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problem of renamed atoms in running

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problem of renamed atoms in running

Hi all,

I am running for my ligand to get the .params file, but the .params file generated by this script is not matched with .mol2 file that I use. This script changes the name of atoms and gives me a new pdb file in which name of atoms are different from my original .mol2 file. Moreover, I get a warning when running this code (which is copied below).  It is noteworthy to mention that all atom names in my ligand are unique.

I need a .params file which are matched with my original pdb file.

I would be grateful,if you could help me.

Atom names contain duplications -- renaming all atoms.

WARNING:  structure contains double bonds but no aromatic bonds

  Aromatic bonds must be identified explicitly --

  alternating single/double bonds (Kekule structure) won't cut it.

  This warning does not apply to you if your molecule really isn't aromatic.

Total naive charge -4.835, desired charge 0.000, offsetting all atoms by 0.056

WARNING: fragment 1 has 87 total atoms including H; protein residues have 7 - 24 (DNA: 33)

WARNING: fragment 1 has 40 non-H atoms; protein residues have 4 - 14 (DNA: 22)

WARNING: fragment 1 has 30 rotatable bonds; protein residues have 0 - 4

Average 87.0 atoms (40.0 non-H atoms) per fragment

(Proteins average 15.5 atoms (7.8 non-H atoms) per residue)

WARNING:  no root atom specified, using auto-selected NBR atom instead.

Wrote params file XYZ.params

Wrote PDB file XYZ_0001.pdb





Post Situation: 
Wed, 2020-04-22 19:17

So there are several options for that script.

  • --keep-names will keep the names
  • --name SPT will call the ligand SPT
  • Now. Your ligand looks like an amino acid, which has it's own flag (--amino-acid), but requires a substrate with special protective group... Or are you going to manually add UPPER and LOWER instead? If so, you will need to write two connect lines and two internal coordinate lines which you can steal from other amino acids. But the TYPE needs to be POLYMER not LIGAND.
Mon, 2020-05-04 02:16