VIEWS: 7 PAGES: 44 POSTED ON: 12/4/2011
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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