Data for 'Dynamical origins of heat capacity changes in enzyme catalysed reactions'

Dynamical origins of heat capacity changes in enzyme catalysed reactions<br>Marc W van der Kamp, Erica J. Prentice, Kirsty L. Kraakmann, Michael Connolly, Adrian J. Mulholland &amp; Vickery L. Arcus<br>School of Biochemistry, Biomedical Sciences Building, University Walk, University of Bristol, BS8 1TD, UK.Centre of Computational Chemistry, School of Chemistry, Cantock's Close, University of Bristol, BS8 1TS, UK.School of Science, University of Waikato, Hamilton, New Zealand.<br>The data files contained in this repository are as follows: <br>1a. Input coordinates (starting structures) in PDB format are named as enzyme_state.pdb. <br>1b. Input coordinates are named as enzyme_state.inpcrd and are in the standard Amber format (generated with Amber12). <br>2. Topology and parameter files are named as enzyme_state.prmtop and are also in standard Amber format (generated with Amber12).<br>3. Input files for the MD simulations are in the subdirectories KSI_md_input_files and MalL_md_input files. Input files are included for the equilibration, heating and production runs of molecular dynamics, which were performed in this order: a. minsolv.i b. mdsolv.i c. min.i d. heat.i e. npt_release1.i f. npt_release2.i g. npt_release3.i h. npt_release4.i i. eq_npt.i j. md10.i For KSI, a restraint was used in both RS and IS states, which is included in the file r7.RST. A restraint was also used in the MalL states (RS and TSA), which is included in the file d_com.rst. All input files are in the standard Amber format (see e.g. Amber16.pdf manual). <br>

酶催化反应中热容变化的动力学起源
Marc W van der Kamp, Erica J. Prentice, Kirsty L. Kraakmann, Michael Connolly, Adrian J. Mulholland & Vickery L. Arcus
英国布里斯托大学，大学步道生物医学科学大楼生物化学学院，邮编BS8 1TD；英国布里斯托大学化学学院康托克巷计算化学中心，邮编BS8 1TS；新西兰汉密尔顿怀卡托大学理学院
本仓库收录的数据文件如下：
1a. 格式为PDB（Protein Data Bank）的输入坐标（初始结构）文件命名为enzyme_state.pdb。
1b. 输入坐标文件命名为enzyme_state.inpcrd，采用标准Amber格式（使用Amber12生成）。
2. 拓扑与参数文件命名为enzyme_state.prmtop，同样采用标准Amber格式（使用Amber12生成）。
3. 分子动力学（MD, Molecular Dynamics）模拟的输入文件存于KSI_md_input_files和MalL_md_input_files子目录中。本仓库包含了分子动力学模拟的平衡、升温与生产运行阶段的输入文件，执行顺序如下：
a. minsolv.i
b. mdsolv.i
c. min.i
d. heat.i
e. npt_release1.i
f. npt_release2.i
g. npt_release3.i
h. npt_release4.i
i. eq_npt.i
j. md10.i
针对KSI，其RS与IS态均使用了约束文件，该约束文件存于r7.RST中。针对MalL的RS与TSA态，同样使用了约束文件，该约束文件存于d_com.rst中。所有输入文件均采用标准Amber格式（详见Amber16.pdf使用手册）。