- c it distinguishes : c1,c2,c3 as sp3 carbons: primary, sec., tert.
- c it distinguishes : ca = C(sp2), c6 = C(arom), n4 =N(cuaternary)
- c it distinguishes : h = H , o = O
- c it distinguishes : c9 = C(carbonyl, as in C=O)
- c it assigns : c0 = general c1,c2,c3
- c it assigns : c4 = C(cuaternary)
- c (otherwise you can relabel 'c4' to 'c3' if pots are the same)
- c it assigns : n0 = general n1,n2,n3
babel -icar template.car -opdb template.pdb
awk -f pdb2con.awk < template.pdb > fort.9
3. The files fort.11, fort.12 and fort.13 are fixed and they must be in the directory.
4. Run the con2fie executable, which is going to generate the fort.1, fort.10 and fort.14 files. These files are the the input files for DL_POLY (fort.1, fort.10 ) and GULP (fort.14).
./con2fie
5. Run the awk scripts skip-repeated.awk onto fort.14
awk -f skip_repeated.awk < fort.14 > fort.14-1
and
awk -f forcefield_repeated.awk < fort.14-1> fort.14-2
6. If a torsion term makes part of the force field, then add a number code following the rule:
n=3 if Angle= 0.0
n=2 if Angle= 180.0
example:
torsion bond intra
h core c1 core ca core h core 0.0108 0.0
h core ca core ca core h core 0.3254 180.0
Add:
torsion bond intra
h core c1 core ca core h core 0.0108 3 0.0
h core ca core ca core h core 0.3254 2 180.0
7. You're ready to go. The file fort.14-2 is your Hydrocarbon ForceField in GULP format.
8. Files fort.1 and fort.10 are the files needed by DL_POLY FIELD file. fort.1 has information about the 2-Body, 3-Body and Dihedral intramolecular force field. fort.10 is a check-out file with 2, 3 and 4 body connectivity.
9. Charges for the forcefield are obtained from the template.car using the "charges.awk" awk script.
awk -f charges.awk < template.car > template.charges
The output file contains the individual charges of every atom in the molecule and the average charge value for atom type.
