PACKMOL 二：手把手教你用packmol构建含有 1 400 个 PS 单体的纳米球

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已于 2024-09-21 11:18:14 修改

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分类专栏：生物信息学 linux 编译文章标签： linux 运维 packmol

于 2024-09-20 19:37:17 首次发布

本文链接：https://blog.csdn.net/m0_54634272/article/details/142391771

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文章目录

1. 1400个 Polystyrene nanoparticles（PS）单体的纳米球的来源
2. 准备PS单体结构文件
3. 配置PACKMOL输入文件
4.运行PACKMOL
5. 检查和优化结构
6.展出讲讲怎么使用ATB
7. 展开讲讲怎么安装和使用moltemplate
8.展出讲讲怎么使用Sobtop生成拓扑文件
9. 展开讲讲怎么安装和使用sobtop
10. 展开讲讲怎么用Charmm-GUI 生成 GROMACS 拓扑文件
可能遇到的错误
- 1.错误一
- 2. 错误二

1. 1400个 Polystyrene nanoparticles（PS）单体的纳米球的来源

通过复现《Polystyrene nanoparticles trigger aberrant condensation of TDP-43 and amyotrophic lateral sclerosis-like symptoms》文章中的1400个 PS 单体的纳米球来学习。
在这里插入图片描述

2. 准备PS单体结构文件

在纳米球构建之前，你需要PS（聚苯乙烯）单体的结构文件。可以使用以下两种方式获取：
• 在线数据库：通过在线化学数据库（如PubChem或ChemSpider）下载PS单体的PDB或XYZ格式文件。
• 手动构建：如果没有现成的PS单体结构，可以使用分子建模软件（如Avogadro、ChemDraw或GaussView）创建PS单体的3D结构，并保存为PDB、XYZ或MOL2格式。

这里我在PubChem和ChemSpider上没有找到Polystyrene nanoparticles，但是我在pubchem上找到了结构相似的分子2-Phenyl-2-propanol，因此我决定对其进行改造


论文中的结构式	2-Phenyl-2-propanol

改造后的样子符合论文中的结构式（使用的pymol）
在这里插入图片描述

3. 配置PACKMOL输入文件

PACKMOL通过一个输入文件定义分子布局。接下来，创建一个文本文件（如ps_nanoball.inp）来配置PACKMOL的参数。
• PS纳米球的构建思路：我们希望将1400个PS单体分布在一个直径为20纳米的球体内。
• 输入文件示例：

tolerance 2.0
filetype pdb  # 指定输入/输出文件格式
output ps_nanoball.pdb  # 输出文件名

# 定义纳米球的体积
structure ps_monomer.pdb  # PS单体的PDB文件路径
  number 1400  # PS单体的数量
  inside sphere 0.0 0.0 0.0 10.0  # 在中心(0,0,0)构建直径为20 nm的球（半径10 nm）
end structure

4.运行PACKMOL

packmol < ps_nanoball.inp

运行中的样例，3090运行很久，大概需要3个小时吧
在这里插入图片描述
运行成功的样例
热乎的，还在跑。。。。。。

5. 检查和优化结构

• 结构检查：使用分子可视化软件（如VMD、PyMOL或Avogadro）打开生成的PDB文件，查看纳米球的形状和结构是否符合预期。
在这里插入图片描述

• 优化结构：由于PACKMOL生成的结构只是初始的分子排布，你可能需要进一步优化结构。可以使用分子动力学模拟软件（如Gromacs、LAMMPS或NAMD）进行能量最小化和分子动力学模拟，以优化纳米球的几何形状和分子排列。
• 我使用的是Gromacs，使用Gromacs进行能量最小化示例：


gmx grompp -f em.mdp -c ps_nanoball.pdb -p topol.top -o em.tpr
gmx mdrun -v -deffnm em

