求助：蛋白和小分子配体的模拟中，怎么针对某关键氨基酸和配体的距离变动作如下分析

gzcnp_yp · 发表于 Post on 2021-10-21 19:57:04

本帖最后由 gzcnp_yp 于 2021-10-23 09:24 编辑

初学中，请指教, 从原文看"Further analysis shows that one or two hydrogen bonds were formed between the compound 1 and sEH, and some key amino acid residues, including Tyr343, Met369, Ile363, Ser374, Asn378, Trp465, Asn468, and Asn472, emerged in this MD stimulation. Their distances with compound 1 were analyzed and plotted in Fig. 8E–G."，他的distance好象是指氨基酸残基和小分子配体的距离，文章好象通过这个来分析形成氢键的稳定性，

sobereva · 发表于 Post on 2021-10-22 06:23:19

在网上求助计算化学问题的时候必须把问题描述得详细、具体、准确、清楚
http://sobereva.com/620（http://bbs.keinsci.com/thread-25787-1-1.html）
distance是什么都不说明白

gzcnp_yp · 发表于 Post on 2021-10-23 09:19:17

本帖最后由 gzcnp_yp 于 2021-10-23 09:22 编辑

感谢sobereva指正，以后发贴求助要注意细节描述清楚，已改原贴，

gzcnp_yp · 发表于 Post on 2021-10-23 09:52:06

Fig. 8. (A) The potential energy of compound 1 with sEH for 20 ns of MD stimulation. (B) RMSD of compound 1 with sEH for 20 ns of MD stimulation. (C) RMSF of compound 1 with sEH for 20 ns of MD stimulation. (D) The hydrogen bond number of compound 1 with sEH (E) The distance of compound 1 with amino acid residues Tyr343, Met369, and Ile363 for 20 ns of MD stimulation. (F) The distance of compound 1 with amino acid residues Ser374, Asn378, and Trp465 for 20 ns of MD stimulation. (G) The distance of compound 1 with amino acid residues Asn468 and Asn472 for 20 ns of MD stimulation. (H) The position of compound 1 with sEH at the 20th ns of MD stimulation. (I) The interaction of compound 1 with amino acid residues Ser374 via a hydrogen bond at the 20th ns of MD stimulation.
这是文献中MD部分的出图，”International Journal of Biological Macromolecules 183 (2021) 811–817“

gzcnp_yp · 发表于 Post on 2021-10-23 18:48:23

本帖最后由 gzcnp_yp 于 2021-10-23 19:39 编辑

我查了一下，好象用 gmx mindist或gmx distance可以实现，具体还在摸索中，求具体实现方法

夏一天 · 发表于 Post on 2021-10-23 22:31:32

是不是要gmx make_ndx 先索引需要分析的氨基酸？不清楚，还望sobereva老师能指点

gzcnp_yp · 发表于 Post on 2021-10-26 16:40:25

本帖最后由 gzcnp_yp 于 2021-10-26 16:46 编辑

答案在http://bbs.keinsci.com/thread-15180-1-1.html，如果执行成功， -oall 会给出dist.xvg

gzcnp_yp · 发表于 Post on 2021-10-26 16:42:19

但我执行 gmx distance -s md_0_10.tpr -f md_0_10_center.xtc -select "resname JZ4 and name OAB plus resid 102 and name OE1" -oall

出现下行错误，求解决

Program: gmx distance, version 2019.6
Source file: src\gromacs\trajectoryanalysis\modules\distance.cpp (line 204)
Function: void __cdecl gmx::analysismodules::`anonymous-namespace'::checkSelections(const class std::vector<class gmx::Selection,class std::allocator<class gmx::Selection> > &)

Inconsistency in user input:
Selection 'resname JZ4 and name OAB plus resid 102 and name OE1' does not
evaluate into an even number of positions (there are 1 positions)

gzcnp_yp · 发表于 Post on 2021-10-26 19:36:17

Selection 'resname JZ4 and name OAB plus resid 102 and name OE1' 有什么问题，gmx 2019.6 不能正确解析

gzcnp_yp · 发表于 Post on 2021-10-26 20:34:00

gmx distance -s md_0_10.tpr -f md_0_10_center.xtc -select "resname jz4 and name O10 plus resid 102 and name OE1" -oall

改成上面后，通过，主要是配体名字和基团号搞错了，有时间写个总结，给有同样问题的后来者有个参考

		自动登录 Automatic login	找回密码 Forget password
密码 Password			注册 Register

[GROMACS] 求助：蛋白和小分子配体的模拟中，怎么针对某关键氨基酸和配体的距离变动作如下分析

浏览过的版块