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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. -
Notes on MINPERMDIST - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Notes_on_MINPERMDISTNotes 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 -
Connecting Sub-databases - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Connecting_Sub-databases00003_00303 670 811 connectlowest> Distance: 24.67395896. Error creating thumbnail: Unable to save thumbnail to destination. -
Generating pdb, crd and psf for a peptide sequence - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Generating_pdb,_crd_and_psf_for_a_peptide_sequenceNATOM 1 ALAD 1 ALA CAY 24 -0.270000 12.0110 0 0.00000 -0.301140E-02 2 ALAD 1 ALA HY1 3 0.900000E-01 1.00800 0 0.00000 ... 0.900000E-01 1.00800 0 0.00000 -0.301140E-02 11 ALAD 1 ALA CB 24 -0.270000 12.0110 0 0.00000 -0.301140E-02 12 ALAD 1 ALA -
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 -
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 -
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_methodPAC 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.
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