这里需要你有你自己的 em.mdp文件（能量最小化的参数文件）和topol.top 文件（在此文件中包含你使用的分子的适当信息和参数），因为这是纳米材料，普通力场里并没收录，应该使用一些外部工具来生成这些小分子的拓扑文件，例如：
• PRODRG：生成 GROMOS 力场的小分子拓扑文件。
• ATB (Automated Topology Builder)：生成 AMBER、CHARMM 等力场的小分子拓扑文件。
• GAFF (General AMBER Force Field)：如果你使用 AMBER 力场，GAFF 可用于生成小分子拓扑。
em.mdp 文件示例

; Energy minimization
integrator = steep        ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0            ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01             ; Energy step size
nsteps = 5000             ; Maximum number of (minimization) steps
nstenergy = 100           ; Write energy data every 100 steps
energygrps = System       ; Which energy group(s) to write

这里生成拓扑文件我用的ATB网站（需要用学术邮箱注册）
如果没有安装过Gromacs，可以看我这篇文章：手把手教你用linux安装Gromacs（2024 GPU-CUDA）

6.展出讲讲怎么使用ATB

在这里插入图片描述
你也可以自己搜索与自己有关的小分子，我这里只是讲解

可以打开看看结构
在这里插入图片描述
这里配置你的参数

将参数配置好后打开1，另存为GROMOS_54A7_ATB.lt，会看到

下面那四个选择第一个，优化好的全原子力场文件，保存为1XL4_allatom_optimized_geometry.lt,这个名字取决于什么看下图：

在文件2的中间部分，有这么一部分，用三个顿号区分开来的区域，为moltemplate的输入文件，将其另存为system.lt,要去除每行的#|
在这里插入图片描述

中间有两个import，对应于上面提到的两个文件。所有文件准备完成：
之后通过 moltemplate.sh system.lt命令运行，得到以下文件：：
在这里插入图片描述
相关的分子data文件在system.data里面，力场参数如bond_coeff,angle_coeff,pair_coeff等参数在system.in.settings里面。ATB这个力场对应的力场函数形式如下：

units real
        atom_style      full
        bond_style      harmonic
        angle_style     harmonic
        dihedral_style  harmonic
        improper_style  harmonic
        #pair_style      lj/cut/coul/cut \$\{cutoff\}  # for non-period sims
        pair_style      lj/cut/coul/long   \$\{cutoff\}
        kspace_style    pppm 0.0001
        special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 1.0 angle yes dihedral yes

7. 展开讲讲怎么安装和使用moltemplate

下载安装moltemplate，首先进入官网下载
https://www.moltemplate.org/download.html

或者通过wget下载：

wget https://www.moltemplate.org/downloads/moltemplate_2024-2-11.tar.gz

在这里插入图片描述
2. 解压

tar -xzvf moltemplate_2024-2-11.tar.gz

安装依赖

cd moltemplate_2024-2-11
python3 setup.py install

验证安装

moltemplate.sh --version # 在任意位置输入都可

Error可忽略
在这里插入图片描述
之后通过命令 moltemplate.sh system.lt运行即可

会多出这些文件

8.展出讲讲怎么使用Sobtop生成拓扑文件

为什么要用sobtop？因为我从ATB中上传自己的纳米分子没有反应，emm…
Gromacs无法对小分子配体进行处理生成拓扑文件，这里使用Sob老师开发的处理小分子软件Sobtop，实用简单。
1.先将其他形式的文件转换为.mol2文件：使用文本编辑器打开.mol2文件，将图中位置改成配体名称，并保存；(行数多的可以自己写脚本）
我用的 sed 's/UNK/PS/g' ps_nanoball.mol2 > ps_nanoball_rename.mol2
在这里插入图片描述
2. 打开Sobtop，将配体分子ps_nanoball_rename.mol2 路径放进去，并回车；

3. 选择1并回车，生成top文件；

4. 选择3，尽可能使用GAFF力场；

5. 选择0，进入下一步

6. 选择4，如果可能，预先构建成键参数，任意猜测缺少的选项
在这里插入图片描述
7. 回车，生成的top文件生成在sobtop软件根目录下
8. 回车，生成的itp位置限制文件在sobtop软件根目录下

