11/2/2014

vmd - Minot group

Visualizing Molecules with VMD

VMD is a powerful tool for visualizing and analyzing complex molecules like proteins. Below are walkthroughs of some
features. See also this convenient manual [http://www.ks.uiuc.edu/Training/Tutorials/vmd/vmd-tutorial.pdf].

VMD basics
Download PDB file for the molecule you want to visualize
Downloaded PDB files here: protein databank [http://www.pdb.org]
Choose File New Molecule
Set Load files for: to New Molecule
Browse for PDB file & click Load
Choosing Graphics Representations allows you to visualize the protein differently
To create new visual representations click 'Create Rep'
Filters may be applied in the Selected Atoms window.
Examples: all, helix, alpha, alpha and index>1000, waters and vol0>0.5, etc.

Visualizing electrostatics
Create a potential map
Convert PDB file to a PQR file which includes per atom charge information
The conversion can be done online here: Online PDB2PQR [http://kryptonite.nbcr.net/pdb2pqr/]. Or locally
from here: Local PDB2PQR [http://abacus/pdb2pqr/].
Type in PDB # or upload PDB file
Choose PARSE for force field
Choose the internal naming scheme
Use PROPKA to assign a pH value for the environment
The output filetype is .pqr
Look at .pqr file header to check for any errors
PDB2PQR is very picky about what residue codes are used in the PDB files. If an error
occurred the offending residues may need to be renamed in the PDB file or a .mol2 file
needs to be supplied to PDB2PQR so it knows how to deal with them. Some residues can be
built and have .mol2 files generated by PRODRG
[http://davapc1.bioch.dundee.ac.uk/prodrg/index.html].
Run the Applied Poisson-Boltzmann Solver (APBS)
Method 1: run APBS as a plug in from VMD
In VMD choose Extensions Analysis Electrostatics
Edit calculation
Note: the number of grid points needs to be a dime allowable value
[http://www.poissonboltzmann.org/apbs/user-guide/running-apbs/input-files/elec-input-filesection/elec-keywords/dime], you can't set these to whatever value you want. Allowable

values include 65+32*i where i is an integer.

Choose which equation to solve
Note: the linear Poisson-Boltzmann equation is easier to solve but maybe less
accurate?
Run APBS
Note: If you get an error that says 'output file missing or unreadable' it is probably
because there are spaces in the path to the output file. Choose Output Settings
and make sure there are no spaces in the path. Also make sure that there are no
http://www.science.oregonstate.edu/~minote/wiki/doku.php?id=vmd

1/5

11/2/2014

vmd - Minot group

spaces in the .pqr filename that you're inputting.

Method 2: run APBS from the command line. This method is a little more flexible, and avoids bugs
associated with the VMD plug in.
Generate an APBS input file (extension .in).
This can be done manually or with VMD's plug-in (even if the plug-in is misbehaving, it
might still output a good APBS input file that you can run at the command line).
To generate the input file with VMD select Edit Settings in the APBS Tool window.
Check the box labeled 'Setup files only, do not run APBS'
Edit the calculation settings as normal and run APBS from VMD
Locate the output .in file
From DOS run:
working_directory\APBS\APBS.exe working_directory\abps.in
Locate the potential map file APBS made (extension .dx)
To visualize the potential map in VMD: select File New Molecule and load the .dx
potential map onto the molecule for which it was created.
Visualize the potential map
Choose Graphics Representations
Option 1: Isosurfaces
Create a representation & choose Isosurface for the Drawing Method
Choose isosurface value (units are kT/e (= 25 mV at room temperature))
Make this be a blue, positive surface (+ kT/e)
Repeat same procedure except making a red, negative surface (- kT/e)
Option 2: Surface potential map
Create a representation & choose Surf for the Drawing Method
Choose Volume for the Coloring Method
Make sure you select which volume map to color with in the pulldown menu to the right
In the Trajectory tab set the Color Scale Data Range.
Units are kT/e

Calculating the charge on a structure

When you create a pqr file from a pdb file the total charge on the protein is output in the remarks at the top of the
pqr file.
The charge on each atom is stored in the second column from the right in the pqr file. To find the charge of an
arbitrary segment of the protein simply sum up the the atom's charges that make up the segment.
Oftentimes the charge on each domain of a protein is interesting. Under the Sequence Details tab in a protein's
page in the Protein Database the residue numbers of the protein are divided into domains.

Measuring the potential at an atom

Note: There's probably a convenient command that would simplify this but I don't know it (yet).
Choose an atom & record it's index number: xxxx
'query' an interesting atom by pressing '0' & clicking on the atom
Create a new representation
Use Drawing Method: VDW
In the selected atoms box type: index=xxxx and vol0>-500 and vol0<500
The point will be displayed if the potential is between -500 kT/e and 500 kT/e. Close in these values until
the point disappears & you'll know the potential there.

