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  • Batch Search and Replace in Multiple Files Two simple, rather elegant, solutions: perl -pi -w -e ‘s/wrong/right/g;’ *.html Replaces all instances of ‘wrong’ with ‘right’ in html files within the current working directory. grep ...
    Posted May 24, 2013, 10:45 PM by Dong Xu
  • List of Computational Chemistry Software https://docs.google.com/file/d/0BwAR2nWq4Z0eTXpjaGZ3cnVMMFU/edit?usp=sharing ===========================================DatabasesCompoundsACD Symyx www.symyx.com 9, 14ChemBridge ChemBridge www.chembridge.com 12, 14, 15 ChemDiv ChemDiv www ...
    Posted Mar 19, 2013, 11:39 AM by Dong Xu
  • Cresset Installation yast2 -i  xed/forge/torch...rpmbinaries are installed to /opt/cresset
    Posted Jan 17, 2013, 2:11 PM by Dong Xu
  • Amber 12 Installation see http://ambermd.org/bugfixes12.html must run $AMBERHOME/patch_amber.py --update-tree at least several times to get all file patched up before installation.also, install    flex tcsh ...
    Posted Jan 17, 2013, 12:12 PM by Dong Xu
  • ssh server sshd config TCP wapper for IP controlvi /etc/hosts.denyaddALL: ALLvi /etc/hosts.allowadd all allowed IP and domainsALL: hpclogin.inel.gov 204.134.163.222 ...
    Posted Jan 18, 2013, 10:28 PM by Dong Xu
  • Protonation State Great article about basics:http://www.daylight.com/meetings/emug00/Sayle/pkapredict.htmlMore pka examples:https://docs.google.com/file/d/1LqtPkvhwlSDJpkxTV9ZCtz0-XgvHX_1HwNC8c3v9rjL-aFQ9xLJPokHON8py/edit?usp=sharing1 ...
    Posted Apr 11, 2013, 2:54 PM by Dong Xu
  • OpenEye Suite Installation All executables should go in  openeye/arch/suse-SLES11-x64because packages such as rocs or eon use "suse-SLED11-x64" dir, the files should be moved into "suse-SLES11 ...
    Posted Oct 25, 2012, 4:52 PM by Dong Xu
  • List of Computational Chemistry Software http://www.sbgrid.org/software/
    Posted May 8, 2012, 6:02 PM by Dong Xu
  • Check CPU Temperature on Linux A long shot:Reference:http://www.cyberciti.biz/faq/howto-linux-get-sensors-information/   (package called sensors in suse)k10temp patch:http://blog.morrigan.ch/?p=9https://bbs.archlinux ...
    Posted Jan 29, 2012, 3:00 PM by Dong Xu
  • Consistent AM1-BCC Charge Calculation According to an amber-l post, here's the best practice to avoid inconsistency:In my humble opinion, the most important consideration for correct charge derivation is that the conformation ...
    Posted Jan 29, 2012, 10:58 AM by Dong Xu
  • Andy Coombs' Tutorial on 1WMA Docking * Ensure the following files are in the folder you will be working in, copy these files from Andy's folder: LIGAND_NAME.pdb 1WMA_NDP.pdbqtvina.conf* Ensure that ...
    Posted Jan 27, 2012, 11:01 AM by Dong Xu
  • Remote Desktop Putty SSH Tunneling Source port: 127.0.0.2:3389Destination: savor.boisestate.edu:3389ssh to cocoa or kiwihttp://www.engr.wisc.edu/computing/best/rdesktop-putty.html
    Posted Dec 28, 2011, 7:04 PM by Dong Xu
  • SOP-GPU nohup sh -c "sop-gpu ww_1-100_pull.sop 2>&1 | tee  ww_1-100_pull.sop.log"  &
    Posted Nov 9, 2011, 3:55 PM by Dong Xu
  • DNA Script Usage DNA Generation and Manipulation scriptdna.sh help prints this messagedna.sh <input file (.in)> Use a file as the inputdna.sh <output command> <dna commands>    <output command ...
    Posted Nov 8, 2011, 11:07 AM by Dong Xu
  • List of Computational Chemistry Related Journals CHEMICAL PHYSICS     Best        J.Chem.Phys.        Chem.Phys.Lett.        J.Phys.Chem. B        Ann.Rev.Phys.Chem.        J.Comp.Chem.        J. Chem. Theory and Computation     Good        Chem. Phys. Chem.        Mol ...
    Posted May 1, 2012, 4:38 PM by Dong Xu
  • Rosetta export ROSETTA_HOME=/home/apps/rosetta3.3_bundles export ROSETTA3_SRC=$ROSETTA_HOME/rosetta_source export ROSETTA3_DB=$ROSETTA_HOME/rosetta_database export PATH=$PATH:$ROSETTA3_SRC/bin export LD ...
    Posted Nov 3, 2011, 2:39 PM by Dong Xu
  • Linux Cheat Sheet by Matthttps://docs.google.com/document/d/1xdnikGLnzhMlWFT0XTe83URSvzBFajQLPSrjaxWTGrU/edit
    Posted Oct 28, 2011, 4:19 PM by Dong Xu
  • Gromacs MPI Compilation Download gromacs-4.5.5.tar.gz into /usr/local/src/gromacsSee the Installation_Instructions1. Load Environment Modules:module add intel/compiler/64/11.1/075module add ...
    Posted Oct 19, 2011, 3:18 PM by Dong Xu
  • SSH Tunneling between R1 and savor Simplest form: ssh user@host -L <in port>:<destination>:<out port> ssh user@host -R <in port>:<destination>:<out port> Using L will forward any connections to localhost through the ...
    Posted Oct 18, 2011, 10:03 AM by Dong Xu
  • PMEMD.CUDA Memory limit issue (up to patch 17) This might help even more:Go into gpu.cpp, and look for this line:        gpu->sim.randomSteps            = MAX_RANDOM_STEPS;Change to:        gpu->sim.randomSteps            = MAX_RANDOM_STEPS / 2;recompile
    Posted Oct 15, 2011, 2:24 PM by Dong Xu
  • VMD Tachyon Render of High Quality Images Turn on Show and AO in VMD display settingsUse Tychon, not internal tachyon in VMD render and add this to the command line-res 4000 3000See Tachyon doc ...
    Posted Oct 14, 2011, 6:21 PM by Dong Xu
  • Truncated octahedral in NAMD The grid for the FFT is calculated in the crystallographic (so to speak) frame, not along the orthogonal axes. In the case of a truncated octahedral cell -and depending on ...
    Posted Oct 8, 2011, 9:04 AM by Dong Xu
  • R1 cluster info Access from lab/home: ssh cocoa, then ssh r1Wiki: http://wiki.boisestate.edu/research/wiki/research-support/SGE wiki: https://www.nbcr.net/pub/wiki/index.php?title=Using ...
    Posted Nov 7, 2011, 1:57 PM by Dong Xu
  • sed infile search/replace sed -i[.extension] -e "s/XXX/YYY/g" file-i with .ext to back up original files-i without .ext, not to back up
    Posted Oct 7, 2011, 6:21 PM by Dong Xu
  • Unlimited Remote Desktop Connection for Windows XP This is from 5 yrs ago, but should still work Follow this thread, you might wanna go bottom up http://www.golod.com/enabling-multiple-remote-desktop-sessions-in-windows ...
    Posted Oct 7, 2011, 8:49 PM by Dong Xu
  • Script to perserve ssh connection #! /bin/bashwhile :do   echo -ne "."   sleep 180doneexit 0
    Posted Oct 1, 2011, 8:11 PM by Dong Xu
  • Windows NFS Share over Samba Server by Matthew CaylorI got it working and it seems to have the correct permissions. (IE, I can edit my own files, see yours, but not edit yours.)  You need ...
    Posted Sep 22, 2011, 5:20 PM by Dong Xu
  • Query jobs and Sort by CPU Usage ps aux --sort pcpu|tail -10
    Posted Sep 8, 2011, 11:26 PM by Dong Xu
