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Git - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Git6 Jan 2021: 100% (3/3) done refs/remotes/origin/master: fast forward to branch 'master' of file:///Users/athom/tmp/git/tmp/Cambridge old.new: 880aefd.62b3628 Merge made by recursive. -
Simple scripts for LEaP to create topology and coordinate files - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Simple_scripts_for_LEaP_to_create_topology_and_coordinate_files6 Jan 2021: If you have more than one new residue, just load frcmod and prepin files for each of them. -
Loading coordinate files into VMD with the help of an AMBER topology…
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Loading_coordinate_files_into_VMD_with_the_help_of_an_AMBER_topology_file6 Jan 2021: It can be found by going to File >> New Molecule and then browsing for the topology file you need. ... Then check the file type carefully, the new version of VMD automatically assumes that mdcrd files are not periodic, so if your coordinate file is -
Calculating rate constants (GT and fastest path) - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Calculating_rate_constants_(GT_and_fastest_path)6 Jan 2021: Files min.[A,B,data].fastest, ts.data.fastest,points.[min,ts].fastest: a new database containing only the stationary points on the fastest path. ... connect them, and all the individual stationary points in those groups will be written to new. -
Rama upgrade - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Rama_upgrade6 Jan 2021: The ancient OpenPBS queueing system will be replaced with shiny new Torque (it'll look exactly the same to users, but work lots better behind the scenes). -
Compiling AMBER Tools so you can start making input and analyzing…
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Compiling_AMBER_Tools_so_you_can_start_making_input_and_analyzing_output6 Jan 2021: export AMBERHOME=/home/$USER/svn/AMBERTOOLS. Exit vi and then source the file you just altered to export the new variable:. ... Old $PATH:. export PATH=$PATH:/home/csw34/scripts. New $PATH. export PATH=$PATH:/home/csw34/scripts:$AMBERHOME/exe. Once you -
If you need to change the number of atoms (e.g. making a united-atom…
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/If_you_need_to_change_the_number_of_atoms_(e.g._making_a_united-atom_charmm19_.crd_file,_or_if_atoms_are_missing)6 Jan 2021: 2. Sample section of the input for a charmm run:. OPEN UNIT 20 FORM NAME protein_new.pdb READ! ... Excuse the lack of docu for this program ;-) Then paste the new coordinates into your newly-made. -
Relaxing existing transition states with new potential and creating…
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Relaxing_existing_transition_states_with_new_potential_and_creating_new_database6 Jan 2021: 6. next step: creation new binary file points.ts; you will need new pathdata file:. ... Still it is worthy to check where in fact both endpoints are placed in new database. -
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_system6 Jan 2021: to save the ligand you are editing as a new PDB using File>Save and changing the type to. ... R<CILE 385> Created a new atom named: O2 within residue:. R<CILE 385> Added missing heavy atom:. -
Perm-prmtop.py - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Perm-prmtop.py6 Jan 2021: For the new topology file, the energy is invariant to permutation of the aforementioned atoms or groups :). ... How do I use it? /perm-prmtop.py name-of-topology-file name-of-new-topology-file. Where can I find it?
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