Aligning a section of two molecules

http://www.science.oregonstate.edu/~minote/wiki/doku.php?id=vmd

2/5

11/2/2014

vmd - Minot group

Give the molecule to be moved a new name in the vmd console window
set newname [atomselect n all]
Where n is the molecule ID number (found in the VMD Main window)
The protein backbone alpha-carbons probably don't move a lot between the two molecules. So select them using
the two commands
set alpha1 [atomselect n alpha]
set alpha2 [atomselect m alpha]
Where m is the second molecule's ID number
If the backbones DO move a lot between the two molecules modify the part of the command in
parenthesis to specify the part that you want to align. i.e. alpha and index>1054
Both groups of atoms must have the same number of atoms. Verify this using
$alpha1 num
$alpha2 num
Calculate a best fit transformation matrix & call it M
set M [measure fit $alpha1 $alpha2]
Use M to move your molecule
$newname move $M

Other movements of molecules

To move arbitrarily you can follow the general directions in the above 'Aligning a section of two molecules' section,
except use a different transformation matrix M . For example, to rotate 90 degrees around the z-axis:
set newname [atomselect n all]
set M [transaxis z -90]
$newname move $M

Loading/saving coordinates and volume maps into a molecule

The x,y,z coordinates & orientation of a molecule may be saved:
Select File Save Coordinates
Save the file
Choose the file extension you want
Volume maps created by APBS can be saved so the calculation doesn't need to be redone every time you need it
Find the .dx file APBS creates in /usr/tmp/ & copy it to a safe place.
To find the the file sort the folders according to modification date & look for a recent one starting with APBS
To load saved coordinates & orientation or a volume map (an old APBS calculation say) into a molecule:
Load a molecule into VMD
Select File New Molecule
Next to Load files for: choose your molecule
Browse for the volume map you want loaded
Click Load

Creating a potential difference volume map

Find PDB numbers for two conformations of the same molecule
Use the molecular morphing database [http://www.molmovdb.org/] to find good protein morphs
Create PQR files from both PDB files
Load both PQR files into VMD
http://www.science.oregonstate.edu/~minote/wiki/doku.php?id=vmd

3/5

11/2/2014

vmd - Minot group

Align a section of both molecules

It would be worthwhile to save this alignment
Run APBS for both molecules
Important: make sure both volume map options are identical with regards to origin, fine grid options,
number of gridpoints, etc. Verify this by clicking Edit in the APBS Tool window.
Copy the .dx volume map files APBS just created into home folder
Default location: /usr/tmp/ . Organize files by modification date & look for folders starting with APBS
Subtract one volume map from the other using the program volumer (Volumer is an in-house program for doing 3D
potential map subtractions. If you stumbled on this wiki from the abyss of the internet and are interested in
obtaining a free copy we'd be happy to share. Contact Landon Prisbrey ([email protected]))
In a terminal window run the program by typing /home/landon/volumer
The program will ask for both filenames, preform the subtraction, & output a file: filename1-filename2.dx
The footer of the new .dx file might be missing. If so, just copy-paste the footer from one of the .dx files
used to create it
Load the new volume map into VMD.

Creating aesthetically pleasing PR images

Good colors:
violet: red 52 green 53 blue 50
green: red 64 green 82 blue 71
tan: red 82 green 71 blue 55
Good Representation combo (backbone=violet, sidechain=green, Oxygens=tan spheres):
Licorice violet backbone
Licorice green sidechain
VDW tan name O.*^J
Good representation combo (random):
Licorice violet backbone
Licorice green sidechain or name CA
VDW tan sphere scale=0.9
Licorice green sheet
Licorice green coil
Load everything up and choose 'diffuse' for the material type
Render image as a tachyon filename.dat file
In a terminal window add ambient occlusion lighting with the command
LINUX: /usr/local/lib/vmd/tachyon_LINUXAMD64 -rescale_lights 0.4 -add_skylight 0.7 filename.dat -o
newfilename.tga -aasamples 8
Windows 7: C:\Program Files (x86)\University of Illinois\VMD\tachyon_WIN32 -rescale_lights 0.4 add_skylight 0.7 c:/inputfilename.dat -o c:/outputfilename.tga -aasamples 8
It will take a long time to render. To do test renders add -res xxx yyy before -rescale_lights to specify a smaller xxx
by yyy resolution. This can also be used to make extra large resolution images!
see VMD's Tachyon tutorial [http://www.ks.uiuc.edu/Research/vmd/minitutorials/tachyonao/] for information on this
command and how to modify it

Useful links
Details about PDB files [http://www.wwpdb.org/docs.html]
Details about PQR files [http://www.poissonboltzmann.org/file-formats/biomolecular-structurw/pqr]
Generating nanotube and graphene PDB files [http://turin.nss.udel.edu/research/tubegenonline.html]
Tutorials about VMD [http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/]
ABPS program working in VMD [http://www.ks.uiuc.edu/Research/vmd/plugins/apbsrun/]
http://www.science.oregonstate.edu/~minote/wiki/doku.php?id=vmd

4/5

11/2/2014

vmd - Minot group

Details on DX files (Volume map files) [http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dxplugin.html]

http://www.science.oregonstate.edu/~minote/wiki/doku.php?id=vmd

5/5