ROSETTA使⽤技巧随笔--RottaLigandDocking
时间不充分，简单记录下⾃⼰实践过程中的做法:
1. ⾸先，⾮标准残基都需要转换成.params⽂件，使⽤ <path-to-Rotta>/main/source/scripts/python/public/molfile_to_params.py -n l2 --chain=F --clobber --keep-names 转换，此命令会产⽣TPP_0001.pdb和TPP.params两个⽂件；
3. 如果经过上⼀步产⽣了ligand_conformers.sdf，就需要为 <path-to-Rotta>/main/source/scripts/python/public/molfile_to_params.py -n GAD -p GAD --chain=X --center=-31,-35.5,8 --clobber --keep-names --conformers-in-one-file GAD_confs.sdf 命令多加⼀个参数 --conformers-in-one-file GAD_confs.sdf ，这个参数会在产⽣的.params⽂件末尾加⼀句 PDB_ROTAMERS GAD_conformers.pdb 来表明你的多重构象的⽂件，此命令会产⽣GAD.pdb，GAD.params和GAD_conformers.pdb三个⽂件，其中GAD.pdb是以conformers中第⼀个构象为结构；
4. 多底物对接的问题，经过查阅⼿册和论坛，得出的结论是通过控制需要dock的链("X/Y/F/。。。")来指定需要对接的⼩分⼦，⽐如我要对接TPP和GAD，就需要在single movers后⾯及前⾯LIGAND_AREAS和INTERFACE_BUILDERS那⾥指定分别对“F”和“X”链进⾏dock，并在MOVERS处指定两底物分⼦分别对应的操作，options不必特意根据双底物改变，下⾯给出了我做的两个XML⽂件的⽰例；秋天不会来
5. StartFrom,Transform,Translate和Rotate的差别和⽐较。StartFrom是在底物不在蛋⽩⼝袋内部，需要程序先将底物以Coordinates为基准放到⼝袋中的程序；Transform是使⽤蒙特卡洛的⽅法，对对接过程的底物和蛋⽩⼩分⼦随机取样的过程；Translate和Rotate则是对处于⼝袋中的⼩分⼦进⾏平移旋转的操作。底物在蛋⽩⼝袋中时，就可以不使⽤StartFrom；使⽤Transform时，则需要指定GRID。
6. 执⾏过程中报 cannot find chain_id X 错误，这个错误很奇怪，有时候出现，有时候不出现，解决⽅法为在pdb⽂件开头指定号HETATM 的chain id，如下所⽰：
HEADER xx-MMM-xx
HETNAM HEM F 498 HEM
HETNAM KAE X 499 KAE
ATOM 1 N PRO A 134.936 -10.914 -32.4801.000.00 N
ATOM 2 CA PRO A 135.217 -12.093 -33.3491.000.00 C
ATOM 3 C PRO A 136.671 -12.422 -33.4261.000.00 C
欧美人体艺术照......
......
7. 下⾯的high_resolution_dock XML⽂件，⽤途是在你已经知道你的底物的位置的情况下，对底物及周边残基进⾏⾼分辨率的对接，与其说对接，可能说packing和minimizing更恰当，因为它是对周围的残基优化的同时变换底物的构象，以求找到最优结果。
分享⼀下⾃⼰的两个xml⽂件及对应的flags：
low_resolution_dock+high_resolution_dock
This protocol will simply do low-resolution followed by high-resolution docking.
It will also report the binding energy (ddg) and buried-surface area (sasa) in the score file.
