AUTODOCK大分子去除里面的小分子

pdh1015

求助：我从PDB数据库下载的酶晶1CVZ.pdb文件，用ChemBio3D去除ligand后保存为11CVZ.pdb，备用
   
   一下操作在ADT中进行
1、Read Molecule 11CVZ.pdb，去水、加氢，保存
2、Flexible Residules,选11CVZ.pdb，

点Yes，出现的对话框继续点Yes合并没有极性的氢
3、柔性残基选择点Add时报错



IDLE 1.2.2      ==== No Subprocess ====
>>> The following nonpolar hydrogens had more than one bond
22PAD:A:SER70:HN2-2 bonds
ERROR *********************************************
Traceback (most recent call last):
  File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto
    result = command( *args, **kw )
  File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\Pmv\selectionCommands.py", line 924, in doit
    escapeCharacters)
  File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\MolKit\stringSelector.py", line 82, in select
    msg = msg + str(m)
UnicodeEncodeError: 'ascii' codec can't encode character u'\uff0c' in position 5: ordinal not in range(128)
no secondary structure set for chain:   !
no secondary structure set for chain:   !
Sorry, there are no Gasteiger parameters available for atom 11CVZ: :ASN212:OXT
ERROR *********************************************
Traceback (most recent call last):
  File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto
    result = command( *args, **kw )
  File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\Pmv\selectionCommands.py", line 924, in doit
    escapeCharacters)
  File "C:\Program Files\MGLTools-1.5.6\lib\site-packages\MolKit\stringSelector.py", line 82, in select
    msg = msg + str(m)
UnicodeEncodeError: 'ascii' codec can't encode character u'\uff0c' in position 5: ordinal not in range(128)


   求高人解释

1、怎么经常报丢失命令？Traceback (most recent call last):
2、为什么删除大分子里原来的配体后就no secondary structure set for chain:   !
3、怎么最后一个氨基酸残基分配不了电荷？Sorry, there are no Gasteiger parameters available for atom 11CVZ: :ASN212:OXT

川大-灰太狼

不要使用 Chem3D去删除，然后再保存。你手动在记事本里面，或者yasara view （论坛里面有下载的）或者pymol，打开后删除，然后保存pdb。

pdh1015

谢谢，用该方法直接在记事本里删除已解决问题