User contributions for Frodo

18:1918:19, 9 March 2014 diff hist +237‎ Nm User talk:Qixiaolong ‎ Welcome! current
18:1918:19, 9 March 2014 diff hist +86‎ Nm User:Qixiaolong ‎ Creating user page for new user. current

20:1620:16, 6 March 2014 diff hist −34‎ IPMI ‎No edit summary
20:1520:15, 6 March 2014 diff hist +596‎ N IPMI ‎ Created page with "This page is about IPMI. = House rules= IPMI is always configured on the private network. Until configured, IPMI is always deactivated. We use the hundreds (decimal) number..."

17:2817:28, 5 March 2014 diff hist +715‎ N Remote control your virtual box vm ‎ Created page with "Imagine your userid is henry and your desktop machine where you have a virtualbox VM is called nirvana. You should be able to start the VM (at any time) by running (from the..."

18:0218:02, 25 February 2014 diff hist +73‎ DOCK 3.7 ‎ →‎Molecular docking
18:0118:01, 25 February 2014 diff hist +26‎ DOCK 3.7 ‎ →‎Molecular docking
18:0018:00, 25 February 2014 diff hist +29‎ DOCK 3.7 ‎ →‎Molecular library preparation for docking
17:5617:56, 25 February 2014 diff hist +94‎ Running docking 3.7 ‎No edit summary current
17:3417:34, 25 February 2014 diff hist +554‎ N Running docking 3.7 ‎ Created page with "To set up directories for docking using DOCK 3.7, use: setup_db2_lots.py <num_dirs> <prefix> /path/to/db2/files Then to start the docking using the queuing system sub..."
17:2817:28, 25 February 2014 diff hist +159‎ N Ligand preparation 3.7 ‎ Created page with "To build a db2 format database from SMILES for use by DOCK 3.7, use: build_smiles_ligand <smiles_file.smi> Return to DOCK 3.7 Category:Tutorial"
04:3704:37, 25 February 2014 diff hist +194‎ DOCK 3.7 ‎ →‎Highest level scripts
04:3404:34, 25 February 2014 diff hist −6‎ Blastermaster ‎ →‎Simple default usage
04:3304:33, 25 February 2014 diff hist +3,500‎ N OUTDOCK 3.7 ‎ Created page with " = Explanation of header = Here we explain line by line the meaning of the header in the OUTDOCK 3.7 file. DOCK v. 3.7, compiled 20140211 Version of program, date create..." current
04:2304:23, 25 February 2014 diff hist +36‎ DOCK 3.7 ‎ →‎Molecular docking
04:1604:16, 25 February 2014 diff hist +155‎ Getting started with DOCK 3.7 ‎ →‎Test 4. Dock custom library
03:1103:11, 25 February 2014 diff hist +139‎ Getting started with DOCK 3.7 ‎No edit summary
00:5200:52, 25 February 2014 diff hist +10‎ DOCK 3.7 ‎ →‎Protein preparation for docking
00:5200:52, 25 February 2014 diff hist +266‎ DOCK 3.7 ‎No edit summary
00:4900:49, 25 February 2014 diff hist +367‎ N Be blasti ‎ Created page with "be_blasti is a script to download a PDB entry, locate the receptor and ligand, and prepare other files for docking using blastermaster Author: Trent Balius, based on an o..."
00:3400:34, 25 February 2014 diff hist +41‎ Getting started with DOCK 3.7 ‎No edit summary
00:1000:10, 25 February 2014 diff hist +42‎ OGS/GE ‎No edit summary
00:1000:10, 25 February 2014 diff hist +33‎ Get a queuing system working ‎No edit summary
00:0900:09, 25 February 2014 diff hist +20‎ N SGE ‎ Redirected page to OGS/GE current

