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Using BHINTERP to find minima between two end points - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Using_BHINTERP_to_find_minima_between_two_end_points6 Jan 2021: Often they are initial and final structures of studied path or reaction (however, here reaction means geometrical change in the system, not breaking and forming new bonds). ... overwrite! Update: new version of PATHSAMPLE does not overwrite this file, -
Creating movies (.mpg) of paths using OPTIM - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Creating_movies_(.mpg)_of_paths_using_OPTIM6 Jan 2021: If this doesn't help, then the NEWCONNECT commands in odata will tell OPTIM to try to bridge the gap by finding new TSs in the usual way to form a -
Using VMD to display and manipulate '.pdb' files - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Using_VMD_to_display_and_manipulate_%27.pdb%27_files6 Jan 2021: Formyl. Vinyl. Chloride. Hydroxyl. Methyl. Those you can start a new molecule from are:. -
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). -
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. -
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. -
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. -
Upgrading destiny - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Upgrading_destiny6 Jan 2021: Upgrading destiny. From CUC3. Destiny is to be upgraded to SuSE and at the same time have a new disk installed to give a bigger /scratch and /usr/local. -
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:. -
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. -
Other IT stuff - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Other_IT_stuff6 Jan 2021: Other IT stuff. From CUC3. Made this page so I can provide links to older IT pages and not clutter up the 'headlines' on the front page. Retrieved from "". Navigation menu. Personal tools. Namespaces. Variants. Views. More. Search. Navigation. -
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? -
Visitor policy - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Visitor_policy6 Jan 2021: This information is used to set up UCS computer accounts in advance and is needed for any new member of staff. -
Maui compilation - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Maui_compilation6 Jan 2021: Maui compilation. From CUC3. It's 7/6/06 at time of writing. On new mek-quake torque-2.1 does not work with current Maui because they have chnaged the -
Computer Office services - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Computer_Office_services6 Jan 2021: Computer Office services. From CUC3. This has moved to the COs' wiki. COs only! And even more recently, this has gone public on (Raven password needed, but if you got here then you already have one). Retrieved from "". Navigation menu. Personal tools -
General queueing problems - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/General_queueing_problems6 Jan 2021: General queueing problems. From CUC3. This page is for general queueing discussion. There are specific pages for discussing mek-quake and tardis. I have moved the paragraph from the page for me-quake as it is more appropriate here. --Catherine 09:55, -
GPU processing - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/GPU_processing6 Jan 2021: I need a new version of the image without those SuSE libs to use on these machines. ... The auto-patching script doesn't do kernels on 10.2 so it will always need a computer officer's intervention to do a new kernel anyway.
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