请问从全原子到Martini粗粒化粒子映射的规则从哪里寻找？

不想飞的猫头鹰 · 发表于 Post on 2023-2-13 16:41:50

最近在做Martini粗粒化磷脂分子模拟，使用insane脚本构建出粗粒化细胞膜。我的体系包含多种不同的磷脂分子，想要找到如图一样类似的能明确指出哪些全原子作为一个粗粒化粒子的映射规则，方便之后能对其他种类的磷脂分子做出类似的映射图，但是从Martini官网http://www.cgmartini.nl/并没有找到这样的说明，希望热心网友能指条路，十分感谢！

Acee · 发表于 Post on 2023-2-13 22:22:42

映射规则在martini 07年的原文里写的很清楚

rpestana94 · 发表于 Post on 2023-2-13 23:59:11

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

不想飞的猫头鹰 · 发表于 Post on 2023-2-14 14:52:44

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！

不想飞的猫头鹰 · 发表于 Post on 2023-2-14 15:09:00

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.

rpestana94 · 发表于 Post on 2023-2-14 17:19:34

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

不想飞的猫头鹰 · 发表于 Post on 2023-2-15 09:14:04

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!

Azrael · 发表于 Post on 2023-11-23 16:35:34

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！

不想飞的猫头鹰 · 发表于 Post on 2023-11-23 21:44:09

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

Azrael · 发表于 Post on 2023-11-24 09:04:08

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

不想飞的猫头鹰 · 发表于 Post on 2023-11-24 09:36:10

Azrael 发表于 2023-11-24 09:04
跪谢

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[GROMACS] 请问从全原子到Martini粗粒化粒子映射的规则从哪里寻找？

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