orca

install

    1  ls
    2  cd /root/
    3  ls
    4  apt update
    5  tar -xf openmpi-4.1.6.tar.bz2
    6  apt install bzip2 -y
    7  tar -xf openmpi-4.1.6.tar.bz2
    8  mkdir -p /sob/openmpi416
    9  ./configure --prefix=/sob/openmpi416 --disable-builtin-atomics
   10  cd openmpi-4.1.6
   11  ./configure --prefix=/sob/openmpi416 --disable-builtin-atomics
   12  sudo apt install linux-headers-$(uname -r) build-essential
   13  apt install linux-headers-$(uname -r) build-essential
   14  apt update
   15  sudo add-apt-repository ppa:ubuntu-toolchain-r/test
   16  add-apt-repository ppa:ubuntu-toolchain-r/test
   17  apt install build-essential -y
   18  add-apt-repository ppa:ubuntu-toolchain-r/test
   19  sudo apt-get update
   20  sudo apt-get install gcc-12 g++-12 -y
   21  apt-get install gcc-12 g++-12 -y
   22  update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-12 12
   23  update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-12 12
   24  update-alternatives --config gcc
   25  gcc --version
   26  g++ --version
   27  ./configure --prefix=/sob/openmpi416 --disable-builtin-atomics
   28  make all install -j
   29  make clean
   30  make
   31  make install
   32  vim ~/.bashrc
   33  vi ~/.bashrc
   34  nano  ~/.bashrc
   35  apt install -y vim
   36  vim ~/.bashrc
   37  source ~/.bashrc
   38  mpiexec -V
   39  cd ~
   40  ls
   41  tar -xf orca_6_0_0_linux_x86-64_avx2_shared_openmpi416.tar
   42  tar -xf orca_6_0_0_linux_x86-64_avx2_shared_openmpi416.tar.xz
   43  ls
   44  cd orca_6_0_0_shared_openmpi416_avx2/
   45  ls
   46  cd ..
   47  ls
   48  cd orca_6_0_0_shared_openmpi416_avx2/
   49  pwd
   50  vim ~/.bashrc
   51  source ~/.bashrc
   52  /sob/orca600/orca test.inp > test.out
   53  /root/orca_6_0_0_shared_openmpi416_avx2/orca test.inp > /root/test.out
   54  ls
   55  rm -rf test.out
   56  cd ..
   57  ls
   58  vim test.inp
   59  /root/orca_6_0_0_shared_openmpi416_avx2/orca test.out > test.out
   60  /root/orca_6_0_0_shared_openmpi416_avx2/orca test.inp > test.out
   61  vim ~/.bashrc
   62  source ~/.bashrc
   63  /root/orca_6_0_0_shared_openmpi416_avx2/orca test.inp > test.out
   64  apt-get update
   65  apt-get install -y openssh-client
   66  /root/orca_6_0_0_shared_openmpi416_avx2/orca test.inp > test.out
   67  cat test.out
   68  history > history.txt

grid

https://www.moldiscovery.com/software/grid/

需要edu邮箱申请，等待批准

All GAMESS requestors MUST agree to the following license agreement which covers all versions of GAMESS (source code, and binaries for Windows, Macintosh and ChemOffice). With regard to the ab initio quantum chemistry code GAMESS, together with its associated graphics and utility programs, with which you have supplied me a copy, I agree to the following conditions: I will not supply a copy of the code to anyone outside my institution or corporation for any reason whatsoever. Instead, I will refer any requests for copies of the program to you at ISUQCG. This in no way limits my making of copies of the code for backup purposes, or for running on more than one computer system at my institution or home. I understand that copyright or ownership rights to GAMESS are retained by ISUQCG and contributors to the GAMESS package. I will not incorporate any part of GAMESS into any other program system, either for sale or for non-profit distribution, without written permission from ISUQCG, I understand that no large program such as GAMESS can be considered to be bug free, and accordingly the ISUQCG supplies the GAMESS software on an "as is" basis, with no additional responsibility or liability, If results obtained with GAMESS are published in the scientific literature, I will reference the program from the article: G. MJ. Barca, C. Bertoni, L. Carrington, D. Datta, N. De Silva, J. E. Deustua, D. G. Fedorov, J. R. Gour, A. O. Gunina, E. Guidez, T. Harville, S. Irle, J. Ivanic, K. Kowalski, S. S. Leang, H. Li, W. L., J. J. Lutz, I. Magoulas, J. Mato, V. Mironov, H. Nakata, B. Q. Pham, P. Piecuch, D. Poole, S. R. Pruitt, A. P. Rendell, L. B. Roskop, K. Ruedenberg, T. Sattasathuchana, M. W. Schmidt, J. Shen, L. Slipchenko, M. Sosonkina, V. Sundriyal, A. Tiwari, J. L. Galvez Vallejo, B. Westheimer, M. Wloch, P. Xu, F. Zahariev, M. S. Gordon J. Chem. Phys. 152 154102 (2020). Using specific methods included in GAMESS may require citing additional articles, as described in the manual. I agree to honor the request to cite additional papers, as appropriate. See HERE For proper citation etiquette. This license is considered a "Research Group" license. Thus anyone directly associated with your research group is covered by the license and may share your copy of GAMESS on all of your group's computer resources.

