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Using the implicit membrane model IMM1 - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Using_the_implicit_membrane_model_IMM11 2. New Terms in GMIN. Two new terms have been included for use with the implicit membrane. -
Basic linux commands everyone should know! - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Basic_linux_commands_everyone_should_know!mkdir. mkdir newdir newdir2. This will create two new directories, newdir and newdir2. -
List of output files for PATHSAMPLE - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/List_of_output_files_for_PATHSAMPLEodata.<n> -- OPTIM input file. odata.new.<n> -- files generated by OPTIM for restarting from that point (non-CHARMM varieties of OPTIM). -
ElaborateDiff - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/ElaborateDiffTo create a new /.svndiffrc file, write $progname --create-rc >/.svndiffrc -c, --diffcmd x Use x as the diff command. ... item B<--create-rc> Send a configuration file example to stdout. To create a new F</.svndiffrc> file, write $progname --create-rc -
CamCASP/Programming/7 - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/CamCASP/Programming/76 Jan 2021: Needs commands. SET NEW-PROP KERNEL-EPS 0.00001 END BEGIN POLARIZABILITY MOLECULE <name> NEW-PROP. ... Can now be used in energy routines. Just add NEW-PROP to the commands. -
Removing minima and transition states from the database - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Removing_minima_and_transition_states_from_the_database6 Jan 2021: First off back up the directory. The minima specified in files min.remove and ts.remove are removed and new files min.data.removed, ts.data.removed, min.A.removed, -
Short 'awk' examples - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Short_%27awk%27_examplesPlease notify me if you find errors or new commands to add to this list (total length under 65 characters). -
Loading OPTIM's min.data.info files into PATHSAMPLE - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Loading_OPTIM%27s_min.data.info_files_into_PATHSAMPLEmin.data.info.initial. In a new directory copy the following files:. coords.inpcrd, coords.prmtop, min.data.info.initial, perm.allow, pathdata. -
Revamping the modules system - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Revamping_the_modules_systemThen someone's going to have fftw2 loaded and forget about it, and suddenly find they can't load a new compiler. ... A few months later I tried a variant of this by installing the new 64-bit cluster tardis without 32-bit Portland modules. -
Removing minima and transition states from the database - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Removing_minima_and_transition_states_from_the_databaseFirst off back up the directory. The minima specified in files min.remove and ts.remove are removed and new files min.data.removed, ts.data.removed, min.A.removed, -
Running a G\=o model with the AMHGMIN - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Running_a_G%5C%3Do_model_with_the_AMHGMIN1 2. New Terms in GMIN. Two new terms have been included for use with the implicit membrane. -
Using GMIN to generate endpoints (CHARMM) - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Using_GMIN_to_generate_endpoints_(CHARMM)Setting up CGMIN. Copy the metenk.crd file you have just created into a new directory, and rename it input.crd. ... We now need to create a new file, data, which contains the GMIN keywords we would like to use. -
Environment modules - CUC3
wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Environment_modules6 Jan 2021: If you do module avail after loading the use.own module, you'll see there's a new section: /home/${USER}/privatemodules. -
Symmetrising AMBER topology files - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Symmetrising_AMBER_topology_filesjob). Also, it would be helpful once you've done this if you add your new cofactor to the group8 list. -
CamCASP/Numerical - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/CamCASP/Numerical6 Jan 2021: Aux basis: aTZ Basis type as indicated. New mid-bond set used: 3s3p3d2f1g. -
Running Wales Group software on Windows 7 - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Running_Wales_Group_software_on_Windows_7New packages can be selected later by running the setup wizard again. -
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, -
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:. -
OPTIM and PY ellipsoids tutorial - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/OPTIM_and_PY_ellipsoids_tutorialIf you are unsatisfied with the topology, it's time to try a new connection scheme. ... permissions? JOBSPERNODE/PBS vs CPUS again? "Operation not permitted". "error code returned by host stdio - 1." -> close the terminal and open a new one! -
Makerestart - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/Makerestart6 Jan 2021: up restart run in the current directory' echo 'Number of steps completed='$oldsteps echo 'Number of additional steps requested='$1 echo 'Total number of steps after restart='$steps # CREATING THE NEW ... Prints the top of the data file up to (but not -
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 -
Biomolecules in the energy landscape framework - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Biomolecules_in_the_energy_landscape_frameworkThe new libraries are found in the AMBERTOOLS/dat/leap/lib directory, you will need to copy them to your AMBER version (AMBER12 or newer!). -
Comprehensive Contents Page - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Comprehensive_Contents_PageCan be very useful for visualizing your system and for rapidly implementing and testing new ideas. ... rough outline of the subroutines that need to be changed to add a new model to GMIN. -
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. -
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, -
Relaxing existing minima with new potential and creating new database …
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Relaxing_existing_minima_with_new_potential_and_creating_new_database6. next step: creation new binary file points.min; you will need new pathdata file:. ... Still it is worthy to check where in fact both endpoints are placed in new database. -
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:. -
Connecting Sub-databases - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Connecting_Sub-databasesThis new reorganised file we give the rather unimaginative name of lowest_to_highest_distances_tot. ... Assuming all of the connections were successfully made, all we need to do now is to merge these new connected databases together. -
Notes on MINPERMDIST - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Notes_on_MINPERMDISTThe best permutation is returned in the LPERM array. SAVEPERM is set to NEWPERM with the new permutation applied. ... Updates to permutation vector and coordinates (l870-l912). ALLPERM is updated with the new swaps. -
Calculating order parameters - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Calculating_order_parametersCHARMM to calculate the order parameters charmm_new < order_parameters.inp > charmm.out. -
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. -
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. -
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. -
GMIN - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/GMINThe program knows many different empirical potentials, and it is straightforward to add new systems. ... symmetry.f. mdiff is used to test whether a generated symmetry operation is new. -
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 -
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. -
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. -
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 -
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 -
Getting started with SLURM - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Getting_started_with_SLURMChange 'jwrm2' to your own username. We copy only the files GMIN needs in order to run, then change to the new directory. ... the files back and adds new stationary points to the database, then deletes the temporary directory. -
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. -
Maui compilation - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Maui_compilationMaui compilation. From Docswiki. 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 -
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. -
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. -
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 -
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 -
SuSE 10.1 workstation image - CUC3
https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php/SuSE_10.1_workstation_image6 Jan 2021: OpenSSH (SSH client) DONE. Pan (news client) DONE. Pine (mail/news client) DONE. ... rasmol (molecular visualisation) DONE. TeX/LaTeX (document preparation system) DONE. Thunderbird (mail/news client) DONE. -
If you need to change the number of atoms (e.g. making a united-atom…
https://wikis.ch.cam.ac.uk/ro-walesdocs/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)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. -
GMIN TESTS module - Docswiki
https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/GMIN_TESTS_moduleIt will contain tests of routines such as those in the new GMIN MOVES module. -
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.
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