<ROSETTASCRIPTS>
<SCOREFXNS>
<ligand_soft_rep weights="ligand_soft_rep">
</ligand_soft_rep>
<hard_rep weights="ligand">
</hard_rep>
</SCOREFXNS>
<LIGAND_AREAS>
<docking_sidechain_X chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>
<final_sidechain_X chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>
<final_backbone_X chain="X" cutoff="7.0" add_nbr_radius="fal" all_atom_mode="true" Calpha_restraints="0.3"/>
</LIGAND_AREAS>
<INTERFACE_BUILDERS>
<side_chain_for_docking ligand_areas="docking_sidechain_X"/>
<side_chain_for_final ligand_areas="final_sidechain_X"/>
<backbone ligand_areas="final_backbone_X" extension_window="3"/>
</INTERFACE_BUILDERS>
<MOVEMAP_BUILDERS>
<docking sc_interface="side_chain_for_docking" minimize_water="true"/>
<final sc_interface="side_chain_for_final" bb_interface="backbone" minimize_water="true"/>
</MOVEMAP_BUILDERS>
<MOVERS>
single movers
<StartFrom name="start_from_X" chain="X">
<Coordinates x="-31" y="-35.5" z="8"/>
</StartFrom>
<CompoundTranslate name="compound_translate" randomize_order="fal" allow_overlap="fal">
<Translate chain="X" distribution="uniform" angstroms="2.0" cycles="50"/>
</CompoundTranslate>
<Rotate name="rotate_X" chain="X" distribution="uniform" degrees="360" cycles="500"/>
<SlideTogether name="slide_together" chains="X"/>
<HighResDocker name="high_res_docker" cycles="6" repack_every_Nth="3" scorefxn="ligand_soft_rep" movemap_builder="docking"/>
<FinalMinimizer name="final" scorefxn="hard_rep" movemap_builder="final"/>
<InterfaceScoreCalculator name="add_scores" chains="X" scorefxn="hard_rep"/>
compound movers
<PardProtocol name="low_res_dock">
<Add mover_name="start_from_X"/>
<Add mover_name="compound_translate"/>
<Add mover_name="rotate_X"/>
<Add mover_name="slide_together"/>
</PardProtocol>
<PardProtocol name="high_res_dock">
<Add mover_name="high_res_docker"/>
<Add mover_name="final"/>
</PardProtocol>
</MOVERS>
<PROTOCOLS>
<Add mover_name="low_res_dock"/>
<Add mover_name="high_res_dock"/>
<Add mover_name="add_scores"/>
</PROTOCOLS>
</ROSETTASCRIPTS>
对应的flag options⽂件：
-in:file:s inputs_GAD/GALS_TPP_GAD.pdb
-in:file:extra_res_fa inputs_GAD/TPP.params inputs_GAD/GAD.params
-packing
一岁宝宝玩具
-ex1
-ex2aro
-
ex2
-no_optH fal
-flip_HNQ true
-ignore_ligand_chi true
-parr
-protocol inputs_GAD/l
-out
-path:all outputs_GAD
-nstruct 1000
-overwrite
high_resolution_dock_only
This protocol will simply do high-resolution docking.
It will also report the binding energy (ddg) and buried-surface area (sasa) in the score file.
<ROSETTASCRIPTS>
<SCOREFXNS>
<ligand_soft_rep weights="ligand_soft_rep">
</ligand_soft_rep>
<hard_rep weights="ligand">
</hard_rep>
</SCOREFXNS>
<LIGAND_AREAS>
<docking_sidechain_X chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>
<final_sidechain_X chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>
<final_backbone_X chain="X" cutoff="7.0" add_nbr_radius="fal" all_atom_mode="true" Calpha_restraints="0.3"/>
</LIGAND_AREAS>
<INTERFACE_BUILDERS>
<side_chain_for_docking ligand_areas="docking_sidechain_X"/>
<side_chain_for_final ligand_areas="final_sidechain_X"/>
<backbone ligand_areas="final_backbone_X" extension_window="3"/>
</INTERFACE_BUILDERS>
<MOVEMAP_BUILDERS>
<docking sc_interface="side_chain_for_docking" minimize_water="true"/>
<final sc_interface="side_chain_for_final" bb_interface="backbone" minimize_water="true"/>
</MOVEMAP_BUILDERS>
<SCORINGGRIDS ligand_chain="X" width="15">
<classic grid_type="ClassicGrid" weight="1.0"/>
</SCORINGGRIDS>
<MOVERS>
<Transform name="transform" chain="X"box_size="7.0" move_distance="0.2" angle="20" cycles="500" repeats="1" temperature="5"/> <HighResDocker name="high_res_docker" cycles="6" repack_every_Nth="3" scorefxn="ligand_soft_rep" movemap_builder="docking"/> <FinalMinimizer name="final" scorefxn="hard_rep" movemap_builder="final"/>
<InterfaceScoreCalculator name="add_scores" chains="X" scorefxn="hard_rep"/>
</MOVERS>
<PROTOCOLS>
<Add mover_name="transform"/>
<Add mover_name="high_res_docker"/>
<Add mover_name="final"/>
<Add mover_name="add_scores"/>
</PROTOCOLS>
</ROSETTASCRIPTS>
对应的flag_options⽂件：
-in:file:s inputs_IMA/GALS_IMA.pdb
-in:file:extra_res_fa inputs_IMA/IMA.params
-packing
-ex1
-
ex2aro
-ex2
-no_optH fal
-flip_HNQ true
-ignore_ligand_chi true
-parr
-protocol inputs_IMA/l
-out
-path:all outputs_IMA
小鸡孵化技术
-nstruct 1000
-overwrite
多底物对接（两个⼩分⼦的链分别对应“X”和“F”）
1. ⼿动指定两个⼩分⼦（“X”，“F”）的位置（使⽤StartFrom mover指定，对应的Coordinates）
This protocol will simply do low-resolution followed by high-resolution docking.
