Getting Started
Computational simulations are performed on a system. What do I mean by a system? Just a simple pdb file that has the required number of molecules of the compounds or elements you wish to work on.
Sidenote
Remember: Packmol works with mol2 and xyz format files too. Changes: You need to change ".pdb" to ".xyz" or ".mol2", as per the need!
The quick three steps
- Get the pdb/xyz/mol2 files for each component of your system.
- Get a suitable packmol script.
- Run the script using the command:
./packmol < mixture.txt
The Proper Elucidation
Equipments required:
1) Crystal Pdb file for each of the compounds/elements.
2) Packmol software. It is an open source
software:
PS: Don't forget to register. ;)
That's all you need.
I will assume that you followed the installation process on their website and did
the needful.
If you face any installation problems you can direct those
mails to their owners.
1. Pdb
We need the pdb files containing the coordinates of a single molecule of
our compound.
If it is a complex that you are working on, then you need
the pdb of the complex.
But make sure it has the coordinates of only one
such complex.
How to get the pdb file:
- a. Geometry optimization using Quantum Calculations
- b. Get it from pdb databank. (Recommended method)
- c. From other source (as per your need)
2. Script
To run packmol, you need a .txt file
that will specify the quantity of
different molecules and constraint that you want to apply to get a desired
system. Packmol gives it's user the ability to specify the size of the
system and the number of molecules of each compound in the system.
Apart from these, you can also specify whether you want Packmol to
randomly distribute the molecules inside the box or to place it exactly
at a fixed coordinate. There are some other options too (manual).
Here is a
nicely commented Packmol script file to help you out.
Save this file as mixture.txt, and read it through to get a feel. Feel free to refer to the
manual
for more help.
3. Run
If you have come this far, then we are almost done!! Open cmd or terminal, crawl to the present directory and type:
Linux: ./packmol < mixture.txt CMD: packmol.exe < mixture.txt
The code should run (without error) and an output file will be created.
You can visualize the output in
VMD
or any other visualizing tool of your choice.
Danke!! :)
Let me know if I erred!!