  • Query GPU Status and Enable Multi-GPUs nvidia-smi -q -aor/home/apps/NVIDIA_GPU_Computing_SDK/C/bin/linux/release/deviceQuerynvidia-xconfig -a --multigpu=on
    Posted Aug 30, 2011, 2:46 PM by Dong Xu
  • Putty Home/End Key on OpenSuse/SUSE Home Key when using PuTTy in Windows… By default, in /etc/inputrc on lines 135 & 136, the Home key is configured to do something entirely different to the normal "beggining ...
    Posted Aug 12, 2011, 4:52 PM by Dong Xu
  • Compile PMEMD on Teragrid ------------ ABE ----------------- Abe uses the Softenv environment to control compilers, mpi implementations etc. While AMBER can be compiled with any number of combinations of compiler and MPI library I suggest you ...
    Posted Aug 5, 2011, 9:45 PM by Dong Xu
  • Compile PMEMD on Triton SDSC Background at http://tritonresource.sdsc.edu/# 1) tar up the pmemd directory from the current AMBER11 CVS tree:        cd amber11/src/pmemd        make clean        cd ..        tar cfvj pmemd.tar.bz2 ...
    Posted Aug 5, 2011, 9:41 PM by Dong Xu
  • Compile NetCDF and PMEMD on Inel Use PGI: module load pgi/7.1andmodule load mvapich2-pgi-7.1/1.6NETCDFC preprocessor should be export CPP='pgcc -E'So use./configure CPP="pgcc ...
    Posted Aug 5, 2011, 9:33 PM by Dong Xu
  • How to print off of Catnip in the Lab by Matthew Caylor and Adam Ehrlichler Two things, add this to the top:To connect to Catnip from linux workstation:1. Open a console and type showcatnip2. A window ...
    Posted Aug 18, 2011, 12:20 PM by Dong Xu
  • VMD SASA Calculation by Rance Shawto start up VMD in text mode go to directory in which your files are located. In ourcase it is Desktop/INL_files/IGB_restrain_backbone ...
    Posted Jul 29, 2011, 5:19 PM by Dong Xu
  • Enable Multiple GPUs nvidia-xconfig --multigpu=onTo get it to show both gpus in deviceQuery and vmd.
    Posted Jul 29, 2011, 3:52 PM by Dong Xu
  • Amber PMEMD MPI Error If you get errors like these:[mpiexec@chili] HYDU_sock_read (./utils/sock/sock.c:222): read errno (Bad file descriptor)[mpiexec@chili] control_cb (./pm/pmiserv/pmiserv_cb.c ...
    Posted Jun 17, 2011, 11:03 AM by Dong Xu
  • Comparison of reference management softwareost http://en.wikipedia.org/wiki/Comparison_of_reference_management_software
    Posted Jun 8, 2011, 10:12 PM by Dong Xu
  • Gromacs 3.3 Installation wget ftp://ftp.gromacs.org/pub/prerequisite_software/fftw-3.0.1.tar.gzOr use system fftw installed from yast2tar xzf Arch/fftw-3.0.1.tar.gz ...
    Posted Jun 7, 2011, 2:27 PM by Dong Xu
  • RMSD calculation difference in Autodock and ADT This is from Ruth at Scripps:What I am saying is that the distance between each atom in the docked conformation and the closest atom of the same element  in ...
    Posted Jun 2, 2011, 7:31 PM by Dong Xu
  • Autodock Tutorial Docking of mitochondrial respiratory complex II (PDB code: 1ZPO)/home/apps/ActivePython-2.5.4.4/bin/python /home/apps/pdb2pqr-1.7/pdb2pqr.py --ff=amber --ffout=amber  --with ...
    Posted Oct 7, 2011, 11:44 AM by Dong Xu
  • Amber Tutorial http://ambermd.org/tutorials/http://sf.anu.edu.au/~vvv900/amber-tutorial/
    Posted May 31, 2011, 5:40 PM by Dong Xu
  • PDB2PQR installation PROPKA MUST be compiled with g77, gfortran does not work and give Segmentation faultso need to export F77 and FC before ./configure stepand Numeric 24.2 is preferred ...
    Posted Jun 2, 2011, 12:11 PM by Dong Xu
  • Pymol installation If you get"pymol Fatal Python error: can't initialize module _opengl"To share a single copy on NFS mount /home/apps, add user to video groupchgrp -R video ...
    Posted May 20, 2011, 5:31 PM by Dong Xu
  • Parallel or GPU autodock MPI implementation: 1. by Khodade, Autodock v4.0.1 (old version)http://proline.physics.iisc.ernet.in/autodock/http://scripts.iucr.org/cgi-bin/paper?S0021889807011053http://mgldev.scripps.edu ...
    Posted Jun 10, 2011, 2:03 PM by Dong Xu
  • GNU Parallel Script for Job Submission by Matthew CaylorUsage: parallel.sh pipe  [log[=<file>] [append]] [mydir[=<dir>]] [: <arguments for paralle >] :: <Program to run with its arguments>parallel.sh count=<positive integer> [log[=<file>] [append]] [mydir ...
    Posted May 26, 2011, 1:46 PM by Dong Xu
  • Hard drive problems Seagate drives often cause:[   23.064454] ata11: exception Emask 0x10 SAct 0x0 SErr 0x10000 action 0xe frozen[   23.064459] ata11: SError: { PHYRdyChg }[   23.064468] ata11: hard resetting linkSo far ...
    Posted May 19, 2011, 12:07 PM by Dong Xu
  • Amber11 Installation https://docs.google.com/open?id=0B8ACWG4kGvuBYjUwZWM3OTgtMDEzMy00MGZmLThlMjUtNGIyOTA0NjZjNzA5Needs package flex, zlib, zlib-devel, libbz2, libbz2-develSo far intel compiler + mpich2 works better than gnu and openmpiif Amber is ...
    Posted Oct 27, 2011, 7:16 PM by Dong Xu
  • Gromacs 4.5 Installation requires cmake, FFTW3, ZlibFFTW3 single and double precision libs (including devel libs) are installed from yast2. Zlib (and devel) is installed from yast2This should be done on all ...
    Posted May 18, 2011, 6:13 PM by Dong Xu
  • Softcore Potential http://archive.ambermd.org/200602/0108.htmlBest use gromacs!
    Posted May 18, 2011, 3:52 PM by Dong Xu
  • Linux Load Average explained http://www.andymillar.co.uk/blog/2006/12/24/linux-load-average-explained/
    Posted May 18, 2011, 3:48 PM by Dong Xu
  • Map ata#.# numbers to /dev/sd numbers lsscsi command and combine info from dmesg
    Posted May 18, 2011, 3:32 PM by Dong Xu
  • Vim browsing directory http://vim.runpaint.org/other-uses-vim/browsing-directories/
    Posted May 18, 2011, 3:28 PM by Dong Xu
  • Graphics Card Hierarchy Chart http://www.tomshardware.com/reviews/gaming-graphics-card-radeon-hd-6870-geforce-gtx-570,2834-7.html
    Posted May 17, 2011, 10:56 PM by Dong Xu
  • List of Computational Chemistry Software List of software for molecular mechanics modelinghttp://en.wikipedia.org/wiki/List_of_software_for_molecular_mechanics_modelingList of molecular graphics systemshttp://en.wikipedia.org/wiki/List ...
    Posted May 17, 2011, 10:56 PM by Dong Xu
  • GPU Molecular Dynamics Simulation Benchmark ACEMDacemd inputNAMDMulti-core CPU-only, 4-core jobnamd2_mc +p4 dhfr.namd GPU+CPU job  (Max 14 CPU cores can be used to share 1 GPU ...
    Posted Jun 13, 2011, 4:49 PM by Dong Xu
  • Add Audio Track/Music to Movie Using FFMPEG by Cameron Wilcockhttp://stackoverflow.com/questions/43890/crop-mp3-to-first-30-secondsfirst specify your input music file, and then crop it to how long you want it ...
    Posted May 17, 2011, 2:26 PM by Dong Xu
  • Non-Root User USB Drive Mount Solution /usr/bin/polkit-gnome-authorizationThat program controlls the permissions that include mounting usb drives. You will need to set them because the program needs the root password.go to ...