It will also report the binding energy (ddg) and buried-surface area (sasa) in the score file.
<ROSETTASCRIPTS>
<SCOREFXNS>
<ligand_soft_rep weights="ligand_soft_rep">
</ligand_soft_rep>
<hard_rep weights="ligand">
</hard_rep>
</SCOREFXNS>
查询营业执照
<LIGAND_AREAS>
<docking_sidechain_X chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>
<final_sidechain_X chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>
<final_backbone_X chain="X" cutoff="7.0" add_nbr_radius="fal" all_atom_mode="true" Calpha_restraints="0.3"/>
<docking_sidechain_F chain="F" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>
<final_sidechain_F chain="F" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>
<final_backbone_F chain="F" cutoff="7.0" add_nbr_radius="fal" all_atom_mode="true" Calpha_restraints="0.3"/>
</LIGAND_AREAS>
<INTERFACE_BUILDERS>
<side_chain_for_docking ligand_areas="docking_sidechain_X,docking_sidechain_F"/>
<side_chain_for_final ligand_areas="final_sidechain_X,final_sidechain_F"/>
<backbone ligand_areas="final_backbone_X,final_backbone_F" extension_window="3"/>
</INTERFACE_BUILDERS>
<MOVEMAP_BUILDERS>
<docking sc_interface="side_chain_for_docking" minimize_water="true"/>
<final sc_interface="side_chain_for_final" bb_interface="backbone" minimize_water="true"/>
</MOVEMAP_BUILDERS>
<MOVERS>
single movers_X
<StartFrom name="start_from_X" chain="X">
<Coordinates x="-31" y="-35.5" z="8"/>
</StartFrom>
<StartFrom name="start_from_F" chain="F">
<Coordinates x="-27.26" y="-34.56" z="4.87"/>
</StartFrom>
<CompoundTranslate name="compound_translate" randomize_order="fal" allow_overlap="fal">
<Translate chain="X" distribution="uniform" angstroms="2.0" cycles="50"/>
<Translate chain="F" distribution="uniform" angstroms="2.0" cycles="50"/>
</CompoundTranslate>
<Rotate name="rotate_X" chain="X" distribution="uniform" degrees="360" cycles="500"/>
<Rotate name="rotate_F" chain="F" distribution="uniform" degrees="360" cycles="500"/>
<SlideTogether name="slide_together" chains="X,F"/>
<HighResDocker name="high_res_docker" cycles="6" repack_every_Nth="3" scorefxn="ligand_soft_rep" movemap_builder="docking"/> <FinalMinimizer name="final" scorefxn="hard_rep" movemap_builder="final"/>
<InterfaceScoreCalculator name="add_scores" chains="X,F" scorefxn="hard_rep"/>
compound movers
<PardProtocol name="low_res_dock">
<Add mover_name="start_from_X"/>
<Add mover_name="start_from_F"/>
<Add mover_name="compound_translate"/>
<Add mover_name="rotate_X"/>
<Add mover_name="rotate_F"/>
<Add mover_name="slide_together"/>
</PardProtocol>
<PardProtocol name="high_res_dock">
<Add mover_name="high_res_docker"/>
<Add mover_name="final"/>
</PardProtocol>
</MOVERS>
<PROTOCOLS>
<Add mover_name="low_res_dock"/>
<Add mover_name="high_res_dock"/>
<Add mover_name="add_scores"/>
</PROTOCOLS>
</ROSETTASCRIPTS>
2. 其中⼀个⼩分⼦（“F”）位置已知，另⼀个⼩分⼦（“X”）的位置需要指定（⾸先需使⽤SCORINGGRIDS为已知位置的⼩分⼦指定盒⼦，然后使⽤Transform 指定其动作模式）
This protocol will simply do low-resolution followed by high-resolution docking.
