MacroDox Brownian Dynamics Software 
 
 

Online Tutorial Table of Contents

1. Importing Proteins into MacroDox and Assigning Charges pdf
2. Calculating the Electrostatic Field around a Protein html pdf
3. Preparing a Second Protein for BD html pdf
4. Setting Up and Running BD Simulations html pdf
5. Analyzing a BD Simulation html pdf
6. Using the BD Helix Algorithm html pdf

General Suggestions for Using MacroDox

MacroDox comes compiled for different size systems. The executables in the MacroDox directory are named according to the upper limit for the number of atoms it can treat. It is more efficient to use the version that fits your particular molecule's needs. The larger versions of MacroDox require so much memory that some functions are nolonger functional (look for notes concerning this within the tutorials).

The different exacutables found in /disk06/macrodox3.0.0/program/ are

• macrodox5K for 5000 or fewer atoms
• macrodox12K for 12000 or fewer atoms
• macrodox18K for 18000 or fewer atoms
• macrodox21K for 21000 or fewer atoms

The tutorial is written using a small protein as an example and will function with the 5K version.

For novice Unix users, I recommend creating aliases in your .cshrc file in your personal user directory (e.g., mine is /usr/people/kathryn/). These aliases appear at the bottom of the file. Each time you login, this file will be noted so that you don't have to type long commands to reach whatever version of MacroDox you want.

Examples from my .cshrc file

• alias mdx5k /disk06/macrodox3.0.0/program/macrodox5K
• alias mdx12k /disk06/macrodox3.0.0/program/macrodox12K
• alias mdx18k /disk06/macrodox3.0.0/program/macrodox18K
• alias mdx21k /disk06/macrodox3.0.0/program/macrodox21K

I you wish to use these yourself, edit your .cshrc file using the jot editor and add these lines to the bottom of the file. Save the changes. Then logout and back in; this will activate the changes you made. Then when you want to access the version for 5000 atoms all you need to type is mdx5k. If you want the version for 21000 atoms all you need to type is mdx21k.

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TUTORIAL SESSION I (v. 3.0.0)
Importing Proteins into MacroDox and Assigning Charges

The following is an example tutorial session which reads in a Protein Data Bank file for the protein yeast iso-1-cytochrome c (1ycc) and assigns the charges to every atom based on a Tanford-Kirkwood calculation at a specified pH, temperature and ionic strength.

Basically the types of operations exemplified here can be summarized as follows:

1. A Protein Data Bank file is imported using the NEW command. Default charge assignments are made from the 'macprep.chg' file of charges.
2. The file of atoms is edited, the waters are eliminated and the resultant file is saved as an 'mdx' formatted file using SAVE.
3. The status of charge assignments and the global properties of the molecule are looked at using the STATUS and PROPERTIES command, respectively.
4. A Tanford-Kirkwood calculation is set up and run using the TK menu of commands.
5. The ASSIGN command is used to implement these TK-recommended set of charges.
6. The ADJUST command is used to tweak the charge on the FE to be what it should be
7. Finally, the PROPERTIES command is used for the properly assigned set of charges and a list of atoms near the resultant dipole vector is output to the file 'DIPOLE.LIS'.

1.1 Importing a Protein Data Bank File Using the NEW Command

The program is initiated by typing the command mdx5k, which brings up the main menu:

MacroDox Main Menu

File	Charges	Modify	Calculate	Dock
---------------------------------------------------------------atoms---------
Current file 1 = untitled
Current file 2 = untitled
Terminal type = IRIS workstation
-------------------------------------------------v3.0.1
new	assign	addh	properties	init
open	adjust	delh	surface	search
save	tk	mutate	field	rate
save as	status	xtrans	contour	review
swap		edit	slice
help		compare
settings		compare
quit

To import a brand new coordinate file for ycc in PDB format, use the NEW command. Commands can be all upper case, or all lower case, but not a mixture.