    Posted May 13, 2011, 1:15 PM by Dong Xu
  • Day One in the Lab 1. VMD http://www.ks.uiuc.edu/Research/vmd/Go over thoroughly the tutorials:http://www.ks.uiuc.edu/Research/vmd/current/docs.html#tutorialsParticularly "VMD Molecular Graphics" and ...
    Posted May 6, 2011, 12:01 PM by Dong Xu
  • Membrane protein simulation using the CHARMM force field There has been some recent interest/questions among group members in simulating membrane proteins, and when it comes to using the CHARMM force field, I thought I'd point to ...
    Posted Apr 28, 2011, 7:27 PM by Dong Xu
  • Movie Making in Chimera By Cameron WilcockChimera Movie Making TutorialRequired Software:ChimeraProcedures:Step 1: Going over the functionsFunctions:savepos     this function is used to save any view point/position we ...
    Posted Apr 24, 2011, 9:43 PM by Dong Xu
  • HighPoint RocketRAID 620 Controller Card Driver Installation 1. install gcc and kernel source/header from DVD2. cd rr62x-linux-src-v1.xx/product/rr62x/linux/3. make4. cp rr62x.ko /lib/modules/2.6.32 ...
    Posted Apr 8, 2011, 8:38 PM by Dong Xu
  • SSH-RSYNC Backup Set Up by Matthew CaylorPresteps:Chose or make a non-root user on all the computers that are involved.Create pass-wordless ssh for that user in all locations.Add the ...
    Posted Mar 16, 2011, 6:57 PM by Dong Xu
  • Ricoh Printer Setup on Linux by Matthew CaylorLinux Network Printer for SUSE.   1. Open yast in the console. This requires use of sudo.   2. Go to Hardware → Printer   3. Go to Print via Network ...
    Posted Mar 19, 2011, 2:22 PM by Dong Xu
  • Running Office 2007 on Linux Using Wine From what I read, Office 2010 is not working properly yet at this point, but Office 2007 (Office12) is.From SUSE repository http://download.opensuse.org/repositories/Emulators:/Wine/SLE ...
    Posted Mar 15, 2011, 4:25 PM by Dong Xu
  • VMD View Change Rendering Tutorial by Cameron WilcockVMD 1.8 (or later)For this tutorial we will be using View Change Render 1.1 by Barry Isralewitzhttp://www.ks.uiuc.edu/Research/vmd ...
    Posted May 20, 2011, 11:03 AM by Dong Xu
  • ACEMD Manualhttp://multiscalelab.org/acemd/manualPlumed pluginhttp://multiscalelab.org/acemd/pluginsGoogle grouphttp://groups.google.com/group/acemdSupported GPU listhttp://www.gpugrid.net/forum_thread ...
    Posted Feb 10, 2011, 8:36 PM by Dong Xu
  • Math Stuff Symbolic: Maxima vs. Maple/Mathematicahttp://www.math.utah.edu/faq/maxima/maxima.html#FAQ-9Numerical: Octave vs. Matlabhttp://www.gnu.org/software/octave/FAQ.html#MATLAB-compatibility
    Posted Feb 9, 2011, 7:59 PM by Dong Xu
  • Job submission using multiple nodes and cores GNU Parallelhttp://www.gnu.org/software/parallel/Youtube intro:http://www.youtube.com/watch?v=OpaiGYxkSuQ&feature=relatedhttp://www.youtube.com/watch?v=P40akGWJ_gY&feature=relatedhttp ...
    Posted Jun 9, 2011, 9:54 PM by Dong Xu
  • Autodock/Vina/MGLTools Installation by Kevin WuOn Savor:   1. Compiled autodock and autogrid from source. All make tests pass, no problems here.   2. Downloaded vina 32-bit binaries.   3. Installed Python 2.5 ...
    Posted Mar 9, 2013, 9:54 PM by Dong Xu
  • Passwordless SSH Set Up:1. Run ssh-keygen -t dsa2. Choose a spot to save the file, default location is the best.3. Choose a password, or leave blank for no ...
    Posted Oct 13, 2011, 2:07 PM by Dong Xu
  • CUDA Support and Testing To verify which video adapter your system uses, find the model number by going to your distribution's equivalent of System Properties, or, from the command line, enter: lspci | grep ...
    Posted Jan 14, 2013, 12:33 PM by Dong Xu
  • Sysadmin Stuff "octave: error while loading shared libraries: liboctave.so: cannot open shared object file: No such file or directory"/sbin/ldconfig /usr/lib64/octave-3.2.2/Mount an ISO file ...
    Posted Jan 18, 2013, 10:26 PM by Dong Xu
  • CyberPower UPS Battery Setup 1. Plug in the computer to the UPS device and plug in the usb lead.2. Go to http://www.cyberpowersystems.com/products/management-software/ppl.html?selectedTabId=resources&imageI ...
    Posted Feb 4, 2011, 1:27 PM by Dong Xu
  • OpenSUSE repositories for SLES from here http://en.opensuse.org/Package_repositorieshttp://en.opensuse.org/Additional_package_repositoriesWe added OpenSUSE 11.2 repositorieshttp://download.opensuse.org/distribution/11.2/repo/oss ...
    Posted Mar 9, 2013, 9:26 PM by Dong Xu
  • Intel Compiler Setup http://ariadne.mse.uiuc.edu/Cluster/intel_setup.html
    Posted Feb 9, 2011, 12:02 AM by Dong Xu
  • Enable CUDA in VMD-1.8.7 Add everyone to the video group locally in /etc/group, works!===========================If you get an error message ""No CUDA accelerator devices available", then do this:you can change the permissions ...
    Posted Feb 5, 2011, 3:48 PM by Dong Xu
  • SUSE/SELS NFS/NIS Setup server side: rw,no_root_squash,syncclient side: defaultsNFS explained: http://www.novell.com/coolsolutions/feature/15986.htmlNFS: http://www.novell.com/documentation/sles10/book_sle_reference ...
    Posted Jan 15, 2013, 1:05 PM by Dong Xu
  • NOVELL SUSE/SELS Support Site http://www.novell.com/support/microsites/microsite.dochoose "SUSE Linux Enterprise Server"
    Posted Jan 22, 2011, 2:52 PM by Dong Xu
  • File server backup with rsync http://www.mikerubel.org/computers/rsync_snapshots/Rsync for Backup Purposes1. To use rsync over ssh do: rsync -e ssh host:/path/to/source /path/to/destination2. To ...
    Posted Feb 11, 2011, 4:55 PM by Dong Xu
  • Installing the NVIDIA Driver by Rance Shaw December 17, 2010   1. Make sure the DVD drive with the SLES 11 DVD is in it.   2. Computer->Install Software          * Search: GCC               1. make sure the ...
    Posted Jan 10, 2013, 3:59 PM by Dong Xu
  • ATI Catalyst Driver installation for SUSE/SLES by Matthew Caylor1. Launch the Terminal Application/Window and navigate to the /usr/share/ati folder.2. With superuser permissions, enter the command "sh ./fglrx-uninstall.sh".3. Reboot ...
    Posted Jan 10, 2013, 1:11 PM by Dong Xu
  • VMD Movie Making by Madison Block and Sam BatteyWhen setting or changing your working directory or destination folder in the command prompt make sure that if there is a space in your ...
    Posted Jan 6, 2012, 2:42 PM by Dong Xu
  • Analyze NAMD and Amber MD trajectories with Gromacs 4.5 Gromacs 4.5 can be linked to VMD libraries so that it can read any trajectory format that VMD can read, so now there is no file conversion necessary. The ...
    Posted Sep 17, 2011, 1:47 PM by Dong Xu
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Batch Search and Replace in Multiple Files

