求助TAO工具包prep文件无法被程序识别的问题

hhhnano

最近在学习TAO ONIOM工具包，按照作者提供的教程文件，运行TAO正常，但是作自己的蛋白时，发现小分子配体无法识别 ，按照教程所说，需要将小分子prep文件放在ESPT/prepfiles文件夹中，我将prep文件放在该文件下，文件名参考教程中的小分子（SB3_resp_int.prep，蛋白配体为SB3）修改为（UNK_resp_int.prep，蛋白配体为UNK），但是仍无法识别，不知有人是否遇到同样的问题？

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.

Element type cannot be decided for atom H03 in residue UNK 299.

Atom type cannot be assigned to atom C2 in residue UNK 299.

Partial charge cannot be assigned to atom C2 in residue UNK 299.

Element type cannot be decided for atom C2 in residue UNK 299.

Atom type cannot be assigned to atom H04 in residue UNK 299.

Partial charge cannot be assigned to atom H04 in residue UNK 299.

Element type cannot be decided for atom H04 in residue UNK 299.

Atom type cannot be assigned to atom H05 in residue UNK 299.

Partial charge cannot be assigned to atom H05 in residue UNK 299.

Element type cannot be decided for atom H05 in residue UNK 299.

Atom type cannot be assigned to atom C3 in residue UNK 299.

Partial charge cannot be assigned to atom C3 in residue UNK 299.

Element type cannot be decided for atom C3 in residue UNK 299.

Atom type cannot be assigned to atom H06 in residue UNK 299.

Partial charge cannot be assigned to atom H06 in residue UNK 299.

Element type cannot be decided for atom H06 in residue UNK 299.

Atom type cannot be assigned to atom H07 in residue UNK 299.

Partial charge cannot be assigned to atom H07 in residue UNK 299.

Element type cannot be decided for atom H07 in residue UNK 299.

Atom type cannot be assigned to atom C4 in residue UNK 299.

Partial charge cannot be assigned to atom C4 in residue UNK 299.

Element type cannot be decided for atom C4 in residue UNK 299.

Atom type cannot be assigned to atom H08 in residue UNK 299.

Partial charge cannot be assigned to atom H08 in residue UNK 299.

Element type cannot be decided for atom H08 in residue UNK 299.

Atom type cannot be assigned to atom H09 in residue UNK 299.

Partial charge cannot be assigned to atom H09 in residue UNK 299.

Element type cannot be decided for atom H09 in residue UNK 299.

Atom type cannot be assigned to atom C5 in residue UNK 299.

Partial charge cannot be assigned to atom C5 in residue UNK 299.

Element type cannot be decided for atom C5 in residue UNK 299.

Atom type cannot be assigned to atom C6 in residue UNK 299.

Partial charge cannot be assigned to atom C6 in residue UNK 299.

Element type cannot be decided for atom C6 in residue UNK 299.

Atom type cannot be assigned to atom C7 in residue UNK 299.

Partial charge cannot be assigned to atom C7 in residue UNK 299.

Element type cannot be decided for atom C7 in residue UNK 299.

Atom type cannot be assigned to atom H13 in residue UNK 299.

Partial charge cannot be assigned to atom H13 in residue UNK 299.

Element type cannot be decided for atom H13 in residue UNK 299.

Atom type cannot be assigned to atom H14 in residue UNK 299.

Partial charge cannot be assigned to atom H14 in residue UNK 299.

Element type cannot be decided for atom H14 in residue UNK 299.

Atom type cannot be assigned to atom H15 in residue UNK 299.

Partial charge cannot be assigned to atom H15 in residue UNK 299.

Element type cannot be decided for atom H15 in residue UNK 299.

Atom type cannot be assigned to atom H11 in residue UNK 299.

Partial charge cannot be assigned to atom H11 in residue UNK 299.

Element type cannot be decided for atom H11 in residue UNK 299.

Atom type cannot be assigned to atom H12 in residue UNK 299.

Partial charge cannot be assigned to atom H12 in residue UNK 299.

Element type cannot be decided for atom H12 in residue UNK 299.

Atom type cannot be assigned to atom H10 in residue UNK 299.

Partial charge cannot be assigned to atom H10 in residue UNK 299.

Element type cannot be decided for atom H10 in residue UNK 299.

Atom type cannot be assigned to atom C8 in residue UNK 299.

Partial charge cannot be assigned to atom C8 in residue UNK 299.