23:4923:49, 24 February 2014 diff hist +651‎ N Get a queuing system working ‎ Created page with "Here is how to get a queuing system up and running, our way, and integrate it with [[DOCK 3.7]. We assume you have already [[build a computer cluster | built a computer clust..."
23:4123:41, 24 February 2014 diff hist +503‎ Getting started with DOCK 3.7 ‎No edit summary
23:3623:36, 24 February 2014 diff hist +1‎ RDKit ‎No edit summary
23:3523:35, 24 February 2014 diff hist +21‎ RDKit ‎No edit summary
23:3523:35, 24 February 2014 diff hist +6‎ Chemical informatics ‎ Redirected page to Category:Cheminformatics current
23:3423:34, 24 February 2014 diff hist +12‎ OEChem ‎No edit summary
23:3423:34, 24 February 2014 diff hist +134‎ OEChem ‎No edit summary
23:3223:32, 24 February 2014 diff hist +21‎ N OpenEye Scientific Software ‎ Redirected page to OpenEye current
23:3123:31, 24 February 2014 diff hist +35‎ OpenEye ‎No edit summary
23:2923:29, 24 February 2014 diff hist +16‎ Getting started with DOCK 3.7 ‎No edit summary
23:2823:28, 24 February 2014 diff hist −249‎ Getting started with DOCK 3.7 ‎No edit summary
23:2523:25, 24 February 2014 diff hist +17‎ Getting started with DOCK 3.7 ‎No edit summary
23:2223:22, 24 February 2014 diff hist −3‎ Getting started with DOCK 3.7 ‎No edit summary
23:2123:21, 24 February 2014 diff hist −39‎ Getting started with DOCK 3.7 ‎No edit summary
23:1823:18, 24 February 2014 diff hist +592‎ Getting started with DOCK 3.7 ‎No edit summary
23:0523:05, 24 February 2014 diff hist −96‎ Getting started with DOCK 3.7 ‎ →‎set up .cshrc (or .bashrc equivalent)
22:4422:44, 24 February 2014 diff hist +120‎ Getting started with DOCK 3.7 ‎ →‎Acquire 3rd party software
22:3822:38, 24 February 2014 diff hist +422‎ Centos ‎No edit summary
22:3422:34, 24 February 2014 diff hist +84‎ Python ‎No edit summary
22:3322:33, 24 February 2014 diff hist +19‎ m Getting started with DOCK 3.7 ‎No edit summary
21:4321:43, 24 February 2014 diff hist +196‎ Supported platforms for DOCK 3.7 ‎No edit summary
21:4021:40, 24 February 2014 diff hist +2‎ Supported platforms for DOCK 3.7 ‎ →‎Support requested
21:4021:40, 24 February 2014 diff hist +214‎ N Supported platforms for DOCK 3.7 ‎ Created page with "= Support = * Centos 6.3 = Support planned - May 2014 = * OSX (Mac) * = Support requested = * Debian * Raspbian * make your suggestion here Category:Internal [[C..."
21:3221:32, 24 February 2014 diff hist +34‎ Molinspiration ‎No edit summary
21:3121:31, 24 February 2014 diff hist +207‎ OGS/GE ‎No edit summary
21:3021:30, 24 February 2014 diff hist +97‎ Getting started with DOCK 3.7 ‎ →‎Acquire 3rd party software
21:2721:27, 24 February 2014 diff hist +442‎ N Vbox windows ‎ Created page with "How to manage your Virtual Box running Windows from outside the lab. 1. ssh to a portal $ ssh <userid>@<your_desktop> vboxmanage startvm LabWindows 2. To power off the VM ..." current
21:2321:23, 24 February 2014 diff hist +313‎ N Disk Quotas ‎ Created page with "Quota management on XFS disks: xfs_quota -xc 'limit bsoft=1t bhard=1.5t teague' /raidb xfs_quota -xc report /raidb xfs_quota -xc help Also see the website: [https://acc..."
16:5616:56, 24 February 2014 diff hist +227‎ N Centos ‎ Created page with "We develop on and recommend Centos. Our software should work on * RedHat (versions) * It should be possible to use MacOS, but we are still not quite ready. We do not sup..."
16:4016:40, 24 February 2014 diff hist +51‎ Getting started with DOCK 3.7 ‎ →‎Acquire 3rd party software
16:3716:37, 24 February 2014 diff hist +139‎ OGS/GE ‎No edit summary
16:3616:36, 24 February 2014 diff hist +254‎ N OGS/GE ‎ Created page with "Open Grid Scheduler / Grid Engine is the open source batch queuing system that succeeds the Sun Grid Engine. It is available at [http://gridscheduler.sourceforge.net gridsched..."
16:3516:35, 24 February 2014 diff hist +45‎ Getting started with DOCK 3.7 ‎No edit summary
16:2716:27, 24 February 2014 diff hist −4‎ Getting started with DOCK 3.7 ‎ →‎Test 2: Docking preparation from receptor and ligand alone
16:1116:11, 24 February 2014 diff hist +245‎ N RDKit ‎ Created page with "Rdkit is an incredibly useful cheminformatics software package available from [http://rdkit.org it's website]] or from [http://github.org/rdkit/rdkit github]]. [[Catego..."
16:0916:09, 24 February 2014 diff hist +51‎ Getting started with DOCK 3.7 ‎No edit summary
16:0716:07, 24 February 2014 diff hist +335‎ Python ‎No edit summary
16:0516:05, 24 February 2014 diff hist +439‎ N Python ‎ Created page with "Python is probably the single most useful programming language you can learn today. Most of our new code is written in Python. The interface to many programs we use such as [..."
16:0216:02, 24 February 2014 diff hist −107‎ Getting started with DOCK 3.7 ‎No edit summary
15:5915:59, 24 February 2014 diff hist +34‎ PyMol ‎No edit summary
15:5915:59, 24 February 2014 diff hist +237‎ N Omega ‎ Created page with "Omega is a conformation generation program from OpenEye Scientific Software. Request a license (free to qualified academics) at [http://eyesopen.com eyesopen.com]. [[Catego..."
15:5615:56, 24 February 2014 diff hist +4‎ Getting started with DOCK 3.7 ‎No edit summary
15:5615:56, 24 February 2014 diff hist +1,000‎ Getting started with DOCK 3.7 ‎No edit summary
02:1602:16, 24 February 2014 diff hist +52‎ m Ligand preparation ‎No edit summary
02:1602:16, 24 February 2014 diff hist +75‎ m Ligand preparation ‎No edit summary

