Search results

Information on how to use the Shoichet Lab Cluster. Note this information is only relevant if you have ssh access to the cluster.

...le, the number of the cluster of interest, and names for the output files. Information is sent to the screen while the spheres are being read in, and while the su

== SGE Cluster Information == ...head.compbio.ucsf.edu' is the submit machine for the Sun Grid Engine (SGE) cluster. wilco is also authorized to submit jobs.

...ty. You need to ask the [[sysadmin]]s about portal access. We do not post information about portals or how they function in a public forum. Ever. Please. What this means in practice is that you cannot ssh to our cluster unless you follow very specific instructions. You may however ssh *out* and

...ueues, flags, ...) can be found in the [https://salilab.org/qb3cluster QB3 cluster wiki]. It is password-protected and will be accessible once you have obtain ...ser name, name of PI) to Joshua Baker-LePain (jlb at salilab dot org), the cluster administrator.

...erience. If there are repeat offenders (three crashes without any further information), we should consider dismantling the machine.

This wiki contains information for both members of the lab as well as the general public. ...n software on our cluster is [[TLDR]]. Of course, since you are using our cluster, it won't be as fast as if you had it installed locally on your own system.

Cluster 4 is our self-centric name for the SciNet cluster in Canada. (1.4) In your personal information.

To use the CLI, you'll need to be on alpha, where puppet is hosted on Cluster 2. More information

''Pascal'': the write load on a disk even when the entire cluster is filled with DOCK jobs is negligible, i.e., it rarely happens that two jo ...t2</tt> files, which should be appended to <tt>amb.crg.oxt</tt>. Find more information [[Preparing the protein#Tarting the protein|here]].

On our cluster, you only need to type: The output is a csv file, containing the strain energy and detailed information for each compound in mol2 or each conformation in db2.

Click "Override" on '''variant''' and enter "Cluster" in Value at the bottom # Additional Information

Meaning the script will find all vendor information and smiles associated with the provided zinc ids or vendor codes. ...find the script and environment @ /nfs/soft/zinc22/search_zinc on the BKS cluster.

...ring a job. Here you upload your data to the DOCK Blaster server. For more information about the data formats, please see [[DOCK Blaster:Prepare Input | Prepare I ...the server, and the Scrutinizer checks the data for consistency. For more information about the Scrutinizer, and the many ways it can complain about your data, p

* Go to marketplace, search for "hpc". Find a stack called simply "HPC Cluster". Click on that, accept the agreement, select the compartment you just crea * Click next to proceed past the first step, "Stack Information". In the second step, "Configure Variables", paste the ssh key you just gen

On our cluster, you may source my environment. The output is a csv file, containing the total strain energy and detailed information of each dihedral sorted by its torsion energy.

If you do not already have a cluster with middleware, see: [[So you want to set up a lab]]. ** More information [http://www.eyesopen.com/oechem-tk here for OEChem TK]

...of DOCK) to flood the surface of the protein with spheres, which are then cluster by distance. OUTSPH is the file containing the information about sphere genereation

This tutorial shows how to do parallel search of smi files on the cluster. The files and scripts can be found in /nfs/home/jizhou/ex7/2D/test-paralle ...up searching. The performance of qsub depends on the workload of the whole cluster. Generally, searching with qsub has good scalability.

Our puppet modules exist in two places: /opt/bks/src/cluster/puppet/modules & /etc/puppet/modules <br /> To generate a new Puppet module, we first go to /opt/bks/src/cluster/puppet/modules. Decide on what you want to call it. Notice in this direct

This is a list of machines/servers that we have on our cluster. Additionally, we'll try to keep this page updated with the compatible RAM ===File Server RAID drives Information===

* All tar.gz can be found in /nfs/home/xyz/soft on our cluster. Ask JJI about remote access. * [[Building_The_3D_Pipeline_ZINC22]] for information on running the script.

* Extract the following information from MYSQL into files and bins. ...ion that has been loaded in to the MySQL data base on SGEHEAD of the BKSLB cluster.

