Protein Volume and Voids

(1) McVol:

• Developed by Matthias Ullmann's team
• omictools (https://omictools.com/mcvol-tool) can be used to download  McVol
• McVol uses a Monte Carlo method to compute volumes of protein cavities
• McVol requires a .pqr file as an input. There are many online tools available to create a .pqr file from .pdb file. We tried with pdb2pqr server (http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/) and it worked fine. You need to upload input pdb file from your desktop (accessing the pdb file from rcsb did not work!). In doing so, you need to make sure that only protein coordinates are present in the pdb file (exclude heteroatoms, water, and ions). We could use pdb2pqr server to get atomic radii and charges (CHARMM) of atoms of a system of interest (You may need them to quickly compute vdW and electrostatic energies).
• McVol also requires a setup file. This file contains all necessary input parameters needed to compute the void volume of the system of interest.
  
  nmc 50       ! Number of Monte Carlo steps per A^3 molecule
  surfPT 2500    ! Number of surface points per atom
  probe 1.3     ! Probe sphere radius
  membZmin -10  ! Minimum Z coordinate for the membrane
  membZmax 10   ! Maximum Z coordinate for the membrane
  startgridspacing 1.0   ! Grid spacing fo the initial search
  membgridspacing 2.0    ! Grid spacing for the membrane
  cavgridspacing 0.5     ! Grid spacing for the cavity refinement
  minVol 7       ! Minimum volume for cavities to be treated
  waterVol 18     ! Volume of one water molecule
  DummyRad 1.7    ! Radius of the dummy atoms placed as membrane
  blab 0          ! Output level
  MembDim 4      ! Thickness of the membrane in x/y direktion
  CoreZMin 0     ! Membrane Core region minimum Z coordinate
  CoreZMax 0      ! Membrane Core region maximum Z coordinate
  CoreDim 0       ! Allowed distance of membrane points not in core region
  CleftDim 3     ! Kind of a inverse probe sphere radius for a cleft
  CleftRel 70
  CleftMethod 2
  SurfaceCluster 1.5

Ubuntu - useful tips

(1) Important shortcut keys for computer:

CTRL+A. . . . . . . . . . . . . . . . . Select All

CTRL+C. . . . . . . . . . . . . . . . . Copy

CTRL+X. . . . . . . . . . . . . . . . . Cut

CTRL+V. . . . . . . . . . . . . . . . . Paste

CTRL+Z. . . . . . . . . . . . . . . . . Undo

CTRL+B. . . . . . . . . . . . . . . . . Bold

CTRL+U. . . . . . . . . . . . . . . . . Underline

CTRL+I . . . . . . . . . . . . . . . . . Italic

F1 . . . . . . . . . . . . . . . . . . . . . . Help

F2 . . . . . . . . . . . . . . . . . . . . . Rename selected object

F3 . . . . . . . . . . . . . . . . . . . . . Find all files

F4 . . . . . . . . . . . . . . . . . . . . . Opens file list drop-down in dialogs

F5 . . . . . . . . . . . . . . . . . . . . . Refresh current window

F6 . . . . . . . . . . . . . . . . . . . . . Shifts focus in Windows Explorer

F10 . . . . . . . . . . . . . . . . . . . . Activates menu bar options

ALT+TAB . . . . . . . . . . . . . . . . Cycles between open applications

ALT+F4 . . . . . . . . . . . . . . . . . Quit program, close current window

ALT+F6 . . . . . . . . . . . . . . . . . Switch between current program windows

ALT+ENTER. . . . . . . . . . . . . . Opens properties dialog

ALT+SPACE . . . . . . . . . . . . . . System menu for current window

ALT+¢ . . . . . . . . . . . . . . . . . . opens drop-down lists in dialog boxes

BACKSPACE . . . . . . . . . . . . . Switch to parent folder

CTRL+ESC . . . . . . . . . . . . . . Opens Start menu

CTRL+ALT+DEL . . . . . . . . . . Opens task manager, reboots the computer

CTRL+TAB . . . . . . . . . . . . . . Move through property tabs

CTRL+SHIFT+DRAG . . . . . . . Create shortcut (also right-click, drag)

CTRL+DRAG . . . . . . . . . . . . . Copy File

ESC . . . . . . . . . . . . . . . . . . . Cancel last function

SHIFT . . . . . . . . . . . . . . . . . . Press/hold SHIFT, insert CD-ROM to bypass auto-play

