Optimal Paste

When you have a crystal structure, and want to minimize it with a rigid molecule (using DMACRYS), but with a slightly different molecular conformation, you need to use OptimalPaste. The normal time when you would want to do this are if you are minimizing an experimental crystal structure determination with the fully optimized molecular conformation.

The executable is found at /home/cposs/UTILITIES/OptimalPaste/OptimalPasteNonNAG/OptimalPaste on Xenon.

You need two files to run OptimalPaste

• The crystal structure file, which must be called expcrys.res
• The molecular conformation that you want to paste in, which must be called optmolstr.geomG

The expcrys.res file can be any .res file, with any format. Only the atomic coordinates are changed. The optmolstr.geomG is a .geomG format file, ie the molecular conformation that can be used in a GAUSSIAN optimization or charge density calculation. The order of the atoms in both files must be identical.

OptimalPaste works by minimizing the differences in the atomic positions of the non-hydrogen atoms. The resulting file is called pasted.res

Note: When NEIGHCRYS is run, the order of the atoms is changed to have all the atoms of the same type together. This may require you to reorder the experimental crystal structure file.

If you have more than 1 molecule in your crystal structure, you will need to separate them into two expcrys.res files and paste the optimized conformation in separately. Then join the two files back together. Although the order of the atoms is critical, the names are not - if you have higher numbers in your second molecule, the pasted.res file comes out with those higher numbers.

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