posted May 24, 2013, 10:42 PM by Dong Xu   [ updated May 24, 2013, 10:45 PM ]

Two simple, rather elegant, solutions:

perl -pi -w -e ‘s/wrong/right/g;’ *.html
Replaces all instances of ‘wrong’ with ‘right’ in html files within the current working directory.

grep -rl “wrong” /home/jerrywaller  | xargs sed -i ‘s|wrong|right|g’
Recursively replaces ‘wrong’ with ‘right’ within the designated directory.

Just make sure you use plain single and double quotation marks, and not the smart quotes that may show up in the formatting above.  Hat tip to the author and commenters here and here. 

=============================================================

You could also use find and sed, but I find that this little line of perl works nicely.


perl -pi -w -e 's/search/replace/g;' *.php


-e means execute the following line of code.

-i means edit in-place

-w write warnings

-p loop


Example I had the following style sheet in a section:

<link rel="stylesheet" type="text/css" href="../includes/style.css">

and I wanted the following instead:

<link rel="stylesheet" type="text/css" href="admin.css">


As each expression is a regular expression you've got to escape the special characters such as forward slash and .

\.\.\/includes\/style\.css


So the final line of code ends up as

perl -pi -w -e 's/\.\.\/includes\/style\.css/admin\.css/g;' *.php

List of Computational Chemistry Software

posted Mar 19, 2013, 11:33 AM by Dong Xu   [ updated Mar 19, 2013, 11:39 AM ]

https://docs.google.com/file/d/0BwAR2nWq4Z0eTXpjaGZ3cnVMMFU/edit?usp=sharing
===========================================

Databases

  1. Compounds

    ACD Symyx www.symyx.com 9, 14

    ChemBridge ChemBridge www.chembridge.com 12, 14, 15 ChemDiv ChemDiv www.chemdiv.com 14

    ChemDB University of

    California, Irvine

    ChemSpider Royal Society of Chemistry

    cdb.ics.uci.edu 1

    www.chemspider.com 1, 2

    CSD CCDC www.ccdc.cam.ac.uk/pro- 4 ducts/csd

    eMolecules eMolecules, Inc. www.emolecules.com 1

    GDB-13 University of Berne www.dcb-server.unibe.ch/ groups/reymond/gdb/

    home.html

    1

    (Continued)