Firefly

Multiwfn可以计算的分子描述符一览

3D-QSAR 选择记录

对于 3D-QSAR（三维定量构效关系）分析，选择工具时需要考虑易用性、教程资源、功能完整性和学习曲线等因素。以下是几款常见工具的比较和推荐：

GRID 易用性：GRID 是一款非常成熟且广泛使用的工具，专门用于生成 CoMSIA 和 CoMFA 所需的分子相互作用场（MIF）。它在结构基础药物设计中应用广泛。教程资源：GRID 提供了官方文档、教程和一些示例案例，用户可以从中学习如何生成 MIF 并进行后续分析。官方提供了丰富的技术支持和参考资料，适合初学者。优点：专注于 3D-QSAR，生成 CoMSIA 所需的分子场。支持多种化学探针类型，适应不同的设计需求。提供可视化工具和 3D模型绘制功能，帮助用户更好地理解分子相互作用。缺点：是商业软件，可能需要购买许可证。
SYBYL（特别是 SYBYL-X）易用性：SYBYL 是用于分子建模和药物设计的经典软件，提供了 CoMFA 和 CoMSIA 的强大支持。它的用户界面相对友好，适合药物化学和生物学研究人员使用。教程资源：SYBYL 提供了大量的教程、培训材料和示例案例，用户可以轻松上手并逐步深入。优点：支持 CoMFA 和 CoMSIA，可用于药物设计和 3D-QSAR。具备强大的可视化功能，用户可以直观地查看计算结果。提供深度学习支持和机器学习接口，帮助进行更先进的模型构建。缺点：同样是商业软件，需要购买许可证。
Open3DQSAR 易用性：Open3DQSAR 是一款开源的 3D-QSAR 工具，专为生成 CoMFA 和 CoMSIA 场设计。其命令行界面可能相对不如图形界面工具直观，但对于有经验的用户来说非常高效。教程资源：作为开源工具，Open3DQSAR 的文档相对简洁，但社区支持和教程较为有限。用户可以在网上找到一些教程，但整体支持不如商业软件丰富。优点：开源免费。支持 CoMFA 和 CoMSIA 场计算。适用于定量构效分析，并且可以与其他工具结合使用。缺点：相比商业软件，易用性较低，需要一定的命令行操作经验。文档和社区支持相对较少。
MOE（Molecular Operating Environment）易用性：MOE 提供了丰富的图形用户界面（GUI），使得 3D-QSAR 分析更加直观和易于操作。用户可以轻松地进行分子对接、构效关系建模和药物设计。教程资源：MOE 提供了丰富的在线文档和教程，帮助用户快速上手并深入学习。优点：拥有强大的图形用户界面，适合初学者和非计算化学专业的人士使用。提供多种分子模拟功能，包括 3D-QSAR、对接、药物设计等。广泛用于学术界和制药行业。缺点：商业软件，许可证费用较高。推荐选择：初学者：如果您是 3D-QSAR 的初学者，MOE 和 SYBYL 是非常合适的选择，因为它们提供了图形界面和全面的教程支持，容易上手，且功能强大。MOE 的图形界面更适合快速学习和操作，而 SYBYL 提供了更强大的专业功能。开源爱好者：如果您偏好开源工具，可以选择 Open3DQSAR。尽管其易用性较差，但它支持 CoMSIA 和 CoMFA 的计算，且不需要许可证费用。预算有限的用户：如果您预算有限，且具备一定的命令行操作经验，可以选择 Open3DQSAR 或 GRID（如果能够购买许可证）。如果您不希望投入太多金钱，开源工具可能是最好的选择。总结：

易用性：MOE > SYBYL > GRID > Open3DQSAR 教程和文档：SYBYL > MOE > GRID > Open3DQSAR 开源性：Open3DQSAR > GRID > SYBYL = MOE

README.md Unescape Escape