9. 选择2，生成gro文件

10. 回车，生成的gro文件在sobtop软件根目录下
11. 回车，退出sobtop软件

12. 处理过后得到ps_nanoball_rename.itp/.gro/.top文件。将这三个文件剪切至工作目录中。

mv ps_nanoball_rename.gro ps_nanoball_rename.itp ps_nanoball_rename.top /mnt/data/zf/packmol/

在这里插入图片描述

9. 展开讲讲怎么安装和使用sobtop

Sobtop 官网：http://sobereva.com/soft/Sobtop/#download
在这里插入图片描述
或者使用wget：

wget "http://sobereva.com/soft/Sobtop/sobtop_1.0(dev5).zip"

在这里插入图片描述
解压

 unzip 'sobtop_1.0(dev5).zip'
 mv 'sobtop_1.0(dev5)' sobtop_1.0
 cd sobtop_1.0
 chmod +x sobtop # 赋予sobtop可执行权限

使用

./sobtop # 因为没加入环境变量，必须在sobtop_1.0文件夹下执行，有兴趣的可以自己加

在这里插入图片描述

10. 展开讲讲怎么用Charmm-GUI 生成 GROMACS 拓扑文件

对于纳米材料的模拟，常见的分子力场不一定适用于这些系统，因为它们通常是为有机分子或生物分子设计的。纳米材料的原子间相互作用和结构属性比较独特，尤其是当涉及到金属、氧化物、碳基材料（如石墨烯、碳纳米管）等时。因此，选择合适的力场至关重要。因此sobtob并不擅长这个，只能再次更换！
Charmm-GUI 是另一个在线平台，支持生成适合 GROMACS 的拓扑文件，尤其适合分子较大的系统（如纳米材料）。

访问网站https://www.charmm-gui.org/
需要先用教育邮箱注册
在界面中选择“Input Generator”。
上传小分子或者纳米材料的 .pdb 文件。
在等待注册中，让我等24h内。。。
选择合适的力场，并指定生成 GROMACS 的输入文件。
Charmm-GUI 会生成 .top 文件、坐标文件 .gro 以及力场参数文件，可以直接下载并在 GROMACS 中使用

