24小时热门版块排行榜

返回列表

本帖产生 1 个模拟EPI ，点击这里进行查看

smutao

禁虫 (著名写手)

模拟EPI: 6
应助: 247 (大学生)
金币: 6380.1
散金: 4740
红花: 57
帖子: 1402
在线: 598.8小时
虫号: 2880224
注册: 2013-12-18

[交流] [smutao文集-自编教程]如何快速构建单链Polymer模型？已有1人参与

最近做了一点和polymer有关的工作，想到了一个快速构建单链polymer的方式。
希望对大家有帮助。
Sometimes, when we need to do some research on polymers using the MD simulation methods, we have to construct models of them first. It is a common way to construct such models using commercial software packages such as Material Studio, Discovery Studio and so forth. But what can we do without them?

The main tool we need to construct such models is Open Babel.

Following is the protocol:
1. Get the structure information of the polymer you study(usually the 2D structure);
2. Draw a short sample of the polymer in Chemdraw saving as ".cdx" file or 3D modeling software such as GaussView saving as ".mol2" file;
3. Using Open Babel to convert the ".cdx" or ".mol2" file into SMILES format;
4. Look at the SMILES string and learn how it is organized;
5. Write the SMILES string for the polymer you study;
6. Using Open Babel to convert the SMILES format into a ".mol2" file.

So the raw model has been constructed.
However, there are a little problems before using it for MD simulation.
Firstly, there will be same atom names, and we have to adjust them to avoid conflicts.
Secondly, no other problems found... :-)

Enjoy!

回复此楼