Hi,
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.
| Attachment | Size |
|---|---|
 pdb output | 1.9 KB |
| params output | 3.33 KB |
| Mol2 file generated in iqmol for my AA | 1.41 KB |
I think you will at least need to add to the end of the mol file, or as a separate file with the flag --m-ctrl=file.txt with numbering based on the ordering in the mol file
M ROOT [the number of the N-terminal atom]
M POLY_N_BB [ditto, unless for some reason the most N terminal atom in your residue type is not ]
M POLY_CA_BB [the CA atom number]
M POLY_C_BB [the C atom number]
M POLY_O_BB [the O atom number]
M POLY_IGNORE [all the atoms of the capping groups except UPPER and LOWER]
M POLY_UPPER [the nitrogen atom number of the C-terminal methyl amide]
M POLY_LOWER [the carbonyl atom number of the N-terminal acetyl]
M POLY_PROPERTIES [any properties, like PROTEIN and CHARGED, etc.]
M END