The topolgy files were generated using pdb2gmx on tripeptides built in pymol. The error message is as follows:
"
Traceback (most recent call last):
File "/Users/rmuraglia/alchemical-setup-master/alchemical-setup.py", line 564, in
buildAtoms() # Part II.
File "/Users/rmuraglia/alchemical-setup-master/alchemical-setup.py", line 296, in buildAtoms
xyz_A, name_alpha_counter, hh, oo = preprocessAtoms(molA, defaultdict(int), [], [])
File "/Users/rmuraglia/alchemical-setup-master/alchemical-setup.py", line 236, in preprocessAtoms
l['xyz'] = "%8.3f%8.3f%8.3f" % tuple(xyz_A[i])
IndexError: index 17 is out of bounds for axis 0 with size 17
"
Hello, my attempt to carry out an amino acid mutation using the following input files failed:
GAG.top GLG.top map.txt
The topolgy files were generated using pdb2gmx on tripeptides built in pymol. The error message is as follows:
" Traceback (most recent call last): File "/Users/rmuraglia/alchemical-setup-master/alchemical-setup.py", line 564, in
buildAtoms() # Part II.
File "/Users/rmuraglia/alchemical-setup-master/alchemical-setup.py", line 296, in buildAtoms
xyz_A, name_alpha_counter, hh, oo = preprocessAtoms(molA, defaultdict(int), [], [])
File "/Users/rmuraglia/alchemical-setup-master/alchemical-setup.py", line 236, in preprocessAtoms
l['xyz'] = "%8.3f%8.3f%8.3f" % tuple(xyz_A[i])
IndexError: index 17 is out of bounds for axis 0 with size 17
"
The rest of the printed output is attached in alchemical-setup.err.
It is unclear to me why I am running into this issue or what steps I can take to fix it. Any help would be greatly appreciated. Thank you in advance!