请选择 进入手机版 | 继续访问电脑版

分子模拟论坛 Molecular Simulation Forums

 找回密码
 立即注册

QQ登录

只需一步,快速开始

搜索
查看: 312|回复: 1

Wrong binding energy using the autodock4.0?

[复制链接]

20

主题

81

帖子

186

积分

注册会员

Rank: 2

积分
186
发表于 2008-10-3 10:11:00 | 显示全部楼层 |阅读模式
HI. I have tried to use AutoDock4.0 to bind several substrates to a protein. This is what I do in the following:
For the first substrate, I first manually dock to the active side, and then run autodock, I get a resonable binding energy,
While for the second substrate, because it is similiar to the firstone, so I just use all the grid file from the first one, and then I gota huge binding energy, 100000, I dont see why.
Because the coordinate of the first substrate is in the 30.0 32.0 31.0
while the second oneis-1.885-1.547-0.672 .
Is this the problem? If this is, does that mean everyone I need tomanually dock first? so frustrate, hope someone can help me, THanks,
回复

使用道具 举报

23

主题

109

帖子

247

积分

中级会员

Rank: 3Rank: 3

积分
247
发表于 2010-5-27 14:00:00 | 显示全部楼层
If you just want your 2nd substrate orignal coodinate locate as the 1st one, you could modify in.dpf file copy -1.885-1.547-0.672instead of 30.0 32.0 31.0
回复

使用道具 举报

您需要登录后才可以回帖 登录 | 立即注册

本版积分规则

Archiver|手机版|小黑屋|分子模拟论坛

GMT+8, 2020-12-2 16:52 , Processed in 0.069127 second(s), 22 queries .

Powered by Discuz! X3.4

© 2001-2017 Comsenz Inc.

快速回复 返回顶部 返回列表