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Molfile to params creating invalid params output

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Molfile to params creating invalid params output


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 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 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. 

Post Situation: 
Sun, 2021-08-29 01:54

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.]


Sun, 2021-08-29 11:15