I am using the Surface Probe script from Stephen Todd that is available on the discussion boards through this link: https://community.accelrys.com/thread/1794
Thank you for the script. I have downloaded the *.zip file and run the demo successfully.
I would like to now modify the script to evaluate the surface energies in my model, but I am having a problem getting the correct Settings read into the script.
I am using a user-defined forcefield (CLAYFF) and properties as specified in my Calculation-Settings file. The script is opening the file through the "LoadSettings" command and reading some of the relevant information (summation method (group vs. atom vs. Ewald) and cutoff distances). But, it does not appear to be finding the Forcefield file (CLAYFF) and thus defaults to "Universal". If I open the calculation settings document through the GUI, it lists my forcefield (CLAYFF) for the Calculation. But the output files (see below) indicate that "Universal" is the chosen forcefield and the script job fails because there are forcefield types that are not part of the chosen forcefield (Universal).
I have placed a copy of CLAYFFin all the locations that I think the script might be looking for it (root diretory of the project and in the ../share/Discover/res/ directory). But this doesn't seem to matter, the error persists. Where does this user-defined forcefield file (*.off format)need to be? Or, can I specify it's location through a line in the SurfaceProbe.pl script? I have attached the "LoadSettings" file if it could be of any help.
Thank you in advance for taking the time to read through my question and share your expertise.
Aric
Forcite
-------
Task : Energy
Version : 5.5
Build date : Mar 22 2011
Host : compute-0-2.local
Threads : Parallel 6
Operating system : linux
Task started : Fri Jun 10 18:42:25 2011
---- Energy parameters ----
Forcefield : Universal
Electrostatic terms:
Summation method : Ewald
Accuracy : 0.001 kcal/mol
Buffer width : 0.5 A
van der Waals terms:
Summation method : Ewald
Accuracy : 0.001 kcal/mol
Repulsive cutoff : 10 A
Buffer width : 0.5 A
---- Current structure ----
The model contains forcefield types that are not part of the selected forcefield.
Script Output
host | 0
======|======
0 : SHM
Prot - All Intra-node communication is: SHM
The model contains forcefield types that are not part of the selected forcefield in Forcite.Calculation (function/property "Run") at -e line 145.
Centroid coordinates are 20.946724213452, 16.0749490996521, 0.0140017061569877
Grid spacing is 1.89284545454545 angstroms
Length in the x direction is 20.8213 and the number of points is 11
Length in the y direction is 66.4346 and the number of points is 35
Length in the z direction is 18.8582 and the number of points is 9
Total number of energy calculations is 1296
Total number of points in the grid is 4320
Translated the probe molecule 1.87884374838847 to place it on the nearest grid point
