Azrael 发表于 2023-11-24 09:04
跪谢

不想飞的猫头鹰 发表于 2023-11-23 21:44
不敢当呀，我也是正在学习的小菜狗insane原文是DOI: 10.1021/acs.jctc.5b00209，可以从http://md.c ...

跪谢

Azrael 发表于 2023-11-23 16:35
猫头鹰大佬，我刚入门磷脂体系，请问你做Martini粗粒化磷脂分子模拟是看的哪篇文献呢，提到的insane脚本是 ...

不敢当呀，我也是正在学习的小菜狗insane原文是DOI: 10.1021/acs.jctc.5b00209，可以从http://md.chem.rug.nl/index.php/tools2/proteins-and-bilayers下载，欢迎多交流呀

猫头鹰大佬，我刚入门磷脂体系，请问你做Martini粗粒化磷脂分子模拟是看的哪篇文献呢，提到的insane脚本是在哪里下载的呢，诚盼佳音！

rpestana94 发表于 2023-2-14 17:19
I just remember, there is a martini database, is quite new, there are several models there, https: ...

I have saved it. Thanks again for your information and help!

不想飞的猫头鹰 发表于 2023-2-14 02:09
Thank you very much for your valuable advice! I will try to model Martini 3 with charmm-gui later. ...

I just remember, there is a martini database, is quite new, there are several models there, https://mad.ibcp.fr/explore

rpestana94 发表于 2023-2-13 23:59
You can try with chamgui which have some martini builder in case you want to build something differe ...

Thank you very much for your valuable advice! I will try to model Martini 3 with charmm-gui later.

Acee 发表于 2023-2-13 22:22
映射规则在martini 07年的原文里写的很清楚

好的，找到了，我在Maritni官网下载到了martini_v2.0_XXXX.itp(代表磷脂分子的itp文件)，里面有对粗粒化粒子种类的说明，在Coarse Grained Model for Semiquantitative Lipid Simulations（doi:10.1021/jp036508g）一文中的Table 3里给出了各种粗粒化粒子对应的映射模块，十分感谢！

You can try with chamgui which have some martini builder in case you want to build something different, also about the mapping you can check: "A Practical Introduction to Martini 3 and its Application to Protein-Ligand Binding Simulations", the first chapter is open and there they describe how to map small molecules but the principles are the same for lipids

映射规则在martini 07年的原文里写的很清楚