Element type cannot be decided for atom C8 in residue UNK 299.

Atom type cannot be assigned to atom H16 in residue UNK 299.

Partial charge cannot be assigned to atom H16 in residue UNK 299.

Element type cannot be decided for atom H16 in residue UNK 299.

Atom type cannot be assigned to atom H17 in residue UNK 299.

Partial charge cannot be assigned to atom H17 in residue UNK 299.

Element type cannot be decided for atom H17 in residue UNK 299.

Atom type cannot be assigned to atom O1 in residue UNK 299.

Partial charge cannot be assigned to atom O1 in residue UNK 299.

Element type cannot be decided for atom O1 in residue UNK 299.

Atom type cannot be assigned to atom C9 in residue UNK 299.

Partial charge cannot be assigned to atom C9 in residue UNK 299.

Element type cannot be decided for atom C9 in residue UNK 299.

Atom type cannot be assigned to atom O2 in residue UNK 299.

Partial charge cannot be assigned to atom O2 in residue UNK 299.

Element type cannot be decided for atom O2 in residue UNK 299.

Atom type cannot be assigned to atom C10 in residue UNK 299.

Partial charge cannot be assigned to atom C10 in residue UNK 299.

Element type cannot be decided for atom C10 in residue UNK 299.

Atom type cannot be assigned to atom C11 in residue UNK 299.

Partial charge cannot be assigned to atom C11 in residue UNK 299.

Element type cannot be decided for atom C11 in residue UNK 299.

Atom type cannot be assigned to atom H18 in residue UNK 299.

Partial charge cannot be assigned to atom H18 in residue UNK 299.

Element type cannot be decided for atom H18 in residue UNK 299.

Atom type cannot be assigned to atom C12 in residue UNK 299.

Partial charge cannot be assigned to atom C12 in residue UNK 299.

Element type cannot be decided for atom C12 in residue UNK 299.

Atom type cannot be assigned to atom H19 in residue UNK 299.

Partial charge cannot be assigned to atom H19 in residue UNK 299.

Element type cannot be decided for atom H19 in residue UNK 299.

Atom type cannot be assigned to atom C13 in residue UNK 299.

Partial charge cannot be assigned to atom C13 in residue UNK 299.

Element type cannot be decided for atom C13 in residue UNK 299.

Atom type cannot be assigned to atom H20 in residue UNK 299.

Partial charge cannot be assigned to atom H20 in residue UNK 299.

Element type cannot be decided for atom H20 in residue UNK 299.

Atom type cannot be assigned to atom C14 in residue UNK 299.

Partial charge cannot be assigned to atom C14 in residue UNK 299.

Element type cannot be decided for atom C14 in residue UNK 299.

Atom type cannot be assigned to atom H21 in residue UNK 299.

Partial charge cannot be assigned to atom H21 in residue UNK 299.

Element type cannot be decided for atom H21 in residue UNK 299.

Atom type cannot be assigned to atom C15 in residue UNK 299.

Partial charge cannot be assigned to atom C15 in residue UNK 299.

Element type cannot be decided for atom C15 in residue UNK 299.

Atom type cannot be assigned to atom C16 in residue UNK 299.

Partial charge cannot be assigned to atom C16 in residue UNK 299.

Element type cannot be decided for atom C16 in residue UNK 299.

Atom type cannot be assigned to atom O3 in residue UNK 299.

Partial charge cannot be assigned to atom O3 in residue UNK 299.

Element type cannot be decided for atom O3 in residue UNK 299.

Atom type cannot be assigned to atom O4 in residue UNK 299.

Partial charge cannot be assigned to atom O4 in residue UNK 299.

Element type cannot be decided for atom O4 in residue UNK 299.

Atom type cannot be assigned to atom C17 in residue UNK 299.

Partial charge cannot be assigned to atom C17 in residue UNK 299.

Element type cannot be decided for atom C17 in residue UNK 299.

Atom type cannot be assigned to atom H22 in residue UNK 299.

Partial charge cannot be assigned to atom H22 in residue UNK 299.

Element type cannot be decided for atom H22 in residue UNK 299.

Atom type cannot be assigned to atom H23 in residue UNK 299.

Partial charge cannot be assigned to atom H23 in residue UNK 299.

Element type cannot be decided for atom H23 in residue UNK 299.

Atom type cannot be assigned to atom C18 in residue UNK 299.

Partial charge cannot be assigned to atom C18 in residue UNK 299.

