Peleffy parameters for a macrocycle causes infinte loop in PELE

[cescgina]

When generating the parameters for plitidepsin (a quite large macrocycle) the resulting template causes PELE to get stuck in an infinite loop generating the sparse atoms. Generating the template with PlopRotTemp does not cause the same issue. I attached the ligand pdb, and the generated templates.

plitidepsin_data.zip

[cescgina]

I found some additional information that I think is related to this bug. Peleffy seems to have problems parsing the topology of the ligand. For example there are dihedrals that contain two times the same atom, e.g.

14 8 -16 14
27 80 -85 27
25 126 -131 25
10 148 -151 10
14 4 -8 14
25 108 -112 25
9 35 -40 9
17 159 -161 17
25 104 -108 25
14 8 -15 14
27 80 -84 27
9 31 -35 9

Also some dihedrals involve atoms that are not bonded together, for example:

43 38 33 14

In this case atom 14 (H22 in the pdb) is not bonded to atom 33 (N1) in the pdb.

[cescgina]

I just checked the same system with the devel branch and works fine now!