    Virtual Screening. Edited by C. Sotriffer

    Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

    ISBN: 978-3-527-32636-5

    Type Software name Developed at or

    provided by

    Reference/ Web site

    Cited in Chapter


    InterBioScreen InterBioScreen www.ibscreen.com 14

    Maybridge Maybridge www.maybridge.com 14, 15

    NCI/DTP National Cancer Institute

    dtp.nci.nih.gov/docs/ 3d_database/Structural_

    information/structural_ data.html

    9, 12, 14,

    15

    SPECS Specs www.specs.net 12

    SureChem SureChem Inc. www.surechem.org 1

    VEHICLe UCB Celltech J. Med. Chem. 2009, 52, 2952. 1

    ZINC UCSF zinc.docking.org 1, 2, 11, 12,

    14

  2. Interactions and targets

AurSCOPE Aureus Pharma www.aureus-pharma.com 1

BioPrint Cerep www.cerep.fr 1

ChEMBLdb EMBL-EBI www.ebi.ac.uk/chembldb 1, 5

ChemBank Broad Institute chembank. 1

broadinstitute.org

DIP University of

California, Los Angeles

dip.doe-mbi.ucla.edu 16

DOCKGROUND University of Kansas dockground. 16

bioinformatics.ku.edu/ index.shtml

DOMINE University of Texas at Dallas

domine.utdallas.edu/ 16

cgi-bin/Domine

DrugBank University of Alberta www.drugbank.ca 1

DUD University of California, San

Francisco

dud.docking.org 2, 7, 10

MDDR MDL www.symyx.com 2, 12, 14 MINT University of Rome mint.bio.uniroma2.it/mint 16

MUV University of Braunschweig

www.pharmchem.tu-bs.de/ 5 lehre/baumann/MUV.html

PDB RCSB, Rutgers, UCSD

www.pdb.org 1, 4, 7, 10,

12, 14, 16

PDBbind University of Michi- gan and Shanghai

Institute of Organic Chemistry

www.pdbbind.org and www. pdbbind.org.cn

7, 10

PIBASE Janelia Farm pibase.janelia.org 16

PRISM Koc University, Istanbul

prism.ccbb.ku.edu.tr 16

PROTCOM Clemson University Nucleic Acids Res. 2007, 16

35, D575.

PubChem NIH, NCBI pubchem.ncbi.nlm.nih.gov 1, 5

ReliBase CCDC relibase.ccdc.cam.ac.uk 4, 7

Type Software name Developed at or

provided by

Reference/ Web site

Cited in Chapter

SCORPIO University of London scorpio.biophysics.ismb.lon. 10

ac.uk

WOMBAT Sunset Molecular www.sunsetmolecular.com 1, 5 World Drug Index Thomson Reuters thomsonreuters.com 5, 15


Chemoinformatic tools and workflow toolkits

ChemAxon ChemAxon www.chemaxon.com 6

Filter OpenEye www.eyesopen.com 6

Inforsense Inforsense www.inforsense.com 2

KNIME KNIME.com GmbH www.knime.org 2

LigPrep Schr€odinger www.schrodinger.com 16

OEChem OpenEye www.eyesopen.com 2

OpenBabel OpenBabel commu- nity project

openbabel.org 2

PipelinePilot Accelrys accelrys.com 2, 5, 6, 13

Taverna myGrid taverna.sourceforge.net 2

Topomers (dbtop) Tripos tripos.com 13

Similarity analysis

ACCS-FP University of Bonn

ChemMedChem 11

2008, 3, 67.

ChemGPS University of Uppsala chemgps.bmc.uu.se 1

Dragon TALETE srl www.talete.mi.it 1

DynaMAD University of Bonn J. Chem. Inf. Model. 2006, 46, 11

1623.

EON OpenEye www.eyesopen.com 13

Fieldscreen Cresset www.cresset-bmd.com 13

FLAP Molecular Discovery J. Chem. Inf. Model. 2007, 47, 279.

5, 12

FTrees, FTrees-FS BioSolveIT www.biosolveit.de 1, 3

GRIND (Almond/ Pentacle)

Molecular Discovery www.moldiscovery.com 12

Meqi Pannanugget

Consulting

www.pannanugget.com 1

MoBSS Pfizer J. Chem. Inf. Model. 2009, 49, 1

745.

ROCS OpenEye www.eyesopen.com 3, 12, 13

Scaffold Hunter TU Dortmund/MPI

Dortmunt

www.scaffoldhunter.com 1

Volsurf Molecular Discovery www.moldiscovery.com 12


Conformer generation

Caesar Accelrys accelrys.com 6

Concord Tripos tripos.com 13, 14

Corina Molecular Networks www.molecular- 6

networks.com

DS Catalyst CONFIRM

Accelrys accelrys.com 5, 6

(Continued)

Type Software name Developed at or

provided by

Reference/ Web site

Cited in Chapter

Omega OpenEye www.eyesopen.com 5, 6

ROTATE Molecular Networks www.molecular- 5

networks.com


Pharmacophore modeling

DS Catalyst Accelrys accelrys.com 5, 12, 13,

15

GALAHAD Tripos tripos.com 5

GASP Tripos tripos.com 5

LigandScout inte:ligand www.inteligand.com 5, 10, 15

MOE Chemical Computing Group

www.chemcomp.com 5, 13

PHASE Schr€odinger www.schrodinger.com 5, 12

UNITY Tripos tripos.com 5, 10,

12–14


De novo design

BREED Chemical Computing Group

www.chemcomp.com 17

CCLD University of Zurich J. Comp. Aided Mol. Des. 1996, 17

10, 372.

GANDI University of Zurich www.biochem-caflisch.uzh. 17

ch/download

HOOK Harvard University Proteins 1994, 19, 199. 17

LEA3D University of Nice bioinfo.ipmc.cnrs.fr/lea. 17

html

LUDI Accelrys accelrys.com 12, 17

PRO_ligand Proteus Molecular Design

Skelgen De Novo

Pharmaceuticals

J Comp. Aided Mol. Des. 1995, 17

9, 13.

www.denovopharma.com/ 17 page2.asp

Protein analysis (binding sites, flexibility, hot spots, interfaces, water sites, etc.)