可能遇到的错误

1.错误一

root@ubuntu20:/mnt/data/zf/moltemplate_2024-2-11# python3 setup.py install
running install
running bdist_egg
running egg_info
creating moltemplate.egg-info
writing moltemplate.egg-info/PKG-INFO
writing dependency_links to moltemplate.egg-info/dependency_links.txt
writing entry points to moltemplate.egg-info/entry_points.txt
writing requirements to moltemplate.egg-info/requires.txt
writing top-level names to moltemplate.egg-info/top_level.txt
writing manifest file 'moltemplate.egg-info/SOURCES.txt'
reading manifest file 'moltemplate.egg-info/SOURCES.txt'
writing manifest file 'moltemplate.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/moltemplate
copying moltemplate/nbody_Impropers.py -> build/lib/moltemplate
copying moltemplate/recenter_coords.py -> build/lib/moltemplate
copying moltemplate/bonds_by_type.py -> build/lib/moltemplate
copying moltemplate/remove_duplicate_atoms.py -> build/lib/moltemplate
copying moltemplate/postprocess_transitions.py -> build/lib/moltemplate
copying moltemplate/nbody_graph_search.py -> build/lib/moltemplate
copying moltemplate/raw2data.py -> build/lib/moltemplate
copying moltemplate/ttree.py -> build/lib/moltemplate
copying moltemplate/ettree.py -> build/lib/moltemplate
copying moltemplate/postprocess_coeffs.py -> build/lib/moltemplate
copying moltemplate/lttree.py -> build/lib/moltemplate
copying moltemplate/ttree_render.py -> build/lib/moltemplate
copying moltemplate/nbody_fix_ttree_assignments.py -> build/lib/moltemplate
copying moltemplate/ttree_lex.py -> build/lib/moltemplate
copying moltemplate/dump2data.py -> build/lib/moltemplate
copying moltemplate/nbody_by_type_lib.py -> build/lib/moltemplate
copying moltemplate/nbody_Angles.py -> build/lib/moltemplate
copying moltemplate/__init__.py -> build/lib/moltemplate
copying moltemplate/nbody_Dihedrals.py -> build/lib/moltemplate
copying moltemplate/ettree_styles.py -> build/lib/moltemplate
copying moltemplate/extract_lammps_data.py -> build/lib/moltemplate
copying moltemplate/nbody_reorder_atoms.py -> build/lib/moltemplate
copying moltemplate/ordereddict.py -> build/lib/moltemplate
copying moltemplate/genpoly_modify_lt.py -> build/lib/moltemplate
copying moltemplate/genpoly_lt.py -> build/lib/moltemplate
copying moltemplate/lttree_postprocess.py -> build/lib/moltemplate
copying moltemplate/ttree_matrix_stack.py -> build/lib/moltemplate
copying moltemplate/charge_by_bond.py -> build/lib/moltemplate
copying moltemplate/interpolate_curve.py -> build/lib/moltemplate
copying moltemplate/nbody_Bonds.py -> build/lib/moltemplate
copying moltemplate/lttree_styles.py -> build/lib/moltemplate
copying moltemplate/ltemplify.py -> build/lib/moltemplate
copying moltemplate/amber2lt.py -> build/lib/moltemplate
copying moltemplate/extract_espresso_atom_types.py -> build/lib/moltemplate
copying moltemplate/nbody_by_type.py -> build/lib/moltemplate
copying moltemplate/postprocess_input_script.py -> build/lib/moltemplate
copying moltemplate/remove_duplicates_nbody.py -> build/lib/moltemplate
copying moltemplate/mol22lt.py -> build/lib/moltemplate
copying moltemplate/renumber_DATA_first_column.py -> build/lib/moltemplate
copying moltemplate/pdbsort.py -> build/lib/moltemplate
copying moltemplate/lttree_check.py -> build/lib/moltemplate
creating build/lib/moltemplate/nbody_alt_symmetry
copying moltemplate/nbody_alt_symmetry/opls_imp.py -> build/lib/moltemplate/nbody_alt_symmetry
copying moltemplate/nbody_alt_symmetry/angles_nosym.py -> build/lib/moltemplate/nbody_alt_symmetry
copying moltemplate/nbody_alt_symmetry/cenJswapIL.py -> build/lib/moltemplate/nbody_alt_symmetry
copying moltemplate/nbody_alt_symmetry/dihedrals_nosym.py -> build/lib/moltemplate/nbody_alt_symmetry
copying moltemplate/nbody_alt_symmetry/cenIswapJK.py -> build/lib/moltemplate/nbody_alt_symmetry
copying moltemplate/nbody_alt_symmetry/gaff_imp.py -> build/lib/moltemplate/nbody_alt_symmetry
copying moltemplate/nbody_alt_symmetry/cenIsortJKL.py -> build/lib/moltemplate/nbody_alt_symmetry
copying moltemplate/nbody_alt_symmetry/cenJsortIKL.py -> build/lib/moltemplate/nbody_alt_symmetry
copying moltemplate/nbody_alt_symmetry/__init__.py -> build/lib/moltemplate/nbody_alt_symmetry
copying moltemplate/nbody_alt_symmetry/impropers_nosym.py -> build/lib/moltemplate/nbody_alt_symmetry
copying moltemplate/nbody_alt_symmetry/bonds_nosym.py -> build/lib/moltemplate/nbody_alt_symmetry
creating build/lib/moltemplate/scripts
copying moltemplate/scripts/cleanup_moltemplate.sh -> build/lib/moltemplate/scripts
copying moltemplate/scripts/emoltemplate.sh -> build/lib/moltemplate/scripts
copying moltemplate/scripts/molc.sh -> build/lib/moltemplate/scripts
copying moltemplate/scripts/moltemplate.sh -> build/lib/moltemplate/scripts
copying moltemplate/scripts/pdb2crds.awk -> build/lib/moltemplate/scripts
creating build/lib/moltemplate/force_fields
copying moltemplate/force_fields/tip3p_1983_oplsaa.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/spce_amber.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/spce.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/graphene_rectangular.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/spce_hybrid.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/sdk.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/drymartini.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/martini.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/spce_ice_rect8.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/tip3p_2004_hybrid.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/spce_oplsaa.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/tip5p_oplsaa.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/graphene.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/spce_ice_rect16.