Itp file generation (printing out parameters)

User discussions
1

GROMACS version: 2023
GROMACS modification: No
Is there a way to print out FF parameters that associate with all lines in itp file (bonds, pairs, angle, dihedral)? I can get those numbers from related ff files but it is very easy to make errors and time consuming for large system. Thank you very much.

2

Yes, Gromologist has the Top.add_ff_params() function exactly for that.

There’s also Top.molecules[0].label_types() that simply puts atom types in the comment of each interaction entry (in [ bonds ], [ angles ] etc).

1 Like
3

That is wonderful. Thank you very much.

1 Like
4

I have run Gromologist to get most of dihedral except the line which has extra info.
"
15 17 19 34 9 0.0 1.75728 3
18 17 19 20 9 0.0 0.0 0
18 17 19 21 9 0.0 0.0 0
18 17 19 34 9 0.0 0.0 0
34 19 21 24 9 torsion_LEU_C_CA_CB_CG_mult1
34 19 21 24 9 torsion_LEU_C_CA_CB_CG_mult2
34 19 21 24 9 torsion_LEU_C_CA_CB_CG_mult3
17 19 21 22 9 0.0 0.65084 3
17 19 21 23 9 0.0 0.65084 3
17 19 21 24 9 0.0 0.65084 3
20 19 21 22 9 0.0 0.65084 3
20 19 21 23 9 0.0 0.65084 3

"
Is there a way to get the value for these guys as well for given geometry set by pdb file? Again, thank you very much for your suggestion.

5

These are values specified elsewhere in the topology with #define keywords (here a standard thing for the ILDN correction), you can replace them with actual numbers with Top.explicit_defines().

6

Thank you very much. I got them.