SHIFT+DRAG . . . . . . . . . . . . Move file

SHIFT+F10. . . . . . . . . . . . . . . Opens context menu (same as right-click)

SHIFT+DELETE . . . . . . . . . . . Full wipe delete (bypasses Recycle Bin)

ALT+underlined letter . . . . Opens the corresponding menu

PC Keyboard Shortcuts

Document Cursor Controls

HOME . . . . . . . . . . . . . . to beginning of line or far left of field or screen

END . . . . . . . . . . . . . . . . to end of line, or far right of field or screen

CTRL+HOME . . . . . . . . to the top

CTRL+END . . . . . . . . . . to the bottom

PAGE UP . . . . . . . . . . . . moves document or dialog box up one page

PAGE DOWN . . . . . . . . moves document or dialog down one page

ARROW KEYS . . . . . . . move focus in documents, dialogs, etc.

CTRL+ > . . . . . . . . . . . . next word

CTRL+SHIFT+ > . . . . . . selects word

Windows Explorer Tree Control

Numeric Keypad * . . . Expand all under current selection

Numeric Keypad + . . . Expands current selection

Numeric Keypad – . . . Collapses current selection

¦ . . . . . . . . . . . . . . . . . . Expand current selection or go to first child

‰ . . . . . . . . . . . . . . . . . . Collapse current selection or go to parent

Special Characters

‘ Opening single quote . . . alt 0145

’ Closing single quote . . . . alt 0146

“ Opening double quote . . . alt 0147

“ Closing double quote. . . . alt 0148

– En dash. . . . . . . . . . . . . . . alt 0150

— Em dash . . . . . . . . . . . . . . alt 0151

… Ellipsis. . . . . . . . . . . . . . . . alt 0133

• Bullet . . . . . . . . . . . . . . . . alt 0149

® Registration Mark . . . . . . . alt 0174

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° Degree symbol. . . . . . . . . alt 0176

¢ Cent sign . . . . . . . . . . . . . alt 0162

1⁄4 . . . . . . . . . . . . . . . . . . . . . alt 0188

1⁄2 . . . . . . . . . . . . . . . . . . . . . alt 0189

3⁄4 . . . . . . . . . . . . . . . . . . . . . alt 0190

PC Keyboard Shortcuts

Creating unique images in a uniform world! Creating unique images in a uniform world!

é . . . . . . . . . . . . . . . alt 0233

É . . . . . . . . . . . . . . . alt 0201

ñ . . . . . . . . . . . . . . . alt 0241

÷ . . . . . . . . . . . . . . . alt 0247

File menu options in current program

Alt + E Edit options in current program

F1 Universal help (for all programs)

Ctrl + A Select all text

Ctrl + X Cut selected item

Shift + Del Cut selected item

Ctrl + C Copy selected item

Ctrl + Ins Copy selected item

Ctrl + V Paste

Shift + Ins Paste

Home Go to beginning of current line

Ctrl + Home Go to beginning of document

End Go to end of current line

Ctrl + End Go to end of document

Shift + Home Highlight from current position to beginning of line

Shift + End Highlight from current position to end of line

Ctrl + f Move one word to the left at a time

Ctrl + g Move one word to the right at a time

MICROSOFT® WINDOWS® SHORTCUT KEYS

Alt + Tab Switch between open applications

Alt +

Shift + Tab

Switch backwards between open

applications

Alt + Print

Screen

Create screen shot for current program

Ctrl + Alt + Del Reboot/Windows® task manager

Ctrl + Esc Bring up start menu

Alt + Esc Switch between applications on taskbar

F2 Rename selected icon

F3 Start find from desktop

F4 Open the drive selection when browsing

F5 Refresh contents

Alt + F4 Close current open program

Ctrl + F4 Close window in program

Ctrl + Plus

Key

Automatically adjust widths of all columns

in Windows Explorer

Alt + Enter Open properties window of selected icon

or program

Shift + F10 Simulate right-click on selected item

Shift + Del Delete programs/files permanently

Holding Shift

During Bootup

Boot safe mode or bypass system files

Holding Shift

During Bootup

When putting in an audio CD, will prevent

CD Player from playing

WINKEY SHORTCUTS

WINKEY + D Bring desktop to the top of other windows

WINKEY + M Minimize all windows

WINKEY +

SHIFT + M

Undo the minimize done by WINKEY + M

and WINKEY + D

WINKEY + E Open Microsoft Explorer

WINKEY + Tab Cycle through open programs on taskbar

WINKEY + F Display the Windows® Search/Find feature

WINKEY +

CTRL + F

Display the search for computers window

WINKEY + F1 Display the Microsoft® Windows® help

WINKEY + R Open the run window

WINKEY +

Pause /Break

Open the system properties window

WINKEY + U Open utility manager

WINKEY + L Lock the computer (Windows XP® & later)

