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					Calculating partial charges for
a nonstandard DNA base with
    ECCE and NWChem
Start the builder from the ECCE toolbar
Choose import from the file menu
Import the PDB file containing thymine-
            glycol geometry
Select the MD toolkit after importing the
               structure
Select the THG residue in the MD toolkit
 In the main Builder window, select (shift-
click) the oxygen atom connecting THG to
            its neighbor cytosine
Using the edit menu, reverse the selection
Again using the edit menu, delete the
 reversed selection to isolate THG
In the MD toolkit, check the Edit column for
 THG to enable the addition of new atoms
   Click on the white H to begin adding
hydrogen, then click on the two circled nubs
  to terminate the residue with hydrogen
                   atoms
With the hydrogen atoms in place, choose
  Geometry Table from the view menu
 Rename the two new hydrogen atoms to
give them unique names such as H5T and
                  H3T
If you cannot see an Atom Name column,
   select All Fields under the view menu
Choose Export from the file menu to write a
PDB file containing the isolated hydrogen-
             terminated THG
Choose a name for the exported PDB file
  and save it; note where it is saved to
Open the reorder.py Python script in a text
 editor. The placeholder atom list needs to
become a real list of all atoms on the base.
The highlighted atoms pictured here belong
  to the base and will go in the atom list
  Select each base atom in the builder by
 clicking it and note the value under the ‘#’
column in the geometry table; these are the
             entries of the atom list
  After filling the atom list, run the script to
        produce a reordered PDB file
• python reorder.py unordered.pdb >
  reordered.pdb
• Now reordered.pdb has all base atoms
  stored and numbered consecutively
• Close all builder windows, restart the
  builder, and import the reordered PDB file
After importing the reordered PDB file,
 choose Save As from the file menu
Choose a name for your calculation and
               save
Do not immediately start the calculation
              manager
  Open the partial charge toolkit from the
toolkits menu. This toolkit will be used to set
up constraints on calculated partial charges.
In the partial charge toolkit, click New to add
 a constraint and choose ‘total charge fixed’
 In the builder, select the same base atoms
that went in the atom list for reordering; use
  shift-click to select multiple atoms at once
  Click ‘populate group #1’ to make these
atoms subject to the total charge constraint.
 Set total charge to 0.121600 to make the
   base interoperable with standard DNA
If not all of the base atoms were reordered,
   or nonconsecutive atoms are otherwise
 selected, the populate group operation will
                       fail
  If the partial charge constraint was
successfully added, save the calculation
 After the partial charge constraint is added
     and the system is saved, start the
calculation manager from the ECCE toolbar
In the calculation manager, select the row
containing your system and then select the
  NWChem calculation editor under tools
Change the charge of the system to -1 to
 match standard interior DNA residues
Change the runtype to ESP
Choose the basis set 6-31G*
Choose theory details
Under theory details, make sure that SCF
 computed is direct; close the panel after
          making the change
Back in the NWChem editor, choose launch
Select a configured machine and launch
      from the ECCE job launcher
A few seconds after launching, you should
  see the green circle of a calculation in
                progress
  2-3 hours later, the green square of a
completed calculation should appear in the
          calculation manager.
With your finished calculation selected, open
      the calculation viewer from tools
   Under partial charges, choose CESP
(constrained electrostatic potential) and then
               assign charges
Open the builder for your system and then
        view the geometry table
 The calculated partial charges have been
assigned. Save your system before exiting.

				
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posted:12/4/2011
language:English
pages:44