{"id":4567,"date":"2020-04-29T16:06:59","date_gmt":"2020-04-29T15:06:59","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=4567"},"modified":"2025-09-10T10:32:56","modified_gmt":"2025-09-10T09:32:56","slug":"acpype","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/acpype\/","title":{"rendered":"ACPYPE"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"https:\/\/pypi.org\/project\/acpype\/\">Acpype<\/a> 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.<\/p>\n<p>Version 0.1.1 is installed on the CSF.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>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.<\/p>\n<h2>Set up procedure<\/h2>\n<p>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 <abbr title=\"add '#$ -V' to your jobscript\">inherit these settings<\/abbr>.<\/p>\n<p>Load one of the following modulefiles:<\/p>\n<pre>\r\nmodule load apps\/python\/acpype\/0.1.1\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p>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 <code>qrsh<\/code> &#8211; see below.<\/p>\n<h3>Serial batch job submission<\/h3>\n<p>Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n<pre>\r\n#!\/bin\/bash --login\r\n#SBATCH -p serial      # (or --partition=) Use the nodes dedicated to 1-core jobs\r\n#SBATCH -n 1           # (or --ntasks=) Number of cores\r\n#SBATCH -t 2-0         # 2 day wallclock time limit (max permitted is 7-0)\r\n\r\nmodule purge\r\nmodule load apps\/python\/acpype\/0.1.1\r\n\r\nacpype -i <em>INPUT<\/em> -o <em>OUTPUT<\/em> <em>args...<\/em>\r\n<\/pre>\n<p>Submit the jobscript using: <\/p>\n<pre>sbatch <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<h3>Interactive Usage<\/h3>\n<p>To run acpype interactively on a compute node, use the <code>srun<\/code> command instead of <code>sbatch<\/code>. For example:<\/p>\n<pre>\r\n# On the login node\r\nmodule purge\r\nmodule load apps\/python\/acpype\/0.1.1\r\nsrun -p interactive -n 1 -t 0-1 acpype -i <em>INPUT<\/em> -o <em>OUTPUT<\/em> <em>args...<\/em>\r\n                             #\r\n                             # 1 hour wallclock - this is the maximum permitted\r\n<\/pre>\n<p>Alternatively, log in to the compute node first then load the modulefile:<\/p>\n<pre>\r\nsrun -p interactive -b 1 -t 0-1 --pty bash\r\n\r\n# Wait to be logged in to the compute node, then\r\nmodule purge\r\nmodule load apps\/python\/acpype\/0.1.1\r\nacpype -i <em>INPUT<\/em> -o <em>OUTPUT<\/em> <em>args...<\/em>\r\n\r\n# When finished, return to the login node\r\nexit\r\n<\/pre>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"https:\/\/pypi.org\/project\/acpype\/\">acpype website<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>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.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/acpype\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-4567","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4567","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=4567"}],"version-history":[{"count":3,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4567\/revisions"}],"predecessor-version":[{"id":10924,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4567\/revisions\/10924"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/86"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=4567"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}