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  2. Notes on MINPERMDIST - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Notes_on_MINPERMDIST
    Notes on MINPERMDIST. From Docswiki. The subroutine that must not be named. Bringing of headaches. Bane of Friday afternoons. Mother of alignment algorithms. This page aims to collect useful information on how MINPERMDIST works to assist in the
  3. Connecting Sub-databases - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Connecting_Sub-databases
    00003_00303 670 811 connectlowest> Distance: 24.67395896. Error creating thumbnail: Unable to save thumbnail to destination.
  4. Adding partially finished OPTIM stationary points to a PATHSAMPLE…

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Adding_partially_finished_OPTIM_stationary_points_to_a_PATHSAMPLE_database
    Navigation. Tools. This page was last edited on 10 May 2019, at 18:24.
  5. Generating parameters using AMBER's built in General Forcefield…

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Generating_parameters_using_AMBER%27s_built_in_General_Forcefield_(gaff)
    Navigation. Tools. This page was last edited on 13 May 2019, at 10:24.
  6. Calculating rate constants (GT and fastest path) - Docswiki

    https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Calculating_rate_constants_(GT_and_fastest_path)
    2100556 Dijkstra> MFPT for fastest path: A<-B value= 0.7030943368E25 B<-A value= 0.2425804971E-08 Dijkstra> rates without conditional probability: A<-B value= 0.1422284248E-24 B<-A value= ... 412234294.2 Dijkstra> rates with conditional probability: A<-B
  7. 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
    PAC A 317 17.578 25.580 63.751 1.00 15.05 C ATOM 2564 C1' PAC A 317 17.351 24.336 62.935 1.00 22.49 C ... 00 15.05 H ATOM 0 H2' PAC A 317 19.077 24.466 61.823 1.00 24.42 H.
  8. 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)
    144.0096582 5.4996 -149.5092547 24.935 17.263 1.969 24.372 18 -149.5092547 0.11279E-01 -149.4979756 3.8322 -153.3301944 6.223 5.891

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