Structural Basis Of Actin Monomer Re-Charging By Cyclase-Associated Protein
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1) table_of_simulations.pdf: table of simulations 2) toppar_HIC.str: methylhistidine (HIC) topologies and parameters -prepared based on analogy -to be used with top_all36_prot.rtf and par_all36_prot.prm 3) simulation_archive.tar.gz The Contents: 1_ADP-Actin--CARP, 2_ADP-Actin--CAP1, 3_ATP-Actin--WH2, 4_ADP-Actin<br> All systems presented in the paper; see table_of_simulations.pdf<br> Each directory contains<br> 000README gromacs_topologies gromacs_tpr_files index.ndx processed_trajectories prod.mdp systems_at_t=0 *** The rosetta models for WH2 domain and the proline-rich loop that connects it to the CARP domain can be found in 2_ADP-Actin--CAP1/rosetta_models <br> _Topologies:<br> toppar_c36_jul16:<br> The charmm force field version used to generate topologies before conversion to gromacs; see 000README in the systems directory<br> <br> ***toppar_c36_jul16/toppar_HIC.str: The topology and parameters for methylated histidine used in the simulations. gromacs_topologies:<br> Contains all itp files (converted from psf file using PyTopol's psf2top utility) and parameters.<br> Note that relevant files can also be found in directories corresponding to each system ( 1_ADP-Actin--CARP 2_ADP-Actin--CAP1 3_ATP-Actin--WH2 4_ADP-Actin)
1) table_of_simulations.pdf：模拟体系一览表 2) toppar_HIC.str：甲基组氨酸（methylhistidine，HIC）拓扑结构与力场参数 - 基于类比法构建 - 需与top_all36_prot.rtf及par_all36_prot.prm配合使用 3) simulation_archive.tar.gz：模拟数据归档包 归档内含以下子目录：1_腺苷二磷酸-肌动蛋白（ADP-Actin）--CARP、2_腺苷二磷酸-肌动蛋白（ADP-Actin）--CAP1、3_腺苷三磷酸-肌动蛋白（ATP-Actin）--WH2、4_腺苷二磷酸-肌动蛋白（ADP-Actin） 本归档涵盖论文中呈现的全部模拟体系；详细信息请参阅table_of_simulations.pdf。 每个子目录均包含以下文件/目录：000README、gromacs_topologies、gromacs_tpr_files、index.ndx、processed_trajectories、prod.mdp、systems_at_t=0 *** WH2结构域及其与CARP结构域相连的脯氨酸富集环的Rosetta模型，可于2_ADP-Actin--CAP1/rosetta_models目录中获取。 _Topologies：拓扑结构说明 toppar_c36_jul16：用于生成转换为GROMACS格式前的拓扑结构的CHARMM力场版本；详细信息请参阅各体系目录中的000README文件 ***toppar_c36_jul16/toppar_HIC.str：本文件为模拟过程中使用的甲基化组氨酸的拓扑结构与力场参数。 gromacs_topologies：包含所有通过PyTopol的psf2top工具从PSF文件转换而来的ITP文件及相关参数。请注意，相关文件亦可于各对应体系的子目录中找到：1_ADP-Actin--CARP、2_ADP-Actin--CAP1、3_ATP-Actin--WH2、4_ADP-Actin