NEW 1ycc.pdb

The NEW command does the following:

• asks for a file name and then opens an ascii Protein Data Bank (PDB) formatted protein coordinate file called 1ycc.pdb
• a list of alternate atom names in a file called 'map.list' is consulted in order to rename certain atoms with other more acceptable name
• it then assigns masses and charges to all identifiable amino acid residues from the default charge file 'macprep.chg'. These are charge assignments in which every atom is assigned a partial charge from the CHARMM16 charge set
• alternative charge assignments can be made subsequently through the ASSIGN menu, which allows different Charge files to be attached in place of the default 'macprep.chg'
• an alert will appear for any amino acid residue or hetero atoms not assignable through the currently attached charge file. A list of these is generated in the temporary file named 'NOASSIGN.LIS' and an edit window opens up with this file
• titratible amino acids are identified for later calculation in Tanford-Kirkwood analysis
• informs the user of the number of atoms read in, and the current position of the center of mass. If the center of mass is not at the origin, the user will be asked if a shift of the center of mass to the origin is desired
• the prospective file generated, which is called the current MDX file is designated with the default name 'untitled' until SAVE or SAVE AS is invoked
• MDX is a special formatted file which is identical to the PDB format through the atom coordinates, but also contains mass, charge assignment, surface accessibility, and other titration site information
• a PDB file opened by NEW can be subject to modification through other commands and the resulting MDX file subsequently saved

After the NEW 1ycc.pdb command, the program should return the following messages:

PAGE UNDER CONSTRUCTION

Number of atoms originally read in = 1014 HEM E name changed to FE HEM N A name changed to NA HEM N B name changed to NB HEM N C name changed to NC HEM N D name changed to ND Warning: 121 atom(s) not found in charge_table file: Consult the output file NOASSIGN.LIS for a listing of atoms with unassigned charge and mass. Present position of center of mass = 4.507 19.824 7.983 Do you want to shift computed center of mass to the origin? To the question "Do you want to shift computed center of mass to the origin?", answer yes. Following this the program advises the user where the center of mass is: New position of center of mass = 0.000 0.000 0.000 and then returns to the MacroDox Main Menu. Also, an edit window should open up containing the list of 121 atoms whose charges could not be assigned. This is the file named 'NOASSIGN.LIS'. Here is a sample of that window containing the list of atoms that were not identified in the file 'macprep.chg', and thus have unassigned masses and charges. Here is a short sample of what that file should contain: HETATM 895 O HOH 105 HETATM 896 O HOH 106 HETATM 897 O HOH 107 HETATM 898 O HOH 108 HETATM 899 O HOH 109 HETATM 900 O HOH 110 HETATM 901 O HOH 111 HETATM 902 O HOH 112 HETATM 903 O HOH 113 HETATM 904 O HOH 114 HETATM 905 O HOH 115 HETATM 906 O HOH 116 HETATM 907 S SO4 117 HETATM 908 O1 SO4 117 HETATM 909 O2 SO4 117 HETATM 910 O3 SO4 117 HETATM 911 O4 SO4 117 HETATM 912 O HOH 118 . . . . . After inspecting this file, we find that these atoms are waters and a sulfate counterion. These are of no consequence to our subsequent treatment. After we exit the 'NOASSIGN.LIS' windows, we should go into the EDIT function and simply delete these from the newly created MDX file. But before we do that, it would not hurt to go ahead and save the assignments that have already been made. Execute the command: SAVE The program will ask you what type of file you want to create, another Protein Data Bank formatted file similar to what you imported with the NEW command, or whether you want the more information-expanded Macrodox-formatted file containing the charge assignments, etc. To this question, answer "mdx". Do you want an MDX or PDB format file? MDX What name shall I give the MDX file? 1ycc.mdx Since we have done a SAVE, we could QUIT the program at this point. Let's do that and then restart it: QUIT

University of North Dakota    

UND Dept. of Chemistry