18:4018:40, 23 February 2014 diff hist +628‎ Getting started with DOCK 3.7 ‎No edit summary
18:2418:24, 23 February 2014 diff hist +70‎ DOCK 3.7 ‎No edit summary
18:2118:21, 23 February 2014 diff hist +14‎ m Getting started with DOCK 3.7 ‎No edit summary
18:2018:20, 23 February 2014 diff hist +2,112‎ N Getting started with DOCK 3.7 ‎ Created page with "You want to install DOCK 3.7 on your own system. These are the notes I made while doing it. These are just recommendations, based on my experience. You are free to simply ..."
17:5717:57, 23 February 2014 diff hist +60‎ Blastermaster files ‎No edit summary
17:5617:56, 23 February 2014 diff hist +1,439‎ N Blastermaster files ‎ Created page with "Meaning of the files created by Blastermaster. These are also documented with each associated program, but since Blastermaster is the widely used interface for docking, t..."
17:3617:36, 23 February 2014 diff hist +111‎ Blastermaster ‎No edit summary
03:5703:57, 23 February 2014 diff hist +159‎ Ligand preparation ‎No edit summary
03:5603:56, 23 February 2014 diff hist +52‎ Ligand preparation ‎No edit summary
03:5503:55, 23 February 2014 diff hist −11‎ DOCK 3.7 ‎No edit summary
03:5403:54, 23 February 2014 diff hist +13‎ DOCK 3.7 ‎No edit summary
03:5403:54, 23 February 2014 diff hist +497‎ DOCK 3.7 ‎ →‎Topics
03:4703:47, 23 February 2014 diff hist +439‎ Mol2db2 format ‎No edit summary
03:4503:45, 23 February 2014 diff hist +187‎ Mol2db2 ‎No edit summary
03:4203:42, 23 February 2014 diff hist +173‎ INDOCK 3.7 ‎No edit summary
03:4003:40, 23 February 2014 diff hist +106‎ Blastermaster ‎No edit summary
03:3903:39, 23 February 2014 diff hist +9,842‎ Blastermaster ‎No edit summary
03:3503:35, 23 February 2014 diff hist +141‎ N Blastermaster ‎ Created page with "Blastermaster Written by Ryan Coleman, based on a prototype in the lab (MakeDOCK/startdockblasterN) which was contributed to by many people."
03:3403:34, 23 February 2014 diff hist +20‎ m DOCK 3.7 ‎ →‎Topics
01:1401:14, 23 February 2014 diff hist +661‎ Github ‎ →‎Lab repositories

User contributions for Frodo

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