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/tip3f_1987_oplsaa.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/tip3p_1983_charmm.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/spc_oplsaa.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/gaff.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/spce_more_comments.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/compass_published.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/oplsaa.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/gaff2.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/dreiding.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/tip3p_1983_charmm_hybrid.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/cooke_deserno_lipid.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/graphite.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/tip3p_1983_hybrid.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/spce_ice_rect32.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/spce_dreiding.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/trappe1998.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/watmw.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/loplsaa.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/tip3p_1983.lt -> build/lib/moltemplate/force_fields
copying moltemplate/force_fields/tip3p_2004.lt -> build/lib/moltemplate/force_fields
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/nbody_Impropers.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/recenter_coords.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/bonds_by_type.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/remove_duplicate_atoms.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/postprocess_transitions.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/nbody_graph_search.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/raw2data.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/ttree.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/ettree.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/postprocess_coeffs.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/lttree.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/ttree_render.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/nbody_fix_ttree_assignments.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/ttree_lex.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/dump2data.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/nbody_by_type_lib.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/nbody_Angles.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/__init__.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/nbody_Dihedrals.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/ettree_styles.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/extract_lammps_data.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/nbody_reorder_atoms.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/ordereddict.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/genpoly_modify_lt.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/genpoly_lt.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/lttree_postprocess.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/ttree_matrix_stack.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/charge_by_bond.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/interpolate_curve.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/nbody_Bonds.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/lttree_styles.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/ltemplify.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/amber2lt.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/extract_espresso_atom_types.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/nbody_by_type.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/postprocess_input_script.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/remove_duplicates_nbody.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/mol22lt.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/renumber_DATA_first_column.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/pdbsort.py -> build/bdist.linux-x86_64/egg/moltemplate
copying build/lib/moltemplate/lttree_check.py -> build/bdist.linux-x86_64/egg/moltemplate
creating build/bdist.linux-x86_64/egg/moltemplate/nbody_alt_symmetry
copying build/lib/moltemplate/nbody_alt_symmetry/opls_imp.py -> build/bdist.linux-x86_64/egg/moltemplate/nbody_alt_symmetry
copying build/lib/moltemplate/nbody_alt_symmetry/angles_nosym.py -> build/bdist.linux-x86_64/egg/moltemplate/nbody_alt_symmetry
copying build/lib/moltemplate/nbody_alt_symmetry/cenJswapIL.py -> build/bdist.linux-x86_64/egg/moltemplate/nbody_alt_symmetry
copying build/lib/moltemplate/nbody_alt_symmetry/dihedrals_nosym.py -> build/bdist.linux-x86_64/egg/moltemplate/nbody_alt_symmetry
copying build/lib/moltemplate/nbody_alt_symmetry/cenIswapJK.py -> build/bdist.linux-x86_64/egg/moltemplate/nbody_alt_symmetry
copying build/lib/moltemplate/nbody_alt_symmetry/gaff_imp.py -> build/bdist.linux-x86_64/egg/moltemplate/nbody_alt_symmetry
copying build/lib/moltemplate/nbody_alt_symmetry/cenIsortJKL.py -> build/bdist.linux-x86_64/egg/moltemplate/nbody_alt_symmetry
copying build/lib/moltemplate/nbody_alt_symmetry/cenJsortIKL.py -> build/bdist.linux-x86_64/egg/moltemplate/nbody_alt_symmetry
copying build/lib/moltemplate/nbody_alt_symmetry/__init__.py -> build/bdist.linux-x86_64/egg/moltemplate/nbody_alt_symmetry
copying build/lib/moltemplate/nbody_alt_symmetry/impropers_nosym.py -> build/bdist.linux-x86_64/egg/moltemplate/nbody_alt_symmetry
copying build/lib/moltemplate/nbody_alt_symmetry/bonds_nosym.py -> build/bdist.linux-x86_64/egg/moltemplate/nbody_alt_symmetry
