rosetta氨基酸参数_rosetta ligand metal ions-程序员宅基地

技术标签: rosetta  蛋白建模  分子动力学模拟  蛋白建模及优化相关  氨基酸参数  

rosetta residue topology file

NAME ALA
NAME The name of the Residue. Must be unique among all residues loaded into Rosetta
IO_STRING ALA A
IO_STRING The 3 letter and 1 letter codes representing the residue. 3 letter code is not unique; it does not need to be the same as the name. 1 letter code is Z by default.
TYPE POLYMER #residue type
TYPE The type of residue being represented, should be ‘LIGAND’ for ligands, or ‘POLYMER’ for amino acids, DNA and RNA bases, or other polymer building-blocks.
AA ALA
AA The amino acid type. Should be “UNK” for ligands, or for most non-canonicals. (Note that this corresponds to the core::chemical::AA enum, internally.)
ROTAMER_AA ALA
ATOM N Nbb NH1 -0.47 -0.350
ATOM CA CAbb CT1 0.07 0.100
ATOM C CObb C 0.51 0.550
ATOM O OCbb O -0.51 -0.550
ATOM CB CH3 CT3 -0.27 0.000
ATOM H HNbb H 0.31 0.250
ATOM HA Hapo HB 0.09 0.000
ATOM 1HB Hapo HA 0.09 0.000
ATOM 2HB Hapo HA 0.09 0.000
ATOM 3HB Hapo HA 0.09 0.000
The first column after the ATOM specifier is the atom name, and the second column (the Nbb/CAbb/etc.) is the Rosetta atom type. The third column (NH1/CT1/C/O) is the CHARMM molecular mechanics atom type, which is not used by default in Rosetta, but is read by certain specialty energy terms (the “MM” terms). (The fourth and fifth columns are partial charges.)
LOWER_CONNECT N
UPPER_CONNECT C
CONNECT Gives an atom a connection to an (unspecified) atom in another residue. This is not to be used for the N and C in the backbone; those are given with LOWER_CONNECT and UPPER_CONNECT respectively.
BOND N CA
BOND N H
BOND CA C
BOND CA CB
BOND CA HA
BOND_TYPE C O 2
BOND CB 1HB
BOND CB 2HB
BOND CB 3HB
BOND Defines a bond connection between two named atoms.
PROPERTIES PROTEIN CANONICAL_AA ALPHA_AA L_AA METALBINDING ALIPHATIC
METAL_BINDING_ATOMS O
PROPERTIES A series of properties describing this ligand type or residue type. Allowed properties include (though this list is not exhaustive): PROTEIN POLYMER LIGAND COARSE METAL METALBINDING DNA RNA CARBOHYDRATE SURFACE POLAR CHARGED AROMATIC TERMINUS LOWER_TERMINUS UPPER_TERMINUS SC_ORBITALS. For an exhaustive list of allowed properties, see the file source/src/core/chemical/residue_properties/general_properties.list in the main Rosetta repository.
NBR_ATOM CB
NBR_ATOM The PDB name of the “neighbor atom”. In the case of ligands, this defaults to the atom that is closest to the geometric center of the ligand
#APL O to CB DISTANCE – MAX O-CB OBSERVED IN UBQ
NBR_RADIUS 3.4473
NBR_RADIUS The radius of gyration of the ligand, used to define the overall size of the ligand.
FIRST_SIDECHAIN_ATOM CB
RAMA_PREPRO_FILENAME scoring/score_functions/rama/fd/all.ramaProb scoring/score_functions/rama/fd/prepro.ramaProb
ACT_COORD_ATOMS CB END
ICOOR_INTERNAL N 0.000000 0.000000 0.000000 N CA C
ICOOR_INTERNAL CA 0.000000 180.000000 1.458001 N CA C
ICOOR_INTERNAL C 0.000000 68.800003 1.523258 CA N C
ICOOR_INTERNAL UPPER 149.999985 63.800007 1.328685 C CA N
ICOOR_INTERNAL O -180.000000 59.200005 1.231015 C CA UPPER
ICOOR_INTERNAL CB -122.800000 69.625412 1.521736 CA N C
ICOOR_INTERNAL 1HB -180.000000 70.500000 1.090040 CB CA N
ICOOR_INTERNAL 2HB 120.000000 70.500000 1.090069 CB CA 1HB
ICOOR_INTERNAL 3HB 120.000000 70.500000 1.088803 CB CA 2HB
ICOOR_INTERNAL HA -119.000000 71.900000 1.090078 CA N CB
ICOOR_INTERNAL LOWER -150.000000 58.300003 1.328685 N CA C
ICOOR_INTERNAL H -180.000000 60.849998 1.010000 N CA LOWER
ICOOR_INTERNAL The internal coordinates of an atom. The format goes backwards and looks like this:
And the fields are the following:
● Child atom
● phi angle (torsion angle between A1, A2, A3, A4)
● theta angle (improper angle = (180 - (angle between A4, A3, A2)))
● distance (between A4 and A3)
● parent atom
● angle atom
● torsion atom

