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STARTING INITIAL PATH JOBS WITH PATHSAMPLE - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/STARTING_INITIAL_PATH_JOBS_WITH_PATHSAMPLEattempts and add new stationary points to the database. -
Using BHINTERP to find minima between two end points - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Using_BHINTERP_to_find_minima_between_two_end_pointsOften 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, -
Using VMD to display and manipulate '.pdb' files - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Using_VMD_to_display_and_manipulate_%27.pdb%27_filesFormyl. Vinyl. Chloride. Hydroxyl. Methyl. Those you can start a new molecule from are:. -
Ligand binding-mode searches with HBONDMATRIX - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Ligand_binding-mode_searches_with_HBONDMATRIXA hydrogen-bond matrix is generated for the new structure, and is compared to all existing groups. ... almost every step would end up in a new mode, and so be rejected. -
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). -
Pathway Gap Filling Post-CHECKSPMUTATE - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Pathway_Gap_Filling_Post-CHECKSPMUTATEThus, there will be gaps in our new, mutated pathway. Hence the need for post-processing to fill these gaps. ... HOWEVER, it must be noted that this new pathway is probably not optimal. -
Generating parameters using RESP charges from GAMESS-US - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Generating_parameters_using_RESP_charges_from_GAMESS-USRun AMBGMIN with new set of RESP charges. Re-calculate RESP charges for new global minimum. ... You can use this file to create AMBER input for complexes containing the new molecule using tleap. -
Creating movies (.mpg) of paths using OPTIM - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Creating_movies_(.mpg)_of_paths_using_OPTIMIf 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 -
Pele - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/PeleIt is not meant to be a replacement for them, but rather as a playground for quickly testing new ideas, finding optimal parameters for the various routines in GMIN and OPTIM, ... You can also generate interactive disconnectivity graphs, which can be used -
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. -
Compiling Wales Group codes using cmake - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Compiling_Wales_Group_codes_using_cmakeNote: If you want to use OPTIM with the new C++ implementation of the NEB routine, you will need to obtain the source code for that separately. ... In that case there are three things you could try: make sure you are building in a new directory, if that -
Piping and redirecting output from one command or file to another -…
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Piping_and_redirecting_output_from_one_command_or_file_to_anotherTo pipe the output to a new command place a '|' character between them. -
Preparing input files for a peptide using AMBER - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Preparing_input_files_for_a_peptide_using_AMBER1 i.e., use tleap again and create new old_coords.prmtop and old_coords.inpcrd file before proceeding to Step 3. ... You might like to check two things a) Symmetrisation of this new topology file by repeating the step 6 b) Whether the A12GMIN and AMBER -
Setting up aliases to quickly log you in to a different machine -…
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Setting_up_aliases_to_quickly_log_you_in_to_a_different_machineSave and exit the file and then open a new shall. -
Simple scripts for LEaP to create topology and coordinate files -…
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Simple_scripts_for_LEaP_to_create_topology_and_coordinate_filesIf 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. -
Identifying the k fastest paths between endpoints using…
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Identifying_the_k_fastest_paths_between_endpoints_using_KSHORTESTPATHSpoints.min.removed. min.data.removed. min.B.removed. min.A.removed. ts.data.removed. points.ts.removed. Stick them in a new directory and rename them by removing the. -
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. -
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_PATHSAMPLEThe bottom of output should look like this:. getallpaths> writing data for new ts to ts.data getallpaths> writing data for 1 new minima to min.data getallpaths> writing data for ... writing data for 1 new minima to min.data setup> The unique A and B
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