creating build/bdist.linux-x86_64/egg/moltemplate/scripts
copying build/lib/moltemplate/scripts/cleanup_moltemplate.sh -> build/bdist.linux-x86_64/egg/moltemplate/scripts
copying build/lib/moltemplate/scripts/emoltemplate.sh -> build/bdist.linux-x86_64/egg/moltemplate/scripts
copying build/lib/moltemplate/scripts/molc.sh -> build/bdist.linux-x86_64/egg/moltemplate/scripts
copying build/lib/moltemplate/scripts/moltemplate.sh -> build/bdist.linux-x86_64/egg/moltemplate/scripts
copying build/lib/moltemplate/scripts/pdb2crds.awk -> build/bdist.linux-x86_64/egg/moltemplate/scripts
creating build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/tip3p_1983_oplsaa.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/spce_amber.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/spce.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/graphene_rectangular.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/spce_hybrid.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/sdk.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/drymartini.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/martini.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/spce_ice_rect8.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/tip3p_2004_hybrid.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/spce_oplsaa.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/tip5p_oplsaa.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/graphene.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/spce_ice_rect16.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/tip3f_1987_oplsaa.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/tip3p_1983_charmm.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/spc_oplsaa.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/gaff.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/spce_more_comments.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/compass_published.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/oplsaa.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/gaff2.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/dreiding.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/tip3p_1983_charmm_hybrid.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/cooke_deserno_lipid.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/graphite.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/tip3p_1983_hybrid.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/spce_ice_rect32.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/spce_dreiding.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/trappe1998.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/watmw.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/loplsaa.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/tip3p_1983.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
copying build/lib/moltemplate/force_fields/tip3p_2004.lt -> build/bdist.linux-x86_64/egg/moltemplate/force_fields
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/nbody_Impropers.py to nbody_Impropers.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/recenter_coords.py to recenter_coords.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/bonds_by_type.py to bonds_by_type.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/remove_duplicate_atoms.py to remove_duplicate_atoms.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/postprocess_transitions.py to postprocess_transitions.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/nbody_graph_search.py to nbody_graph_search.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/raw2data.py to raw2data.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/ttree.py to ttree.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/ettree.py to ettree.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/postprocess_coeffs.py to postprocess_coeffs.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/lttree.py to lttree.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/ttree_render.py to ttree_render.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/nbody_fix_ttree_assignments.py to nbody_fix_ttree_assignments.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/ttree_lex.py to ttree_lex.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/dump2data.py to dump2data.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/nbody_by_type_lib.py to nbody_by_type_lib.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/nbody_Angles.py to nbody_Angles.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/__init__.py to __init__.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/nbody_Dihedrals.py to nbody_Dihedrals.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/ettree_styles.py to ettree_styles.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/extract_lammps_data.py to extract_lammps_data.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/nbody_reorder_atoms.py to nbody_reorder_atoms.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/ordereddict.py to ordereddict.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/genpoly_modify_lt.py to genpoly_modify_lt.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/genpoly_lt.py to genpoly_lt.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/lttree_postprocess.py to lttree_postprocess.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/ttree_matrix_stack.py to ttree_matrix_stack.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/charge_by_bond.py to charge_by_bond.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/interpolate_curve.py to interpolate_curve.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/nbody_Bonds.py to nbody_Bonds.