It will also report the binding energy (ddg) and buried-surface area (sasa) in the score file.
<ROSETTASCRIPTS>
<SCOREFXNS>
<ligand_soft_rep weights="ligand_soft_rep">
</ligand_soft_rep>
<hard_rep weights="ligand">
</hard_rep>
</SCOREFXNS>
<LIGAND_AREAS>
<docking_sidechain_X chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>
<final_sidechain_X chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>
<final_backbone_X chain="X" cutoff="7.0" add_nbr_radius="fal" all_atom_mode="true" Calpha_restraints="0.3"/>
<docking_sidechain_F chain="F" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>
<final_sidechain_F chain="F" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>
<final_backbone_F chain="F" cutoff="7.0" add_nbr_radius="fal" all_atom_mode="true" Calpha_restraints="0.3"/>
</LIGAND_AREAS>
<INTERFACE_BUILDERS>
<side_chain_for_docking ligand_areas="docking_sidechain_X,docking_sidechain_F"/>
<side_chain_for_final ligand_areas="final_sidechain_X,final_sidechain_F"/>
<backbone ligand_areas="final_backbone_X,final_backbone_F" extension_window="3"/>
</INTERFACE_BUILDERS>
<MOVEMAP_BUILDERS>
<docking sc_interface="side_chain_for_docking" minimize_water="true"/>
<final sc_interface="side_chain_for_final" bb_interface="backbone" minimize_water="true"/>
</MOVEMAP_BUILDERS>
<SCORINGGRIDS ligand_chain="F" width="15">
<classic grid_type="ClassicGrid" weight="1.0"/>
哈尔滨特色小吃
</SCORINGGRIDS>
<MOVERS>
single movers_X
<StartFrom name="start_from_X" chain="X">
<Coordinates x="-31" y="-35.5" z="8"/>
</StartFrom>
<Transform name="transform_F" chain="F" box_size="7.0" move_distance="0.2" angle="20" cycles="500" repeats="1" temperature="5"/>
<CompoundTranslate name="compound_translate" randomize_order="fal" allow_overlap="fal">
<Translate chain="X" distribution="uniform" angstroms="2.0" cycles="50"/>
<Translate chain="F" distribution="uniform" angstroms="2.0" cycles="50"/>
</CompoundTranslate>
<Rotate name="rotate_X" chain="X" distribution="uniform" degrees="360" cycles="500"/>
黄芩种子<Rotate name="rotate_F" chain="F" distribution="uniform" degrees="360" cycles="500"/>
茶枯
<SlideTogether name="slide_together" chains="X,F"/>
<HighResDocker name="high_res_docker" cycles="6" repack_every_Nth="3" scorefxn="ligand_soft_rep" movemap_builder="docking"/>
<FinalMinimizer name="final" scorefxn="hard_rep" movemap_builder="final"/>
<InterfaceScoreCalculator name="add_scores" chains="X,F" scorefxn="hard_rep"/>
compound movers
<PardProtocol name="low_res_dock">
<Add mover_name="start_from_X"/>
<Add mover_name="transform_F"/>
<Add mover_name="compound_translate"/>
<Add mover_name="rotate_X"/>
<Add mover_name="rotate_F"/>
<Add mover_name="slide_together"/>
</PardProtocol>
<PardProtocol name="high_res_dock">
<Add mover_name="high_res_docker"/>
<Add mover_name="final"/>
</PardProtocol>
</MOVERS>
<PROTOCOLS>
<Add mover_name="low_res_dock"/>
<Add mover_name="high_res_dock"/>
<Add mover_name="add_scores"/>
</PROTOCOLS>
</ROSETTASCRIPTS>