版权声明:本文为博主原创文章,遵循 CC 4.0 BY-SA 版权协议,转载请附上原文出处链接和本声明。
本文链接:https://blog.csdn.net/m0_37526339/article/details/78942671

智能推荐

java通过netty实现心跳机制_聊聊心跳机制及netty心跳实现-程序员宅基地

文章浏览阅读772次。我们在使用netty的时候会使用一个参数,ChannelOption.SO_KEEPALIVE为true, 设置好了之后再Linux系统才会对keepalive生效,但是linux里边需要配置几个参数,tcp_keepalive_time, tcp_keepalive_invl, tcp_keepalive_probes,如果不配置的时候都会是默认值。tcp_keepalive_time 即给一个..._sendping sendpong

html怎么添加文本内容吗,添加文本内容.html-程序员宅基地

文章浏览阅读948次。添加文本内容$axure.utils.getTransparentGifPath = function() { return 'resources/images/transparent.gif'; };$axure.utils.getOtherPath = function() { return 'resources/Other.html'; };$axure.utils.getReloadPa..._html中function添加文字

eclipse提示SyntaxError: Non-UTF-8 code starting with '\xc4' in file C:\Users\ 怎么解决_syntaxerror: non-utf-8 code starting with '\xc8' i-程序员宅基地

文章浏览阅读9.9k次,点赞2次,收藏9次。一、第一种方法首行增加,已测试可用。# coding=gbk程序中出现中文,运行的时候出现如下错误:SyntaxError: Non-UTF-8 code starting with 'xc1' in file C:...xxx.py on line 8, but no encoding declared; see http://python.org/dev/peps/pep-0263/ _syntaxerror: non-utf-8 code starting with '\xc8' in file c:\users\26743\desk

JAVA笔试代码找错_京东笔试括号匹配问题(代码找错)-程序员宅基地

文章浏览阅读111次。这一题,测试了好几种情况都通过了,例如:())(;((()));)))(((;(())));但是提交只能通过10%,我现在陷入死角了,求各位大佬帮忙;我这一题的思路是,遍历一遍字符串,假如最后结果栈中只有")("那么就判断一次交换可以成功,其他情况都不成功import java.util.Scanner;import java.util.Stack;/*** @Author: Taoyongpan..._笔试代码找错

pandas小记:pandas时间序列分析和处理Timeseries_x must be a pandas object-程序员宅基地

文章浏览阅读10w+次,点赞13次,收藏102次。http://blog.csdn.net/pipisorry/article/details/52209377pandas 最基本的时间序列类型就是以时间戳(TimeStamp)为 index 元素的 Series 类型。其它时间序列处理相关的包[P4J 0.6: Periodic light curve analysis tools based on Information Theory][p4_x must be a pandas object

vue中在哪个生命周期中dom被渲染_Vue.js 组件的生命周期-程序员宅基地

文章浏览阅读2.5k次。本文目录结构问题Vue组件的生命周期答案总共分为8个阶段创建前/后,载⼊前/后,更新前/后,销毁前/后创建前/后: 在 beforeCreate 阶段, vue 实例的挂载元素 el 和数据对象 data 都为undefined ,还未初始化。在 created 阶段, vue 实例的数据对象 data 有了,el还 没有载⼊前/后:在 beforeMount 阶段, vue 实例的 $el 和 ..._vue渲染dom是在哪个环节

