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.