Step 2.  Build a complete input configuration for the isolated molecule.

In this example, we create a modified PDB file that contains information regarding atom identities, positions, connectivities, charges and locations of improper torsions.  

The source code for the program that accomplishes this task, make_pdb_v02.f, and the associated subroutines, are included in the source directory.

To compile this code, move to the directory with the four *.f files and the makefile and type the command

make make_pdb

To execute the code, move the executable, a.out, to the directory with the necessary input files and type the command

a.out

Included in the example directory are 

xyz file (input, output from step 1)
make_pdb_input.txt (input)
charge_input.txt (input)
improper_input.txt (input)
make_pdb_output_tru.pdb (output, standard pdb format)
make_pdb_output_mod.pdb (output, modified pdb format)

Included in the source directory:

make_pdb_v02.f  (main program)
get_tranm.f (subroutine)
read_db.f (subroutine)
xinvmat.f (subroutine)
makefile (compilation instructions)






MSE 614
University of Tennessee, Knoxville
David Keffer
dkeffer@utk.edu
February 24, 2016