gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files. - gmx_MMPBSA/docs/getting-started.md at master · Valdes-Tresanco-MS/gmx_MMPBSA
3.在conda环境下执行以下命令 下面要用到的env.yml文件下载地址: valdes-tresanco-ms.github.ioconda env create --file env.yml conda activate gmxMMPBSA python -m pip install gmx_MMPBSA 验证是否安装成功:gmx_MMPBSA --help 返回结果如下则表明安装成功: 4.运行 准备MMGBSA计算的参数文件mmgbsa.in: ...
.github Update gh-pages.yml Nov 11, 2022 GMXMMPBSA added support for additional histidine variants in residue selection Mar 11, 2025 docs update news.json and changelog.md Mar 12, 2025 examples add docs for user defined amber masks#454 ...
.github GMXMMPBSA docs Q&A assets examples overrides MMPBSA_py_citation.bib MMPBSA_py_citation.ris MMPBSA_py_citation.xml advanced.md analyzer.md api.md changelog.md cite_us.md compatibility.md env.yml getting-started.md gmx_MMPBSA_ana_command-line.md gmx_MMPBSA_ana_running.md gmx_MMPBSA...
Bug summary I am getting a similar error to #95 (comment) Terminal output [INFO ] Building AMBER topologies from GROMACS files... Done. [INFO ] Loading and checking parameter files for compatibility... [INFO ] Preparing trajectories for ...
Bug summary Running the following command for using "Prot-Lig-CHARMM" system mmpbsa.in file gmx_MMPBSA -O -i mmpbsa.in -cs MD.tpr -ci index.ndx -cg 1 13 -ct md_fit.xtc -cp topol.top but didn't successfully run. ###...
Bug summary Here is my test system: MMPBSA_test.zip My PDB file contains two chains (Chain A and Chain B). I'm attempting to compute the PB energy and energy decomposition between Chain A and Chain B. I utilized 'gmx make_ndx' to generat...
Bug summary Error occurs when converting topology files. Amber forcefields are used from charmm-gui webserver. The error is about the pairs func, and I assume in particular from the glycopyranoses, as these have pairs func 2 in topology ...
gmx_MMPBSA provides all the MMPBSA.py functionalities to GROMACS users. In addition, other functionalities have been implemented that ease a number of calculations (e.g. MM/PB(GB)SA with user-defined internal dielectric constant, interaction entropy and C2 entropy calculations). A GUI application...
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