Make_hybrid.py list index out of range error

Hi,

Could someone suggest where my problem is coming from with the following output from make_hybrid.py?

I’m using the charmm36 forcefield and following the latest ligand tutorial.

My only commands to this point:

atoms_to_morph.py -i1 .PEP1.pdb -i2 SPEP1.pdb -o pep_spep_pairs.dat -alignment -H2H

And:
/make_hybrid.py -l1 PEP1.pdb -l2 SPEP1.pdb -itp1 pep.itp -itp2 .spep.itp -pairs pep_spep_pairs.dat -oa pep_spep_merged.pdb -oitp pep_spep_hybrid.itp -ffitp pep_spep_dummy.itp -scDUMd 0.1

returns the below error…

Thank you,

Dan

make_hybrid__log_> Reading ligand 1 from: “…/PEP/PEP1.pdb”
make_hybrid__log_> Reading ligand 2 from: “…/SPEP/SPEP1.pdb”
make_hybrid__log_> Reading itp file 1 from: “…/PEP/pep.itp”
make_hybrid__log_> Reading itp file 2 from: “…/SPEP/spep.itp”
make_hybrid__log_> Assigning forcefield parameters…
make_hybrid__log_> Making pairs…
make_hybrid__log_> Reading file with atom pairs: “pep_spep_pairs.dat”
make_hybrid__log_> Generated 7 atom-atom pairs
make_hybrid__log_> Dummies in state A: 5
make_hybrid__log_> Dummies in state B: 5
make_hybrid__log_> Making B-states…
make_hybrid__log_> Atom…: 1 CG2O3 | 0.57 | 12.01 -> CG2O3 | 0.57 | 12.01
make_hybrid__log_> Atom…: 2 OG2D2 | -0.76 | 16.00 -> OG2D2 | -0.76 | 16.00
make_hybrid__log_> Atom…: 3 OG2D2 | -0.76 | 16.00 -> OG2D2 | -0.76 | 16.00
make_hybrid__log_> Atom…: 4 CG2D1O | -0.25 | 12.01 -> CG2D1O | -0.15 | 12.01
make_hybrid__log_> Atom…: 5 CG2DC3 | -0.46 | 12.01 -> CG2DC3 | -0.42 | 12.01
make_hybrid__log_> Atom…: 11 HGA5 | 0.23 | 1.01 -> HGA5 | 0.21 | 1.01
make_hybrid__log_> Atom…: 12 HGA5 | 0.23 | 1.01 -> HGA5 | 0.21 | 1.01
make_hybrid__log_> Dummy…: 13 DUM_PG2 | 0.00 | 30.97 -> PG2 | 1.60 | 30.97
make_hybrid__log_> Dummy…: 14 DUM_SG2P1 | 0.00 | 32.06 -> SG2P1 | -0.79 | 32.06
make_hybrid__log_> Dummy…: 15 DUM_OG2S1 | 0.00 | 16.00 -> OG2S1 | -0.90 | 16.00
make_hybrid__log_> Dummy…: 16 DUM_OG2S1 | 0.00 | 16.00 -> OG2S1 | -0.90 | 16.00
make_hybrid__log_> Dummy…: 17 DUM_OG2S1 | 0.00 | 16.00 -> OG2S1 | -0.90 | 16.00
make_hybrid__log_> Dummy…: 6 OG303 | -0.13 | 16.00 -> DUM_OG303 | 0.00 | 16.00
make_hybrid__log_> Dummy…: 7 PG2 | 0.84 | 30.97 -> DUM_PG2 | 0.00 | 30.97
make_hybrid__log_> Dummy…: 8 OG2P1 | -0.84 | 16.00 -> DUM_OG2P1 | 0.00 | 16.00
make_hybrid__log_> Dummy…: 9 OG2P1 | -0.84 | 16.00 -> DUM_OG2P1 | 0.00 | 16.00
make_hybrid__log_> Dummy…: 10 OG2P1 | -0.84 | 16.00 -> DUM_OG2P1 | 0.00 | 16.00
make_hybrid__log_> Generating bonded parameters…
Traceback (most recent call last):
File “/Users/danielburns/pmx/pmx/scripts/ligands/make_hybrid.py”, line 1216, in
main( sys.argv )
File “/Users/danielburns/pmx/pmx/scripts/ligands/make_hybrid.py”, line 750, in main
entr = get_ff2_entry([idB1, idB2], itp2, gmx45, what= ‘bond’)
File “/Users/danielburns/pmx/pmx/scripts/ligands/make_hybrid.py”, line 296, in get_ff2_entry
return out[3:][0]
IndexError: list index out of range

If anybody has this issue it is because you need to process your cgenff itp file with a script that was provided to me by Vytas Gapsys. If you need it, let me know.

Right, the topologies used by the hybrid topology generation script need to have all the bonded parameters defined explicitly.