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/lttree_styles.py to lttree_styles.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/ltemplify.py to ltemplify.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/amber2lt.py to amber2lt.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/extract_espresso_atom_types.py to extract_espresso_atom_types.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/nbody_by_type.py to nbody_by_type.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/postprocess_input_script.py to postprocess_input_script.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/remove_duplicates_nbody.py to remove_duplicates_nbody.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/mol22lt.py to mol22lt.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/renumber_DATA_first_column.py to renumber_DATA_first_column.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/pdbsort.py to pdbsort.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/lttree_check.py to lttree_check.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/nbody_alt_symmetry/opls_imp.py to opls_imp.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/nbody_alt_symmetry/angles_nosym.py to angles_nosym.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/nbody_alt_symmetry/cenJswapIL.py to cenJswapIL.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/nbody_alt_symmetry/dihedrals_nosym.py to dihedrals_nosym.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/nbody_alt_symmetry/cenIswapJK.py to cenIswapJK.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/nbody_alt_symmetry/gaff_imp.py to gaff_imp.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/nbody_alt_symmetry/cenIsortJKL.py to cenIsortJKL.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/nbody_alt_symmetry/cenJsortIKL.py to cenJsortIKL.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/nbody_alt_symmetry/__init__.py to __init__.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/nbody_alt_symmetry/impropers_nosym.py to impropers_nosym.cpython-38.pyc
byte-compiling build/bdist.linux-x86_64/egg/moltemplate/nbody_alt_symmetry/bonds_nosym.py to bonds_nosym.cpython-38.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/scripts-3.8
copying moltemplate/scripts/moltemplate.sh -> build/scripts-3.8
copying moltemplate/scripts/cleanup_moltemplate.sh -> build/scripts-3.8
copying moltemplate/scripts/molc.sh -> build/scripts-3.8
copying moltemplate/scripts/pdb2crds.awk -> build/scripts-3.8
copying moltemplate/scripts/emoltemplate.sh -> build/scripts-3.8
creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.8/moltemplate.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.8/cleanup_moltemplate.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.8/molc.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.8/pdb2crds.awk -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.8/emoltemplate.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/moltemplate.sh to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/cleanup_moltemplate.sh to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/molc.sh to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/pdb2crds.awk to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/emoltemplate.sh to 775
copying moltemplate.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying moltemplate.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying moltemplate.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying moltemplate.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying moltemplate.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying moltemplate.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying moltemplate.egg-info/zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO
creating dist
creating 'dist/moltemplate-2.20.20-py3.8.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing moltemplate-2.20.20-py3.8.egg
Copying moltemplate-2.20.20-py3.8.egg to /usr/local/lib/python3.8/dist-packages
Adding moltemplate 2.20.20 to easy-install.pth file
Installing cleanup_moltemplate.sh script to /usr/local/bin
Installing emoltemplate.sh script to /usr/local/bin
Installing molc.sh script to /usr/local/bin
Installing moltemplate.sh script to /usr/local/bin
Installing pdb2crds.awk script to /usr/local/bin
Installing bonds_by_type.py script to /usr/local/bin
Installing charge_by_bond.py script to /usr/local/bin
Installing dump2data.py script to /usr/local/bin
Installing ettree.py script to /usr/local/bin
Installing extract_espresso_atom_types.py script to /usr/local/bin
Installing extract_lammps_data.py script to /usr/local/bin
Installing genpoly_lt.py script to /usr/local/bin
Installing genpoly_modify_lt.py script to /usr/local/bin
Installing interpolate_curve.py script to /usr/local/bin
Installing ltemplify.py script to /usr/local/bin
Installing lttree.py script to /usr/local/bin
Installing lttree_check.py script to /usr/local/bin
Installing lttree_postprocess.py script to /usr/local/bin
Installing mol22lt.py script to /usr/local/bin
Installing nbody_by_type.py script to /usr/local/bin
Installing nbody_fix_ttree_assignments.py script to /usr/local/bin
Installing nbody_reorder_atoms.py script to /usr/local/bin
Installing pdbsort.py script to /usr/local/bin
Installing postprocess_coeffs.py script to /usr/local/bin
Installing postprocess_input_script.py script to /usr/local/bin
Installing raw2data.py script to /usr/local/bin
Installing recenter_coords.py script to /usr/local/bin
Installing remove_duplicate_atoms.py script to /usr/local/bin
Installing remove_duplicates_nbody.py script to /usr/local/bin
Installing renumber_DATA_first_column.py script to /usr/local/bin
Installing ttree.py script to /usr/local/bin
Installing ttree_render.py script to /usr/local/bin