Chimera University of California, San

Francisco

www.cgl.ucsf.edu/chimera 16

Consolv Michigan State University

www.bch.msu.edu/

rv kuhn/software/consolv

4, 10

CS-Map Boston University Proteins 2003, 51, 340. 10

DFprot Centro de Investiga- ciones Biol,ogicas

sbg.cib.csic.es/Software/ 16

DFprot

Electron Density

Server

University of Uppsala eds.bmc.uu.se/eds/ 4, 10

FoldX EMBL foldx.crg.es 10, 16

GRID Molecular Discovery www.moldiscovery.com 4, 5, 10, 15 Harmony NCBS, Bangalore caps.ncbs.res.in/harmony 14

HINT eduSoft www.edusoft-lc.com 4, 10

MCSS Accelrys accelrys.com 17

Type Software name Developed at or

provided by

Reference/ Web site

Cited in Chapter


Mogul CCDC www.ccdc.cam.ac.uk/pro- 4 ducts/csd_system/mogul/

Molprobity Duke University molprobity.biochem.duke. 4

edu

MRC University of

California, San Diego

abagyan.ucsd.edu/MRC 16

ODA MolSoft www.molsoft.com/oda.html 16

PIER University of

California, San Diego

abagyan.ucsd.edu/PIER 16

PPI-Pred University of Leeds bmbpcu36.leeds.ac.uk/ 16

ppi_pred

PQS EMBL/EBI www.ebi.ac.uk/pdbe/pqs/ 4

PROCHECK EMBL/EBI www.biochem.ucl.ac.uk/

rv roman/procheck/ procheck.html

4, 14

PROFACE Bose Institute, Kolkata

PROMATE Weizmann Institute of Science

resources.boseinst.ernet.in/ 16 resources/bioinfo/interface

bioinfo.weizmann.ac.il/ 16

promate

PROTORP University of Sussex www.bioinformatics. 16

sussex.ac.uk/protorp

Q-siteFinder University of Leeds www.modelling.leeds.ac.uk/ 16

qsitefinder

Relibase, Waterbase CCDC relibase.ccdc.cam.ac.uk 4, 7

Robetta University of Washington

robetta.bakerlab.org 16

SuperStar CCDC www.ccdc.cam.ac.uk/pro-

ducts/life_sciences/ superstar/

4, 10

SURFNET University College London

www.biochem.ucl.ac.uk/ 16

rv roman/surfnet/ surfnet.html

UniProt UniProt Consortium www.uniprot.org 4

VMD University of Illinois at Urbana-

Champaign

www.ks.uiuc.edu/Research/ 16 vmd

Watermap Schr€odinger www.schrodinger.com 10

WaterScore University of Cam- bridge/De Novo

Pharmaceuticals

J. Mol. Model. 2003, 9, 172. 4, 10

WHAT_CHECK CMBI swift.cmbi.ru.nl/gv/ 4

whatcheck/

Homology modeling

CODA, FREAD, PETRA

Tripos tripos.com 14


Type

Software name

Developed at or provided by

Reference/ Web site

Cited in Chapter


COILS


MOBILE

EMBnet


University of

www.ch.embnet.org/soft- ware/COILS_form.html

J. Mol. Biol. 2003, 334, 327.

14


14



Modeller

Marburg

University of


salilab.org/modeller


14



MOE

California, San

Francisco

Chemical Computing


www.chemcomp.com


2, 14



PLOP

Group

University of


www.jacobsonlab.org


14



PSIPRED

California, San

Francisco University College


bioinf.cs.ucl.ac.uk/psipred


14



SCWRL

London

Fox Chase Cancer


dunbrack.fccc.edu/scwrl4


15



Sybyl Biopolymer

Center

Tripos


tripos.com


14


Whatif

CMBI

swift.cmbi.kun.nl/whatif/

14

MD S

imulations

Amber

UCSF, Scripps

ambermd.org

6, 7, 9


CHARMM


Gromacs

Harvard University/

Accelrys University of

www.charmm.org


www.gromacs.org

6, 7, 17


14



Groningen



Docking

ADAM IMMD, Toyko Proteins 2006, 63, 878. 8

ADDock Biodelight Biotech Inc.

ASEDock Tokai University School of Medicine

www.biodelight.com.tw/ 6

English

J. Chem. Inf. Model. 2008, 48, 6

583.

Autodock The Scripps Research

Institute

autodock.scripps.edu 6, 9, 10, 14,

15

CDOCKER Accelrys accelrys.com 9

ClusPro Boston University nrc.bu.edu/cluster 16

CombiDOCK University of California, San

Francisco

J. Comp.-Aided Mol. Des. 1

1998, 12, 597.

CombiGlide Schr€odinger www.schrodinger.com 1

DOCK University of California, San

Francisco

dock.compbio.ucsf.edu 6, 7, 9, 12,

14, 16

DREAM þþ University of California, San

Francisco

J. Comp.-Aided Mol. Des. 1

1999, 13, 513.

eHiTS SimBioSys www.simbiosys.ca 6

Type Software name Developed at or

provided by

Reference/ Web site

Cited in Chapter

EUDOC Mayo Foundation for Medical

Education and Research

  1. Comput. Chem. 2001, 22, 12

    1750.

    FITTED McGill University/ Forecaster

    fitted.ca 6, 10

    FlexE BioSolveIT www.biosolveit.de 6, 12, 15 FlexNovo BioSolveIT www.biosolveit.de 1

    FlexScreen BioSolveIT www.biosolveit.de 6, 8

    FlexX BioSolveIT www.biosolveit.de 3, 6, 8–10,

    12, 14, 17

    FlexXC BioSolveIT www.biosolveit.de 1

    FlexX-Pharm BioSolveIT www.biosolveit.de 6, 14

    FLIPDock The Scripps Research Institute

    flipdock.scripps.edu 6, 8

    FRED OpenEye www.eyesopen.com 6, 10, 14

    FRODOCK Centro de Investigaciones

    Biol,ogicas

    FTDock Imperial College London

    GasDock Dalian University of Technology

    sbg.cib.csic.es/Software/ 16

    FRODOCK

    www.sbg.bio.ic.ac.uk/ 16

    docking

    Bioorg. Med. Chem. Lett. 2004, 12

    14, 4671.

    GlamDock Chil2 www.chil2.de 6

    Glide Schr€odinger www.schrodinger.com 6, 9, 10,

    12, 14–17

    GOLD CCDC www.ccdc.cam.ac.uk/pro- ducts/life_sciences/gold


    GRAMM-X University of Kansas vakser.bioinformatics.ku.

    edu/resources/gramm/ grammx

    Haddock University of Utrecht haddock.chem.uu.nl/

    services/HADDOCK/ haddockservereasy.html

    4, 6, 7, 9,

    10, 12, 14,

    15, 17

    16


    16

    Hex INRIA www.loria.fr/rvritchied/hex 14, 16

    ICM MolSoft www.molsoft.com 6, 12, 14,

    16

    ISE-dock Hebrew University of Jerusalem

    Proteins 2008, 71, 1373. 6

    LibDock Accelrys accelrys.com 14

    Ligandfit Accelrys accelrys.com 14

    LIGIN Weizmann

    Institute of Science

    MOE Chemical

    Computing Group

    Proteins 1996, 25, 120. 12

    www.chemcomp.com 14, 15

    Type Software name Developed at or

    provided by

    Reference/ Web site

    Cited in Chapter

    MolFit Weizmann

    Institute of Science

    www.weizmann.ac.il/ 16

    Chemical_Research_ Support//molfit

    PatchDock Tel-Aviv University bioinfo3d.cs.tau.ac.il/ 16

    PatchDock

    PLANTS University of Konstanz

    www.tcd.uni-konstanz.de/ 6 research/plants.php

    Pso@autodock University of Leipzig biophys.biow.uni-

    leipzig.de/ psoatautodock.html

    QXP/FLO Colin McMartin J. Comp.-Aided Mol. Des.

