Dear Amber,
I meet an Issue which the ligand of my protein can not be recoganized by pdb2oniom when I use TAO QM/MM package , I placed the ligand prep file into the ESPT/prepfiles folder of the TAO package according to the tutorial, can anyone help me how to solve the issue?
Any help will be much appreciate.
The ligand in the example of the TAO package can be recoganized very well, but my ligand don't works.
I creat prep file use the following commands,
antechamber -i ligand.pdb -fi pdb -o ligand.mol2 -fo mol2 -c bcc -s 2
antechamber -i ligand.mol2 -fi mol2 -o ligand.prep -fo prepi
I run the following command and the ligand can not recoganized by TAO package.
pdbcore -o 1994_r.pdb -resid corelist.txt -near 6 -i 1994-trunk-new.pdb
Core residues list file corelist.txt provided.
All residues within 3 angstroms from core region are free to move (0) during geometry optimization.
Atom type cannot be assigned to atom H1 in residue MET 1.
Partial charge cannot be assigned to atom H1 in residue MET 1.
Element type cannot be decided for atom H1 in residue MET 1.
Atom type cannot be assigned to atom H2 in residue MET 1.
Partial charge cannot be assigned to atom H2 in residue MET 1.
Element type cannot be decided for atom H2 in residue MET 1.
Atom type cannot be assigned to atom H3 in residue MET 1.
Partial charge cannot be assigned to atom H3 in residue MET 1.
Element type cannot be decided for atom H3 in residue MET 1.
Atom type cannot be assigned to atom OXT in residue ALA 298.
Partial charge cannot be assigned to atom OXT in residue ALA 298.
Element type cannot be decided for atom OXT in residue ALA 298.
Atom type cannot be assigned to atom C1 in residue UNK 299.
Partial charge cannot be assigned to atom C1 in residue UNK 299.
Element type cannot be decided for atom C1 in residue UNK 299.
Atom type cannot be assigned to atom H01 in residue UNK 299.
Partial charge cannot be assigned to atom H01 in residue UNK 299.
Element type cannot be decided for atom H01 in residue UNK 299.
Atom type cannot be assigned to atom H02 in residue UNK 299.
Partial charge cannot be assigned to atom H02 in residue UNK 299.
Element type cannot be decided for atom H02 in residue UNK 299.
Atom type cannot be assigned to atom H03 in residue UNK 299.
Partial charge cannot be assigned to atom H03 in residue UNK 299.
........................................
Your Best,
Zhihong XIn,
Nanjing Agricultural University
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Received on Wed Dec 15 2021 - 01:00:02 PST