OUTLOOK® SHORTCUT KEYS

Alt + S Send the email

Ctrl + C Copy selected text

Ctrl + X Cut selected text

Ctrl + P Open print dialog box

Ctrl + K Complete name/email typed in address bar

Ctrl + B Bold highlighted selection

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WORD® SHORTCUT KEYS

Ctrl + A Select all contents of the page

Ctrl + B Bold highlighted selection

Ctrl + C Copy selected text

Ctrl + X Cut selected text

Ctrl + N Open new/blank document

Ctrl + O Open options

Ctrl + P Open the print window

Ctrl + F Open find box

Ctrl + I Italicize highlighted selection

Ctrl + K Insert link

Ctrl + U Underline highlighted selection

Ctrl + V Paste

Ctrl + Y Redo the last action performed

Ctrl + Z Undo last action

Ctrl + G Find and replace options

Ctrl + H Find and replace options

Ctrl + J Justify paragraph alignment

Ctrl + L Align selected text or line to the left

Ctrl + Q Align selected paragraph to the left

Ctrl + E Align selected.

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

(1) APT configuration (to make apt-get work):

     step1: vi /etc/apt/apt.conf (it is a new file).
     step2: add Acquire::http::Proxy "http://yourproxyaddress:proxyport";
               to /etc/apt/apt.conf file


(2) Installation of java/javac for DL_POLY_GUI (in ubuntu 14.04):
   
     sudo apt-get install openjdk-7-jdk
     javac *.java
     jar cfm GUI.jar manifesto *.class About_DL_POLY Acknowledge CERAMICS MINIDREI    MINIOPLS WATER300K TestInfo Licence Disclaimer
    ./build
    java -jar GUI.jar

(3) To change default applications (for example, to set Adobe Reader as default PDF reader):

 sudo vi /etc/gnome/defaults.list
 change: from "application/pdf=evince.desktop" to "application/pdf=acroread.desktop"

 Add below line into the end:

  application/fdf=acroread.desktop
  application/xdp=acroread.desktop
  application/xfdf=acroread.desktop
  application/pdx=acroread.desktop

  run nautilus -q to apply changes.  (this step may not be required!)

(4) To install acroread:

   sudo add-apt-repository "deb http://archive.canonical.com/ precise partner" (to add the repository)
   sudo apt-get update
   sudo apt install adobereader-enu
   sudo add-apt-repository -r "deb http://archive.canonical.com/ precise partner" (to remove the repository)
   sudo apt-get update

(5) audio recording:

     sudo apt-get install lame
     arecord -f cd -d 3600 -t wav | lame --preset 56 -mm - `date +file_created_on_%d-%m-%Y_at_%H-%M`.mp3

Argon models

Standard LJ parameters used for Argon simulations (ref: A. Rahman's work)

epsilon = 0.238 kcal/mol
sigma   = 3.4 A

These non-bonded parameters should be specified in the NAMD parameter file as follows (use -epsilon and 2^(1/6)*sigma/2 (or 1.12246204831*sigma/2) format):

!Argon
AR 0.000000 -0.238000 1.908100 ! comment

Pioneers

                              Pioneers and Role Models

In India (the list is incomplete; more names will be added soon):
         - Biman Bagchi
         - Rama Kant
         - S.K. Rangarajan
         - K.L. Sebastian
    
Outside of India (more names will be added): 
         - Robert Zwanzig
         - John G. Kirkwood
         - Eugene Wigner
         - Hans C. Andersen
         - David Chandler
         - Bruce Berne
         - Martin Karplus
         - Mark E. Tuckerman
         - Attila Szabo
         - Ludwig E. Boltzmann
         - Josiah Willard Gibbs
         - Noam Agmon

Useful_Scientific_Problems

                               Some useful research problems

(1) Remote Sensing of Explosive Materials

Ambertools16

                                         Installation:

(1) Download AmberTools16.tar.bz2 from http://ambermd.org/AmberTools16-get.html

(2) bunzip2 AmberTools16.tar.bz2

(3) tar xvf AmberTools16.tar

(4) cd amber16

(5)  export AMBERHOME=/home/myname/amber16 # (for bash, zsh, ksh, etc.)
      setenv AMBERHOME /home/myname/amber16 # (for csh, tcsh)
      (if needed, you may need to install csh: sudo apt-get install csh)

(6) You may need to install flex, bison and some compilers and other libraries
      (use synaptic package manager or apt-get)

(7) ./configure gnu  (if needed, switch over to csh)

(8)  source /home/myname/amber16/amber.sh # for bash, zsh, ksh, etc.
      source /home/myname/amber16/amber.csh # for csh, tcsh

(9) make install

(10) make test

Useful tips:

(1) pdb4amber -i input.pdb -o output.pdb [options]
(2) $AMBERHOME/bin/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.DNA.bsc1 -f $AMBERHOME/dat/leap/cmd/leaprc.water.tip3p 
(3) In xleap window: 
      (a) to load a pdb file
            bdi=loadpdb "output.pdb"
      (b) to see and edit the structure
            edit bdi
      (c) to see the list of structures loaded
            list
      (e) to save prmtop and inpcrd:
            saveamberparm bdi bdi.prmtop bdi.inpcrd 

Tutorial: 
(http://ambermd.org/tutorials/advanced/tutorial2/section1.htm)

system:  N-methylacetamide (NMA) in a periodic box of TIP3P water
input PDB: NMA_skeleton.pdb
content of NMA_skeleton.pdb is as follows (missing atoms will be guessed):

ATOM     1   C   ACE     1       0.000   0.000   0.000
ATOM     2   N   NME     2       3.000   1.000  -1.000
TER

step1:  $AMBERHOME/bin/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.protein.ff14SB

step2: nma=loadpdb "NMA_skeleton.pdb"

step3:  edit nma (to energy minimize)

step4: Edit->Relax

step 5:  Unit->Close

step6:  source leaprc.water.tip3 (load solvent parameters)

step7: to add water box:
solvatebox nma TIP3PBOX 15 (here, buffer=15 A, which means that the distance between any atom of NMA and the edge of the box is at least 15 A)
step8:
saveamberparm nma nma.prmtop nma.inpcrd

Our B-DNA model:
step1: remove hydrogens from DNA
step2: add 'TER' after DNAA and DNAB
step3: change residue name of water from TIP3 to TP3
step4: change OH2 of water to O
step5:$AMBERHOME/bin/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.protein.ff14SB -f $AMBERHOME/dat/leap/cmd/leaprc.DNA.bsc1
step6:  In xleap window: source leaprc.water.tip3p
step7: bdna=loadpdb "l_noh.pdb"
step8: saveamberparm bdna bdna.prmtop bdna.inpcrd
step9: savepdb bdna bdna_amber.pdb

For parmbsc1:
 refer: http://mmb.irbbarcelona.org/ParmBSC1/help.php?id=download#instructions

source $AMBERHOME/dat/leap/cmd/leaprc.ff14SB

loadoff parmBSC1.lib
 loadamberparams parmBSC1.frcmod

To visualize AMBER trajectory using VMD:
----------------------------------------

step1: File -> New Molecule -> select file.prmtop (if required, specify the file type as "AMBER7 Parm")
step2: select "Load Data Into Molecule" and load the trajectory file (file.dcd). Here, you need to specify the input dcd file type as "CHARMM,NAMD,XPLOR DCD Trajectory".

To set the topology and parameters for a new residue/fragment:
--------------------------------------------------------------
read: http://ambermd.org/tutorials/advanced/tutorial1/section3.htm

To model proteins:
------------------
Note1: There are three types of histidine (HIS in normal pdb files) residues in AMBER:
      

HID: Histidine with hydrogen on the delta nitrogen (HSD in CHARMM)
HIE: Histidine with hydrogen on the epsilon nitrogen (HSE in CHARMM)
HIP: Histidine with hydrogens on both nitrogens; this is positively charged.
It is up to the user to inspect the environment of each histidine and identify the type that is appropriate.