...stituent spheres, and written out in order of descending size. The largest cluster is typically the ligand binding site of the receptor molecule. The program ...hanging the second to last column of the final sphere file to the critical cluster number (see Output).

==Getting IP information on switch== 101 BKS cluster ch1-3,ch5-6, Static Required

Installer is the shoichet cluster backend dhcp/tftp/anaconda installer. Detailed information on anaconda can be found at: http://www.redhat.com/docs/manuals/linux/RHL-8

See [[DOCK_3.7]] for more up to date information. ...es have also been integrated. To build a set of ligands from SMILES on the cluster, use:

== Development environment inside cluster== == Deployment Information ==

Get help information: ...2, only get molecules with names listed in a file (for example, zincids of cluster heads), and cut at top 100k.

...ockable database]]. It runs entirely on the [[About our cluster | computer cluster ]] in the [[Shoichet Lab]] at [[Mission Bay]] in San Francisco. The graphic More detailed information about problems may be found here:

modes. In these cases, users are encouraged to run CLUSTER in information about the ligand and receptor molecules is required to

*Real Atom Types and Bond Information [x] *arbitrary information to be written into output mol2 file (5th and above M lines) [x]

...mple, we need trk5 to be a member of the public network, VLAN 100, and the cluster 2 private network, VLAN 200. Check the trunk's VLAN memberships after you Status and Counters - VLAN Information - for ports Trk5

In the License Retrieval Assistant, make sure you have the following information for the respective categories: <br /> <b>Cluster 0</b>

DB2 is a text format, with each row of information being printed on a new line (not to exceed 80 characters per line, due to o "M" lines serve a few functions. First is to define information about a db2 molecule entry- molecule name, smiles, properties, etc. The sec

* Build membrane using the '''System Builder''' tool. Use residue information obtained from OPM database (https://opm.phar.umich.edu/), add salts, add so ...'''Molecular Dynamics''' tool to write out a simulation file to run on the cluster. Load the system you built in the previous step from the workspace. Specify

#Flag to read atomic desolvation information from ligand file #included in a particular cluster

On the Wynton cluster, ''/scratch'' only exists on development nodes (not log nodes). Therefore, E.g., on the UCSF Shoichet Lab Gimel cluster (on any node other than 'gimel' itself, such as 'gimel5'):

cluster 1 number of spheres in cluster 50 For more information and more analysis scripts, you can find them on Noam's github repo: https:/

* Cluster - Not yet implamented in DOCK3.7 *T type information (implicitly assumed)

...pose data, and a .scores file containing relevant score information. ...r reading files, due to the way the filesystem works on Wynton. On the BKS cluster, increasing the number of reader threads beyond two will have a negligible

*Use -h or --help to get full help information for the .py (python) scripts *The .csh scripts will automatically print usage information if mis-used

** fill in the required information ** Download the tar.gz file and copy it to your desired location on the cluster.

...ation of ligand binding modes. In these cases, users are encouraged to run CLUSTER in conjunction with SPHGEN and DOCK. ...trostatic scoring, and contact scoring plus force field scoring. Atom-type information and point charges are not required for contact scoring only.

# sshd_config(5) for more information. ...machine by any user; 5 minutes is an ample amount of time to ssh into the cluster.

...ve removed compounds that are known to cause problems in some assays. For information about the additional filtering used, please see [http://filtering.docking.o ...n.2 ; then startdockbks3 `pwd`; you must be on sgehead so you can see the cluster.

...es below and runs a command to list the status of disks. (Does not include cluster 0 machines) === On Cluster 0 's machines ===

...al install (currently in /nfs/soft/modeller/current/bin/mod9.15 on the new cluster) When working with orphans, we typically had information from the Roth lab about one or a few molecules that bound to a given protei

# SGE_ROOT Path, this is basic information # Name of this cluster (used by SMF as an service instance name)

...3.7 is primarily a virtual screening tool is is meant to be run on a Linux cluster. ...y structure of the distribution, what the different directory contain, and information about the scripts.