Dear Sir
I am using antechamber tutorial. First i create parameter and coordinate
files for ligand. Afterward i create a topology and coordinate files for
ligand-protein complex. But it is not accept ligand residues in dock
complex file. When i upload pdb file of dock complex, it shows an error
"The file contained 89 atoms not in residues templates"
>complex=loadpdb best.pdb
Loading PDB file: ./best.pdb
Unknown residues: UNK number 648 type: Terminal/last..relaxing end
constraints to try for a dbase match
- noluck
Created a new atom named: HD1 within residue: .R<HIE 249>
Created a new atom named: HD1 within residue: .R<HIE 573>
Created a new UNIT for residue: UNK sequence: 649
Created a new atom named: C1 within residue: .R<UNK 649>
Created a new atom named: N2 within residue: .R<UNK 649>
Created a new atom named: C3 within residue: .R<UNK 649>
Created a new atom named: C4 within residue: .R<UNK 649>
Created a new atom named: C5 within residue: .R<UNK 649>
Created a new atom named: N6 within residue: .R<UNK 649>
Created a new atom named: N7 within residue: .R<UNK 649>
Created a new atom named: C8 within residue: .R<UNK 649>
...........
............
...........
........
...........
total atoms in file: 9937
leap added 2 missing atoms according to residue templates
2H / lone pairs
The file contained 89 atoms not in residue template
Any one can guide me.
Thanks
Regards
Amen Shamim
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Received on Thu Jul 04 2013 - 02:00:03 PDT
