I am trying to generate a ncAA. My current workflow is using a program called iQmol which has a connection to a QChem server, to produce an appropriate mol file. I then use mol_file_to_params.py to get the params files. It creates a params file with all the atoms quite close together. Running mol_file_to_params gives me this output with the attached files:
edanhabel@Edans-MacBook-Pro-2 molfile2params % python molfile_to_params.py iqmol_pymol_aromatic.mol2 -n f5p --clobber --amino-acid PHE
Centering ligands at ( -0.773, 1.157, 0.117)
Total naive charge -1.725, desired charge 0.000, offsetting all atoms by 0.075
Average 23.0 atoms (17.0 non-H atoms) per fragment
(Proteins average 15.5 atoms (7.8 non-H atoms) per residue)
Wrote params file f5p.params
Wrote PDB file f5p_0001.pdb
I have tried different arguments, such as not specifying the AA. Strangely, the pdb output has the atoms in correct spatial distrubution. I am sure there is something wrong with my input file, but I cannot tell what it is.
Thank you for your help.