software, vmd

One Response to Memasang VMD dari File Binary

  1. terima kasih sebelumnya untuk postingan tutorial instalasi vmd pada ubuntu. kebetulan sy lg butuh instal vmd buat rekan yang sdg studi ttg kimia. tp setelah proses instalasi usai, sy msh blm bs menjalankan aplikasi tersebut.
    pd langkah 14, dimana saya ketikkan perintah 'vmd' ? sy pemula dalam ubuntu, mohon bantuannya. terima kasih

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