acpype
Overview
Acpype is a tool based in Python to use Antechamber to generate topologies for chemical compounds and to interface with others python applications like CCPN or ARIA.
Version 0.1.1 is installed on the CSF.
Restrictions on use
There are no restrictions on accessing the software on the CSF. It is released under the OSI Approved :: MIT License and all usage must adhere to that license.
Set up procedure
We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.
Load one of the following modulefiles:
module load apps/python/acpype/0.1.1
Running the application
Small chemstry files may be converted on the login node. However if converting large files or a large number of files, jobs should be submitted to the compute nodes via batch. You may also run the command interactively via qrsh – see below.
Serial batch job submission
Create a batch submission script (which will load the modulefile in the jobscript), for example:
#!/bin/bash --login #$ -cwd # Job will run from the current directory # NO -V line - we load modulefiles in the jobscript module load apps/python/acpype/0.1.1 acpype -i INPUT -o OUTPUT args...
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Interactive Usage
To run acpype interactively on a compute node, use the qrsh command instead of qsub. For example:
module load apps/python/acpype/0.1.1 qrsh -l short -cwd -V acpype -i INPUT -o OUTPUT args...
Alternatively, log in to the compute node first then load the modulefile:
qrsh -l short # Wait to be logged in to the compute node, then module load apps/python/acpype/0.1.1 acpype -i INPUT -o OUTPUT args... # When finished, return to the login node exit
Further info
Updates
None.