    1997, 11, 333.

    6


    10, 12

    rDock York Structural Biol- ogy Laboratory

    RosettaDock Johns Hopkins

    University

    www.ysbl.york.ac.uk/rDock 12


    rosettadock.graylab.jhu.edu 16

    SEED, FFLD University of Zurich www.biochem-caflisch.uzh. 17

    ch

    SKE-DOCK Kitasato University www.pharm.kitasato-u.ac.jp/ 16

    bmd/files/SKE_ DOCK.html

    SLIDE Michigan State University

    www.bch.msu.edu/

    rv kuhn/software/slide

    8–10

    Sodock National Chiao Tung University

    iclab.life.nctu.edu.tw/sodock 6

    Surflex Tripos tripos.com 6, 12, 14

    ZDOCK Boston University zdock.bu.edu 16

    Scoring functions (SF)

    1. Empirical SF

      AIScore Raub et al., J. Chem. Inf. Model. 2008, 48, 1492. 7

      AutoDock3 SF Morris et al., J. Comput. Chem. 1998, 19, 1639. (7)

      AutoDock4 SF Huey et al., J. Comput. Chem. 2007, 28, 1145. (7)

      ChemScore Eldridge et al., J. Comp.-Aided Mol. Des. 1997, 11, 425. 7, 12, 14

      eHITS SF Zsoldos et al., J. Mol. Struct. Theochem. 2003, 7

      666–667, 659.

      FlexX SF Rarey et al., J. Mol. Biol. 1996, 261, 470. (7)

      Fresno Rognan et al., J. Med. Chem. 1999, 42, 4650. (7)

      GlideScore/GlideXP Friesner et al., J. Med. Chem. 2006, 49, 6177. 7, 16

      Giordanetto’s SF Giordanetto et al., J. Chem. Inf. Comput. Sci. 2004, 44, 7 882.

      Jain’s SF Jain, J. Comp. Aided Mol. Des. 1996, 10, 427. (7)

      LigScore Krammer et al., J. Mol. Graph. Model. 2005, 23, 395. (7)

      PLP Gehlhaar et al., Chem. Biol. 1995, 2, 317. 6, 7

      RankScore Moitessier et al., J. Med. Chem. 2006, 49, 5885. 7

      SCORE Wang et al., J. Mol. Model. 1998, 4, 379. (7)

      SCORE 3.0 Pei et al., Proteins 2006, 62, 934. (7)

      Type Software name Developed at or

      provided by

      Reference/ Web site

      Cited in Chapter


      SCORE1 Boehm, J. Comp. Aided Mol. Des. 1994, 8, 243. (7)

      SCORE2 Boehm, J. Comp. Aided Mol. Des. 1998, 12, 309. (7)

      ScreenScore Stahl et al., J. Med. Chem. 2001, 44, 1035. (7)

      SFCscore Sotriffer et al., Proteins 2008, 73, 395. 7

      SIE (FF) Naim, J. Chem. Inf. Model. 2007, 47, 122. (7)

      SLIDE SF Schnecke et al., Perspect. Drug Discov. Des. 2000, 20, 7 171.

      Surflex-Dock Pham et al., J. Med. Chem. 2006, 49, 5856. 7

      X-Score Wang et al., J. Comp.-Aided Mol. Des. 2002, 16, 11. (7)

      ASP

      Mooij et al., Proteins 2005, 61, 272.

      7

      BLEEP

      Mitchell et al., J. Comput. Chem. 1999, 20, 1165.

      7

      DFIRE

      Zhang et al., J. Med. Chem. 2005, 48, 2325.

      (7)

      DrugScorePDB

      Gohlke et al., J. Mol. Biol. 2000, 295, 337.

      7

      DrugScoreCSD

      Velec et al., J. Med. Chem. 2005, 48, 6296.

      7

      ITScore

      Huang et al., J. Comput. Chem. 2006, 27, 1866.

      (7)

      M-Score

      Yang et al., J. Med. Chem. 2006, 49, 5903.

      7

      PMF

      Muegge, J. Med. Chem. 2006, 49, 5895.

      7

      SMoG

      Ishchenko et al., J. Med. Chem. 2002, 45, 2770.

      7

      Other approaches



      AFMoC

      Gohlke et al., J. Med. Chem. 2002, 45, 4153.

      7

      AutoShim

      Martin et al., J. Chem. Inf. Model. 2008, 48, 861.

      7

      BBCS

      Fukunishi et al., J. Chem. Inf. Model. 2008, 48, 988.

      7

      COMBINE

      Ortiz et al., J. Med. Chem. 1995, 38, 2681.

      7

      CScore

      Clark et al., J. Mol. Graph. Model. 2002, 20, 281.

      14

      GFScore

      Betzi et al., J. Chem. Inf. Model. 2006, 46, 1704.

      7

      HINT

      Cozzini et al., J. Med. Chem. 2002, 45, 2469.

      4, 7, 10

      HYDE

      Reulecke et al., ChemMedChem 2008, 3, 885.

      7

      0

      LIE Aqvist et al., Protein Eng. 1994, 7, 385. 6, 7, 10,

      LIECE

      Huang et al., J. Med. Chem. 2004, 47, 5791.

      7, 17

      MM-GBSA

      Huang et al., J. Chem. Inf. Model. 2006, 46, 243.

      7, 9, 10

      MM-PBSA

      Kollman et al., Acc. Chem. Res. 2000, 33, 889.

      7, 9, 10

      ROTA

      Hartmann et al.,, Proteins 2009, 74, 712.

      14

      SeleX-CS

      Bar-Haim et al., J. Chem. Inf. Model. 2009, 49, 623.

      7

      SIFt

      Deng et al., J. Med. Chem. 2004, 47, 337.

      1, 5–7

      SSM

      Teramoto et al., J. Chem. Inf. Model. 2007, 47, 1858.

      7

      TOP

      Seifert, J. Comp. Aided Mol. Des. 2009, 23, 633.

