>>> ps -ef | grep filename    查看关于filename文件的所有进程状态

>>> find dirpath -name filename   在dirpath目录(绝对路径)下查找关于filename的所有文件

>>> fg %jobsnumber     将后台命令调用到前台运行

>>>  Ctrl + z 挂起当前运行任务  -jobs filename number 查找运行文件filename的PID号  bg %(jobsnumber)将挂起的文件放在后台运行

>>> Ctrl + c 结束当前运行的任务

>>> cat score.sc | sort -nk2 > score_sorted.txt   对得分文件score.sc的第二列按照数值(n)的大小进行排序，并将排序好的信息存储在score_sorted.txt文件中。

>>> 对模板PDB文件进行处理： python rosetta_tools/protein_tools/scripts/clean_pdb.py 2anv.pdb A 

>>>  基于 rosettaCM_1_3.py脚本  同源建模

>>> 基于relax_1_1.py 脚本  模型优化

 

params文件的制备(对于对接小分子的.sdf mol 和mol2)

python rosetta_source/src/python/apps/public/molfile_to_params.py -n MR3 MR3.mol 得到两个文件 MR3.params and MR3_0001.pdb

dock.xml 文件的设置

<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="false" 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="false" 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>
    <FILTERS>
        <AtomicDistance name="S-HEM" residue1="435A" atomtype1="S" residue2="1F" atomtype2="Fe3p" distance="2.60"  confidence="0.9"/>
    </FILTERS>
    <SCORINGGRIDS ligand_chain="F" width="15">
        <classic grid_type="ClassicGrid" weight="1.0"/>
    </SCORINGGRIDS>
    <MOVERS>
    single movers_X        
        <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="false" allow_overlap="false">
            <Translate chain="X" distribution="uniform" angstroms="3.0" cycles="50"/>
            <Translate chain="F" distribution="uniform" angstroms="3.0" cycles="50"/>
        </CompoundTranslate>
        <Rotate name="rotate_X" chain="X" distribution="uniform" degrees="360" cycles="700"/>
        <Rotate name="rotate_F" chain="F" distribution="uniform" degrees="360" cycles="700"/>
        
        <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
        <ParsedProtocol name="low_res_dock">
            <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"/>
        </ParsedProtocol>
        <ParsedProtocol name="high_res_dock">
            <Add mover_name="high_res_docker"/>
            <Add mover_name="final"/>
        </ParsedProtocol>
    </MOVERS>
    <PROTOCOLS>
        <Add mover_name="low_res_dock"/>
        <Add mover_name="high_res_dock"/>
        <Add filter="S-HEM" />    
        <Add mover_name="add_scores"/>        
    </PROTOCOLS>
</ROSETTASCRIPTS>

 

dock.options设置

-in:file:s inputs_AGI/EbF6H_HEM_AGI.pdb
-in:file:extra_res_fa inputs_AGI/HEM.params inputs_AGI/AGI.params

-packing
    -ex1
    -ex2aro
    -ex2 
    -no_optH false
    -flip_HNQ true
    -ignore_ligand_chi true
    
-parser
    -protocol inputs_AGI/ligand_dock.xml

-out
    -path:all outputs_AGI1
    -nstruct 10000
    -overwrite

 

>>> 分子对接  ./rosetta/main/source/bin/rosetta_scripts.linuxgccrelease @dock.options -database /rosetta/main/database -nstruct 1000   构建1000个对接模型 由total_score和其他参数选取最优的对接模型  

 

——————————————————Small-molecule ligand docking into comparative models with Rosett    一篇关于rosettaCM流程详细操作的文章