随便推点

通用技术计算机辅助设计教案,高一通用技术课堂《设计的一般过程》的优秀教案...-程序员宅基地

文章浏览阅读263次。高一通用技术课堂《设计的一般过程》的优秀教案教学过程1. 引入新课多媒体投影展示几个新颖的设计,这些作品基于什么目的而设计的,它解决了什么问题?师:这些作品是怎么来的呢?生:设计出来的。师:我们要知道完成任何一件事情都有一个过程,须遵循一定的步骤,设计也不例外。通过前面的学习,我们已经知道,技术世界因设计而愈加精彩,设计是技术发展的关键。我们设计的最终目的是什么?就是为了解决人们的实际需要。那么同..._高一计算机技术与通用教案

POJ-3415-Common-Substring-后缀数组-并查集_并查集 poj 3415-程序员宅基地

文章浏览阅读172次。题目题目链接内容给两个字符串a,ba,ba,b ,和整数kkk 询问a,ba,ba,b的公共子串中长度大于等于kkk的个数分析对于一个长度为len(len>=k)len(len>=k)len(len>=k) 的公共子串,它对答案的贡献为len−k+1len-k+1len−k+1 ,我们构建后缀数组,将heightheightheight 数组排序,从大到小遍历hei..._并查集 poj 3415

linux脚本while死循环,shell编程之while死循环-程序员宅基地

文章浏览阅读2.5k次。在linux下编程的程序猿都知道shell脚本,就算你不怎么熟悉,也应该听过的吧!那在shell脚本中的死循环该怎么写呢?对于熟悉C语言的猿人们来说,最简单的死循环应该这样写:-------------------------------------------------------------------------while(1){//do something}---------------..._写一个死循环while(1)

成功人士的名言精选——看看你的名言是哪一句?你做到了吗?_brian tracy 名言-程序员宅基地

文章浏览阅读1k次。毋庸置疑,每个人都有自己的名言警句,因为有目标、因为有理想,我们都在拼命努地奋斗着、拼搏着,希望你的名言可以让你距离成功更进一步,相信自己! 1. Success is never a destination, it is a journey.—— Statenig St. Marie  成功不是终点,而是旅程。—— 斯塔特尼格·圣·玛_brian tracy 名言

python程序编译之后、找不到生成的pyc文件_浅谈python编译pyc工程--导包问题解决...-程序员宅基地

文章浏览阅读521次。利用python 编译工程,生产pyc文件pyc文件好处:是一种二进制机器码,并且隐藏了源文件代码,但是有和py文件一样的功能(可以理解为效果一样)所以可以将代码隐藏,便于商业价值,保护代码隐私还能和py文件一样可运行import compileallcompileall.compile_dir(r'/path')所以在一些情况下,需将源文件工程批量生成pyc文件来隐藏代码。上面代码即为 批量生成..._python 没有py文件调用pyc文件失败

抛弃格子衫和冲锋衣,程序员该如何穿?-程序员宅基地

文章浏览阅读111次。在众多人眼中,程序猿是最不会穿衣搭配的物种了,他们一年四季的标配就是格子衫加牛仔裤,冷的时候再加件冲锋衣。每到春夏,码农的大花格子衬衫就会在互联网公司的格子间遍地开花,如同冲锋衣是秋冬标配一样,格子衬衫就是程序员的夏季制服,一堆程序员在一起都不是连连看。人靠衣装,佛靠金装”这句话很多人都听过,但是放在心上的未必有几个,对于不善于穿衣打扮的程...序...员...来说,更是如此。根据聚能...