      7

      TScore

      Matter et al., J. Med. Chem. 2005, 48, 3290.

      7

    2. Knowledge-based SF


(C)


17


Miscellaneous

AMSOL (solvation free energies)


University

of Minnesota


comp.chem.umn.edu/amsol 12

DAIM (molecule decomposition)

University of Zurich www.biochem-caflisch.uzh. 17

ch

Fragment – RECAP method (molecule

fragmentation)

ChemAxon chemaxon.com 1, 3


Cresset Installation

posted Jan 17, 2013, 2:11 PM by Dong Xu

yast2 -i  xed/forge/torch...rpm

binaries are installed to /opt/cresset

Amber 12 Installation

posted Jan 15, 2013, 12:48 PM by Dong Xu   [ updated Jan 17, 2013, 12:12 PM ]

see http://ambermd.org/bugfixes12.html

must run $AMBERHOME/patch_amber.py --update-tree at least several times to get all file patched up before installation.

also, install    flex tcsh zlib-devel bzip2-devel  libXt-devel libXext-devel libXdmcp-devel

may have to break dependency...

gcc-4.4 (opensuse 11.2) and its gfortran work find with GNU install in serial mode.

One problem encountered with leap code, missing -lSM

workaround: cd /usr/lib64
rm libSM.so
cp -s libSM.so.6.0.0 libSM.so

export CC=icc
export F77=ifort
export FC=ifort
export CXX=icpc


For mpi, used mpich2-1.3.2p1 compiled with intel

INL installation

module load ...
Compilation will fail because of ./configure somehow addes incorrect path to mkl libs
don't know why, it didn't happen on desktop because there was no mkl to use, I guess

To fix it, vi config.h and manually replace "/lib/intel64" to ""

Icestorm

Currently Loaded Modulefiles:
  1) pbs                   3) intel-mkl/11.1.046
  2) intel/11.1.046        4) openmpi-intel/1.2.6

Note, need to unload intel 10.1 module after loading openmpi-intel/1.2.6. This works for parallel installation, at least "make test" run fine.

module load intel/11.1.046 intel-mkl/11.1.046 mvapich2-intel/1.0.2
also works, but "make test" parallel did not go through, this may be mvapich restrctions.




ssh server sshd config

posted Jan 10, 2013, 2:53 PM by Dong Xu   [ updated Jan 18, 2013, 10:28 PM ]

TCP wapper for IP control

vi /etc/hosts.deny
add
ALL: ALL

vi /etc/hosts.allow
add all allowed IP and domains
ALL: hpclogin.inel.gov 204.134.163.222

vi /etc/ssh/sshd_config
MaxAuthTries 3
PermitRootLogin no
AllowUsers Myusername  see http://www.cyberciti.biz/tips/openssh-deny-or-restrict-access-to-users-and-groups.html

Protonation State

posted Nov 1, 2012, 9:52 AM by Dong Xu   [ updated Apr 11, 2013, 2:54 PM ]

Great article about basics:

http://www.daylight.com/meetings/emug00/Sayle/pkapredict.html

More pka examples:
https://docs.google.com/file/d/1LqtPkvhwlSDJpkxTV9ZCtz0-XgvHX_1HwNC8c3v9rjL-aFQ9xLJPokHON8py/edit?usp=sharing

1/ You know the pH you want for your simulation and you know the pKa of a certain residue, say His15, and now you want to know what to do about protons on the ND and NE. You have to decide on the following: If pH<pKa you protonate both nitrogens, otherwise you protonate one of them - which one could depend on possibilities of forming hydrogen bonds. 

2/ You want to know the pKa.
You can a/ look it up in a textbook, b/ look it up in a paper if somebody has measured it, c/ get somebody to measure it, d/ calculate it using Poisson-Boltzmann (there is a large literature on this subject)

Examples of Hendersen equation calculations are here:

OpenEye Suite Installation

posted Oct 25, 2012, 4:47 PM by Dong Xu   [ updated Oct 25, 2012, 4:52 PM ]

All executables should go in 

openeye/arch/suse-SLES11-x64

because packages such as rocs or eon use "suse-SLED11-x64" dir, the files should be moved into "suse-SLES11-x64" dir

As for Omega, its start-up script "omega2" should be edited just under the line

version=`grep -i suse /etc/SuSE-release`

from osver="SLE$osver" to osver="SLES$osver"

===================

some packages (vida, fred) are extracted to "suse-SLE11-x64", it works fine, you can either move it to "suse-SLES11-x64" or leave it.

List of Computational Chemistry Software

posted May 8, 2012, 6:02 PM by Dong Xu

Check CPU Temperature on Linux

posted Jan 29, 2012, 2:59 PM by Dong Xu   [ updated Jan 29, 2012, 3:00 PM ]

Consistent AM1-BCC Charge Calculation

posted Jan 29, 2012, 10:58 AM by Dong Xu

According to an amber-l post, here's the best practice to avoid inconsistency:

In my humble opinion, the most important consideration for correct charge
derivation is that the conformation of (especially) flexible molecules is
forced to be as extended as possible to prevent any intramolecular
interactions (H-bonding) that would corrupt the charge fitting method (the
documentation to Openeye's Quacpak clearly quotes Bayly in this
regard...). The simplest way to achieve this is use a program like VegaZZ
to assign charges using their SP4 FF then simply change the signs to be
all positive or all negative. Then use the SP4 FF to minimize the
structure. Since all atoms will repel each other, you will (always?)
achieve the most extended conformation. Then use MOPAC with AM1 to
minimize that structure, and then send it to antechamber. My gut feeling
is that the inconsistent use of the most extended conformations is much
more detrimental to accurate charge derivations than any advantage sqm
might have over MOPAC for assigning the AM1BCC charge.

Without knowing if your structure is highly flexible, it's hard to know if
what I discussed is relevant to your particular situation or not.

At the end of the Ambertools 1.5 it states that for AM1-BCC charges for
585 drug molecules, MOPAC and sqm give essentially similar charges for all
the cases and the average charge difference is 0.005. So what are the
advantages to sqm over MOPAC for AM1-BCC, since there appears to be tight
convergence issues with sqm?

DAC replied:

It was only after sqm was run "in the wild" on many more compounds than
we ever initially tested that we became aware of occasional convergence
issues.

By default, sqm demands tight convergence for both SCF and geometry
optimizations, whereas MOPAC has much less stringent criteria. We may not
have the most appropriate defaults, especially for am1-bcc calcs. This is
discussed in the antechamber chapter of the AmberTools Users' Manual.

==========

So the punch line is sqm tolerance is too tight, maybe try mopac in amber9 or (10?)

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