Element type cannot be decided for atom C18 in residue UNK 299.

Atom type cannot be assigned to atom C19 in residue UNK 299.

Partial charge cannot be assigned to atom C19 in residue UNK 299.

Element type cannot be decided for atom C19 in residue UNK 299.

Atom type cannot be assigned to atom C20 in residue UNK 299.

Partial charge cannot be assigned to atom C20 in residue UNK 299.

Element type cannot be decided for atom C20 in residue UNK 299.

Atom type cannot be assigned to atom H27 in residue UNK 299.

Partial charge cannot be assigned to atom H27 in residue UNK 299.

Element type cannot be decided for atom H27 in residue UNK 299.

Atom type cannot be assigned to atom H28 in residue UNK 299.

Partial charge cannot be assigned to atom H28 in residue UNK 299.

Element type cannot be decided for atom H28 in residue UNK 299.

Atom type cannot be assigned to atom H29 in residue UNK 299.

Partial charge cannot be assigned to atom H29 in residue UNK 299.

Element type cannot be decided for atom H29 in residue UNK 299.

Atom type cannot be assigned to atom H25 in residue UNK 299.

Partial charge cannot be assigned to atom H25 in residue UNK 299.

Element type cannot be decided for atom H25 in residue UNK 299.

Atom type cannot be assigned to atom H26 in residue UNK 299.

Partial charge cannot be assigned to atom H26 in residue UNK 299.

Element type cannot be decided for atom H26 in residue UNK 299.

Atom type cannot be assigned to atom H24 in residue UNK 299.

Partial charge cannot be assigned to atom H24 in residue UNK 299.

Element type cannot be decided for atom H24 in residue UNK 299.

Atom type cannot be assigned to atom C21 in residue UNK 299.

Partial charge cannot be assigned to atom C21 in residue UNK 299.

Element type cannot be decided for atom C21 in residue UNK 299.

Atom type cannot be assigned to atom H30 in residue UNK 299.

Partial charge cannot be assigned to atom H30 in residue UNK 299.

Element type cannot be decided for atom H30 in residue UNK 299.

Atom type cannot be assigned to atom H31 in residue UNK 299.

Partial charge cannot be assigned to atom H31 in residue UNK 299.

Element type cannot be decided for atom H31 in residue UNK 299.

Atom type cannot be assigned to atom C22 in residue UNK 299.

Partial charge cannot be assigned to atom C22 in residue UNK 299.

Element type cannot be decided for atom C22 in residue UNK 299.

Atom type cannot be assigned to atom H32 in residue UNK 299.

Partial charge cannot be assigned to atom H32 in residue UNK 299.

Element type cannot be decided for atom H32 in residue UNK 299.

Atom type cannot be assigned to atom H33 in residue UNK 299.

Partial charge cannot be assigned to atom H33 in residue UNK 299.

Element type cannot be decided for atom H33 in residue UNK 299.

Atom type cannot be assigned to atom C23 in residue UNK 299.

Partial charge cannot be assigned to atom C23 in residue UNK 299.

Element type cannot be decided for atom C23 in residue UNK 299.

Atom type cannot be assigned to atom H34 in residue UNK 299.

Partial charge cannot be assigned to atom H34 in residue UNK 299.

Element type cannot be decided for atom H34 in residue UNK 299.

Atom type cannot be assigned to atom H35 in residue UNK 299.

Partial charge cannot be assigned to atom H35 in residue UNK 299.

Element type cannot be decided for atom H35 in residue UNK 299.

Atom type cannot be assigned to atom C24 in residue UNK 299.

Partial charge cannot be assigned to atom C24 in residue UNK 299.

Element type cannot be decided for atom C24 in residue UNK 299.

Atom type cannot be assigned to atom H36 in residue UNK 299.

Partial charge cannot be assigned to atom H36 in residue UNK 299.

Element type cannot be decided for atom H36 in residue UNK 299.

Atom type cannot be assigned to atom H37 in residue UNK 299.

Partial charge cannot be assigned to atom H37 in residue UNK 299.

Element type cannot be decided for atom H37 in residue UNK 299.

Atom type cannot be assigned to atom H38 in residue UNK 299.

Partial charge cannot be assigned to atom H38 in residue UNK 299.

Element type cannot be decided for atom H38 in residue UNK 299.

There are 1936 residues in the PDB file.

Write PDB file 1994_r.pdb.
Successfully wrote 1994_r.pdb file.

PDBCORE ends.