From Binary distribution

Supported systems

In this new version, binary package support has been included. However, few systems are supported at this moment:.

Systems not included in this list may work without problems (specially RHES 6 clones), but the test were carried out only in these platforms

Common steps

Before installing the binary packages and depending on the target platform, you may need to install certain packages such as OpenBabel and mopac. Also, you will need a OpenEye Academic License in order to run the platform, which is provided free of charge by OpenEye. For more detail about this license see the installation from source section

To set up the license we have to declare the variable OE_LICENSE to the place where the Openeye license file is located (usually at /usr/local/vsdmip/share/oe_license.txt. To this purpose we should edit the file /etc/profile, the file $HOME/.bashrc or the file $HOME/.tcshrc and add the next line for Bash:

export OE_LICENSE=/usr/local/vsdmip/share/oe_license.txt

Or in the case of tcsh/csh

setenv OE_LICENSE /usr/local/vsdmip/share/oe_license.txt

Scientific Linux and Red Hat Enterprise server clones

Download the required packages at the VSDMIP web page and proceed with the next commands:

[user@node $] rpm -ivh vsdmip_local_pack_$platform_$architecture_1.5.rpm
vsdmip_pack_$platform_$architecture_1.5.rpm vsdmip_udf_pack_$platform_$architecture_1.5.rpm
[user@node $]  cd /usr/local/vsdmip/
[user@node $]  $DOWNLOAD_PATH/vsdmip_openbabel-2.3.0-mod_$platform_$architecture_1.5.sh
vsdmip-openbabel-mod Installer Version: 0.1.1, Copyright (c) Humanity
This is a self-extracting archive.
The archive will be extracted to: /usr/local/vsdmip

If you want to stop extracting, please press Ctrl-C
LICENSE
=======

This is an installer created using CPack (http://www.cmake.org). No license provided.



Do you accept the license? [yN]: 
y
By default the vsdmip-openbabel-mod will be installed in:
  "/usr/local/vsdmip/openbabel-2.3.0-mod_vsdmip15"
  Do you want to include the subdirectory openbabel-2.3.0-mod_vsdmip15?
  Saying no will install in: "/usr/local/vsdmip" [Yn]: 
  n

Using target directory: /usr/local/vsdmip
Extracting, please wait...

   

Warning

You must answer no at the second question in order to properyly install OpenBabel 2.3.0_mod in the correct path and not in a subdirectory

Debian and clones (Ubuntu)

Download the required packages at the VSDMIP web page and proceed with the next commands:

[user@node $] dpkg -i vsdmip_local_pack_$platform_$architecture_1.5.dpkg
        vsdmip_pack_$platform_$architecture_1.5.dpkg vsdmip_udf_pack_$platform_$architecture_1.5.dpkg
        [user@node $] cd /usr/local/vsdmip/
        [user@node $] $DOWNLOAD_PATH/vsdmip_openbabel-2.3.0-mod_$platform_$architecture_1.5.sh
        vsdmip-openbabel-mod Installer Version: 0.1.1, Copyright (c) Humanity
        This is a self-extracting archive.
        The archive will be extracted to: /usr/local/vsdmip

If you want to stop extracting, please press Ctrl-C
LICENSE
=======

This is an installer created using CPack (http://www.cmake.org). No license provided.



Do you accept the license? [yN]:
y
By default the vsdmip-openbabel-mod will be installed in:
  "/usr/local/vsdmip/openbabel-2.3.0-mod_vsdmip15"
    Do you want to include the subdirectory openbabel-2.3.0-mod_vsdmip15?
      Saying no will install in: "/usr/local/vsdmip" [Yn]:
        n

Using target directory: /usr/local/vsdmip
Extracting, please wait...

   

Warning

You must answer no at the second question in order to properyly install OpenBabel 2.3.0_mod in the correct path and not in a subdirectory

Now, you have to install openbabel and mopac7-bin packages in order to me able to run the platform properyly.

        [user@node $] apt-get install mopac7-bin openbabel

   

Database modules and schema

Once the software is installed, a database should be created and populated:

[user@dbmaster $] mysql -u root -p -D VSDB < /usr/local/vsdmip/share/define_UDFs.sql
Enter password:
[user@dbmaster $] mysql -u root -p -D VSDB < /usr/local/vsdmip/share/VSDMIP15.sql
Enter password:

For a full explanation of the MySQL installation see the source code installation section.

Windows installation

Download the auto-installer and follow the instructions. Then install PyMOL and the plugin and configure the paths in the application as explained in Plugin manual sections

Plugin installation

Download the file vsdmip.py from the web and install using the PyMOL plugin installer dialog.

Plugin->Manage Plugins->Install

At the first run, configure application paths for the local programs and remote cluster, ensuring you have access to the cluster nodes using passwordless SSH

Warning

In order to run remote commnands from the plugin you should be able to login to the remote machine without a password (using keys) and without any prompt. To configure login using keys, please read the source code installation section about SSH-key login.