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31 - 34 of 34 search results for download |u:wikis.ch.cam.ac.uk

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  2. Preparing an AMBER topology file for a protein plus ligand system -…

    https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Preparing_an_AMBER_topology_file_for_a_protein_plus_ligand_system
    6 Jan 2021: 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

  3. 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_system
    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

  4. Finding an initial path with OPTIM and starting up PATHSAMPLE…

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Finding_an_initial_path_with_OPTIM_and_starting_up_PATHSAMPLE_(CHARMM)
    If you are having problems, you can download a compressed archive of all the files in the PATHSAMPLE directory here, and compare what you have with them!

  5. Calculating binding free energy using the FSA method - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Calculating_binding_free_energy_using_the_FSA_method
    For NADP+, we use slightly modified parameters from the AMBER Parameter Database that you can download here and here.

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