Installed /usr/local/lib/python3.8/dist-packages/moltemplate-2.20.20-py3.8.egg
Processing dependencies for moltemplate==2.20.20
Searching for numpy
Reading https://pypi.org/simple/numpy/
Downloading https://files.pythonhosted.org/packages/59/5f/9003bb3e632f2b58f5e3a3378902dcc73c5518070736c6740fe52454e8e1/numpy-2.1.1.tar.gz#sha256=d0cf7d55b1051387807405b3898efafa862997b4cba8aa5dbe657be794afeafd
Best match: numpy 2.1.1
Processing numpy-2.1.1.tar.gz
error: Couldn't find a setup script in /tmp/easy_install-60v1qrs3/numpy-2.1.1.tar.gz

原因：numpy 包的安装过程无法找到 setup.py 脚本
解决方法：

sudo apt-get install python3-pip  # 如果你使用的是 Ubuntu 或其他基于 Debian 的系统

之后再 python3 setup.py install
成功界面
在这里插入图片描述

2. 错误二

 -1 Select method for deriving rigid parameters: mSeminario
 0 Exit program
 1 Generate GROMACS topology file
 2 Generate GROMACS .gro file
 3 Generate GROMACS .rtp file
 4 Generate .gjf file (for visualizing connectivity in GaussView)
 5 Derive rigid parameter for specific bond/angle/dihedral
 6 Derive rigid parameters for all bonds, angles and dihedrals
 7 Assign atomic charges
 10 Other functions
1
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source             
sobtop             0000000001275B93  Unknown               Unknown  Unknown
libpthread-2.31.s  00007F9B839FD420  Unknown               Unknown  Unknown
sobtop             000000000044A3CF  Unknown               Unknown  Unknown
sobtop             0000000000424781  Unknown               Unknown  Unknown
sobtop             0000000000422322  Unknown               Unknown  Unknown
libc-2.31.so       00007F9B8381B083  __libc_start_main     Unknown  Unknown
sobtop             0000000000422229  Unknown               Unknown  Unknown

原因：大多数情况是由数组越界导致，排除该因素后，考虑到可能是因为Linux系统默认的堆栈过小导致StackOverflow，使用命令：

ulimit -s unlimited

取消堆栈限制后，程序可正常运行。

若要令其永久生效，需要在/etc/security/limits.conf 中加上：

* soft stack unlimited
* hard stack unlimited

在/etc/pam.d/login文件中加上：

session required /lib/security/pam_limits.so

最后重启终端即可。
输入1后成功进行下一步
在这里插入图片描述

PACKMOL 二：手把手教你用packmol构建含有 1 400 个 PS 单体的纳米球

文章目录

1. 1400个 Polystyrene nanoparticles（PS） 单体的纳米球的来源

2. 准备PS单体结构文件

3. 配置PACKMOL输入文件

4.运行PACKMOL

5. 检查和优化结构

6.展出讲讲怎么使用ATB

7. 展开讲讲怎么安装和使用moltemplate

8.展出讲讲怎么使用Sobtop生成拓扑文件

9. 展开讲讲怎么安装和使用sobtop

10. 展开讲讲怎么用Charmm-GUI 生成 GROMACS 拓扑文件

可能遇到的错误

1.错误一

2. 错误二

1. 1400个 Polystyrene nanoparticles（PS）单体的纳米球的来源