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Setting up (CHARMM) - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Setting_up_(CHARMM)NOTE: if your system is NOT a standard peptide/protein, you will need to make the perm.allow file manually! ... Here is some example CHARMM input to do this. You will need to change the set pardir line to point to where you have your copy of the svn -
Preparing an AMBER topology file for a protein plus ligand system -…
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Preparing_an_AMBER_topology_file_for_a_protein_plus_ligand_systemThis is a problem! We will need to add them back in using e.g. ... Molfacture, a tool in VMD. You will need the latest version of VMD to do this so either download and compile it yourself (which is pretty easy - honest!), or use my
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