Contents
Energy-Scans for Display
This is meant to be a very specific example of how the ENERGY-SCAN module can be used to generate the data needed to visualise an energy component on a triangulated surface defined around a molecule (though, in principle, something similar should be possible for an atom in a molecule too).
Get the GRID file
First of all, you need to define the surface. This can be done through Orient or within CamCASP using instructions here.
Important
CamCASP 5.9 and later can generate iso-density grids for the molecule and the atoms-in-the-molecule (the latter using the ISA).
Energy-Scan
Next we need to create a CamCASP command file to perform an energy scan of a molecule with a suitable probe. The idea is to place the probe atom/charge (it must be a spherically symmetrical particle) at each of the points on the triangulated surface, and calculate the required energy at each of those points. To do this, we use the ENERGY-SCAN module like so:
Begin Energy-Scan
Scan formamide with Charge +1.0
Energies E1elst
Units Bohr
Points
Translations-Only
#include formamide_1.00E-02_iso.grid
---
Energy-File formamide_aQZ_iso1.00E-02_Q_elst
EndIn this example, the module is used to calculate the electrostatic energy of the molecule (formamide) with a +1e point charge. The points are read in from file formamide_1.00E-02_iso.grid which is the output of the DISPLAY module (see description here). The output will be in a file with prefix formamide_aQZ_iso1.00E-02_Q_elst.
There are a few points to note:
Translations-Only is needed to tell the code that the points are specified as Rx Ry Rz, that is, without any rotation data. This is the appropriate form for spherically symmetric probes like the point charge.
We could have used an atom such as Ne or Cl$^-$ (needs to be closed shell) as a probe. The latter would have been more appropriate if in addition to $E^{(1)}_{\rm elst}$ we also wanted to scan $E^{(2)}_{\rm ind,tot}$ and/or $E^{(2)}_{\rm disp,tot}$.
The file containing the points needs to contain the points only (this will change in CamCASP 5.9). So we need to edit the file formamide_1.00E-02_iso.grid to comment out or delete the lines that contain text or other information. The edited file will look like:
! MOL-NAME formamide
! DENSITY-TYPE RHO-C
! UNITS BOHR
! BEGIN SITES
! 1 C 6.00 0.7369 -0.2902 0.0000
! 2 O 8.00 -0.4197 -2.2642 0.0000
! 3 N 7.00 -0.3376 2.0382 0.0000
! 4 H1 1.00 2.8209 -0.2060 0.0000
! 5 H2 1.00 -2.2333 2.1962 0.0000
! 6 H3 1.00 0.7228 3.6114 0.0000
! END SITES
! STEP 0.30000000E+00
! POINTS 4696
! TRIANGLES 9388
! BEGIN DATA
-4.2000000 1.2000000 -0.7174596
-4.2358335 1.2000000 -0.6000000
-4.2000000 1.1315009 -0.6000000
-4.2912392 1.2000000 -0.3000000
...
...
5.5275866 0.0000000 -0.3000000
5.5978608 0.0000000 0.0000000
5.5275828 0.0000000 0.3000000
5.4549442 0.3000000 0.0000000
! 1 2 3
! 2 4 5
! 3 2 5
! 4 6 7
! 5 4 7
! ...
! ...
! 4695 4696 4694
! 4680 4695 4674
! 4684 4678 4696
! 4684 4696 4679
! END DATAOf course, you could simply delete the commented out lines, but I prefer not to.
The entire CamCASP command file can be found here.
Process the output
Need to convert units?
As with any ENERGY-SCAN, pay attention to the units of energy: do you want it to be cm-1 or kJ/mol? Or something else? Of course you can convert units later using the PROCESS code, but it's best to get it right at this stage. Here I've used kJ/mol.
To convert units using PROCESS create a file like this:
Global Units kJ/mol End Energy Read formamide_aQZ_iso1.00E-03_Q_elst.dat Write formamide_aQZ_iso1.00E-03_Q_elst_kJ.dat End Finish
Call it convert_to_kJ.prss and run it through PROCESS
$ process < convert_to_kJ.prss
Insert data into GRID file
Next, to use the results in Orient, you need to insert the energies (in appropriate units) into the grid file. The energies will be in a file called formamide_aQZ_iso1.00E-02_Q_elst.dat. Copy the appropriate column (in this case, the electrostatic energy) and insert it in the original grid file (without any lines deleted or commented out!) to get something like this:
$ more formamide_1.00E-03_iso_aQZ_Q.elst
MOL-NAME formamide
DENSITY-TYPE RHO-C
UNITS BOHR
BEGIN SITES
1 C 6.00 0.7369 -0.2902 0.0000
2 O 8.00 -0.4197 -2.2642 0.0000
3 N 7.00 -0.3376 2.0382 0.0000
4 H1 1.00 2.8209 -0.2060 0.0000
5 H2 1.00 -2.2333 2.1962 0.0000
6 H3 1.00 0.7228 3.6114 0.0000
END SITES
STEP 0.30000000E+00
POINTS 4696
TRIANGLES 9388
BEGIN DATA
-4.2000000 1.2000000 -0.7174596 0.135038E+03
-4.2358335 1.2000000 -0.6000000 0.136834E+03
-4.2000000 1.1315009 -0.6000000 0.134023E+03
-4.2912392 1.2000000 -0.3000000 0.140585E+03
-4.2000000 1.0200695 -0.3000000 0.132162E+03
-4.3095228 1.2000000 0.0000000 0.141816E+03
-4.2000000 0.9819806 0.0000000 0.131182E+03
....
....
5.6017083 -0.3000000 0.0000000 0.666641E+02
5.5375572 -0.3000000 0.3000000 0.693236E+02
5.5275866 0.0000000 -0.3000000 0.724044E+02
5.5978608 0.0000000 0.0000000 0.693662E+02
5.5275828 0.0000000 0.3000000 0.724046E+02
5.4549442 0.3000000 0.0000000 0.783642E+02
1 2 3
2 4 5
3 2 5
4 6 7
5 4 7
6 8 9
....
....
4696 4693 4694
4680 4679 4696
4680 4696 4695
4695 4696 4694
4680 4695 4674
4684 4678 4696
4684 4696 4679
END DATAThe energies are in the fourth column. The format is
preable ... BEGIN DATA Rx Ry Rz Energy ... i j k <---triangles ... END DATA
The UNITS line may not (yet) control the units of the energies. But it will soon.
Now the data is ready for use by Orient to visualise the data.