Note2: Change ILE CD to CD1
Note3: Change CGLY OT1 to O;
             Change CGLY OT2 to OXT
Note4:  Remove all hydrogens of the protein from the pdb file

STEP1:  $AMBERHOME/bin/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.protein.ff14SB
STEP2: In xleap window: loadamberparams frcmod.ff99SBnmr (You may need to download frcmod.ff99SBnmr from Bruschweiler's website and copy it to $AMBERHOME/dat/leap/parm folder).
STEP3: source leaprc.water.tip3p
STEP4: ubq=loadpdb "ionized_nohyd.pdb"
STEP5: saveamberparm ubq ubq.prmtop ubq.inpcrd
STEP6: savepdb ubq ubq_amber.pdb

AMBER parameters for simple molecules and cofactors:
------------------------------------------------------------------------------------------
http://research.bmh.manchester.ac.uk/bryce/amber
http://upjv.q4md-forcefieldtools.org/REDDB/projects/F-90/

How to cite Ambertools16:

D.A. Case, R.M. Betz, D.S. Cerutti, T.E. Cheatham, III, T.A. Darden, R.E. Duke, T.J. Giese, H. Gohlke, A.W. Goetz, N. Homeyer, S. Izadi, P. Janowski, J. Kaus, A. Kovalenko, T.S. Lee, S. LeGrand, P. Li, C. Lin, T. Luchko, R. Luo, B. Madej, D. Mermelstein, K.M. Merz, G. Monard, H. Nguyen, H.T. Nguyen, I. Omelyan, A. Onufriev, D.R. Roe, A. Roitberg, C. Sagui, C.L. Simmerling, W.M. Botello-Smith, J. Swails, R.C. Walker, J. Wang, R.M. Wolf, X. Wu, L. Xiao and P.A. Kollman (2016), AMBER 2016, University of California, San Francisco.

voro++/zeo++

zeo++
---------

(1) The radii of atoms are tabulated in networkinfo.cc. If needed, you could define new atom types and assign atomic radii of your choice here.

(2) Box/unit cell vectors: a is aligned with the x-axis and b is in the xy-plane.

(3) The format of the output of the stochastic ray tracing option:
      x y z dx dy dz magnitude
      Here, magnitude = sqrt(dx*dx + dy*dy + dz*dz) and, for a given ray shooted into the free volume region, it provides a measure of the norm of that ray . I think, x y z are the coordinates of the starting point of the ray (not sure!). I think, the way to understand the output is as follows: A given ray starts from (x,y,z) and extends by dx, dy, and dz units along the x-, y-, and z-axes, respectively.

(4) Pore diameters:
     First value: D_i (Diameter of the largest included sphere).
     The largest included sphere points to the location of the largest cavity in the system and D_i measures the size of this cavity.

     Second value: D_f (Diameter of the largest free sphere).
      The largest free sphere corresponds to the largest spherical probe that can diffuse through the structure and D_f measures a minimum restricting aperture on a diffusion path.

     Third value: D_if (Diameter of the largest included sphere along free sphere path).
     D_if is a measure of the size of the largest cavity along free sphere path/diffusion path.

(5) The distance grid option is possible. The energy grid option is not available.
      Distance grid:
      A grid representation of the system is used.  Each grid point is assigned a distance to the surface of the nearest atom. The radius of the largest included sphere is then equal to the maximum value over all grid points. The clusters of neighboring grid points with the assigned distance values above a threshold corresponding to the probe radius are identified and connected to calculate the largest free sphere.

The energy grid option, in principle, can be used to estimate the net activation energy for diffusion of a probe through the system.

 (6) Voronoi netowrk:
        - Voro++ is used
        - voronoi cell associated with each atom is computed individually
        - the collection of edges and vertices/nodes of individual voronoi cell is stored
        - for each edge and vertix of the voronoi cell of an atom, the minimum distance to the atom is also stored. This distance is the distance to the surface of the central atom if its radius is specified (otherwise it is the distance to the center of the atom).

(7) To visualize the network:
      -  cd zeovis
      -  open ZeoVis.tcl and change the path to the network executable. 
      -  vmd -e ZeoVis.tcl
      -  You will be asked to provide the filename of your input file (i.e., the structure file). After providing the input filename, nothing will be displayed on the graphical window of vmd. Do not worry!
      - to show all atoms: show atom all
      - to show all nodes: show node all
      - to show the voronoi cell of an given atom (say, with index 4): show vorcel 4
      - to undo : undo
      - to show unit cell : show unitcell