版块导航: 正在加载中...

登录注册

应《网络安全法》要求，自2017年10月1日起，未进行实名认证将不得使用互联网跟帖服务。为保障您的帐号能够正常使用，请尽快对帐号进行手机号验证，感谢您的理解与支持！

24小时热门版块排行榜

返回列表

当前只显示满足指定条件的回帖，点击这里查看本话题的所有回帖

licaiqin

铜虫 (小有名气)

应助: 0 (幼儿园)
金币: 135.7
散金: 24
红花: 1
帖子: 112
在线: 19.1小时
虫号: 966779
注册: 2010-03-10
专业: 理论和计算化学

[交流] 【求助】PDB文件的处理已有7人参与

Tutorial1中导入PDB文件后出现
Loading PDB file: ./nuc.pdb
Created a new atom named: HO5' within residue: .R
Created a new atom named: H5' within residue: .R
Created a new atom named: H5'' within residue: .R
Created a new atom named: H2' within residue: .R
Created a new atom named: H2'' within residue: .R
Added missing heavy atom: .R.A

  Added missing heavy atom: .R.A
  Added missing heavy atom: .R.A
Created a new atom named: OP1 within residue: .R
Created a new atom named: OP2 within residue: .R
Created a new atom named: H5' within residue: .R
Created a new atom named: H5'' within residue: .R
Created a new atom named: H2' within residue: .R
Created a new atom named: H2'' within residue: .R
  Added missing heavy atom: .R.A
  Added missing heavy atom: .R.A
Created a new atom named: OP1 within residue: .R
Created a new atom named: OP2 within residue: .R
Created a new atom named: H5' within residue: .R
Created a new atom named: H5'' within residue: .R
Created a new atom named: H2' within residue: .R
Created a new atom named: H2'' within residue: .R
  Added missing heavy atom: .R.A
  Added missing heavy atom: .R.A
Created a new atom named: OP1 within residue: .R
Created a new atom named: OP2 within residue: .R
Created a new atom named: H5' within residue: .R
Created a new atom named: H5'' within residue: .R
Created a new atom named: H2' within residue: .R
Created a new atom named: H2'' within residue: .R
  Added missing heavy atom: .R.A
  Added missing heavy atom: .R.A
Created a new atom named: OP1 within residue: .R
Created a new atom named: OP2 within residue: .R
Created a new atom named: H5' within residue: .R
Created a new atom named: H5'' within residue: .R
Created a new atom named: H2' within residue: .R
Created a new atom named: H2'' within residue: .R
  Added missing heavy atom: .R.A
  Added missing heavy atom: .R.A
Created a new atom named: OP1 within residue: .R
Created a new atom named: OP2 within residue: .R
Created a new atom named: H5' within residue: .R
Created a new atom named: H5'' within residue: .R
Created a new atom named: H2' within residue: .R
Created a new atom named: H2'' within residue: .R
  Added missing heavy atom: .R.A
  Added missing heavy atom: .R.A
Created a new atom named: OP1 within residue: .R
Created a new atom named: OP2 within residue: .R
Created a new atom named: H5' within residue: .R
Created a new atom named: H5'' within residue: .R
Created a new atom named: H2' within residue: .R
Created a new atom named: H2'' within residue: .R
  Added missing heavy atom: .R.A
  Added missing heavy atom: .R.A
Created a new atom named: OP1 within residue: .R
Created a new atom named: OP2 within residue: .R
Created a new atom named: H5' within residue: .R
Created a new atom named: H5'' within residue: .R
Created a new atom named: H2' within residue: .R
Created a new atom named: H2'' within residue: .R
  Added missing heavy atom: .R.A
  Added missing heavy atom: .R.A
Created a new atom named: OP1 within residue: .R
Created a new atom named: OP2 within residue: .R
Created a new atom named: H5' within residue: .R
Created a new atom named: H5'' within residue: .R
Created a new atom named: H2' within residue: .R
Created a new atom named: H2'' within residue: .R
  Added missing heavy atom: .R.A
  Added missing heavy atom: .R.A
Created a new atom named: OP1 within residue: .R
Created a new atom named: OP2 within residue: .R
Created a new atom named: H5' within residue: .R
Created a new atom named: H5'' within residue: .R
Created a new atom named: H2' within residue: .R
Created a new atom named: H2'' within residue: .R
Created a new atom named: HO3' within residue: .R
  Added missing heavy atom: .R.A
  Added missing heavy atom: .R.A
Created a new atom named: HO5' within residue: .R

Created a new atom named: H5' within residue: .R

Created a new atom named: H5'' within residue: .R

Created a new atom named: H2' within residue: .R

Created a new atom named: H2'' within residue: .R

Added missing heavy atom: .R

.A
Added missing heavy atom: .R

.A
Created a new atom named: OP1 within residue: .R

Created a new atom named: OP2 within residue: .R

Created a new atom named: H5' within residue: .R

Created a new atom named: H5'' within residue: .R

Created a new atom named: H2' within residue: .R

Created a new atom named: H2'' within residue: .R

Added missing heavy atom: .R

.A
Added missing heavy atom: .R

.A
Created a new atom named: OP1 within residue: .R

Created a new atom named: OP2 within residue: .R

Created a new atom named: H5' within residue: .R

Created a new atom named: H5'' within residue: .R

Created a new atom named: H2' within residue: .R

Created a new atom named: H2'' within residue: .R

Added missing heavy atom: .R

.A
Added missing heavy atom: .R

.A
Created a new atom named: OP1 within residue: .R

Created a new atom named: OP2 within residue: .R

Created a new atom named: H5' within residue: .R

Created a new atom named: H5'' within residue: .R

Created a new atom named: H2' within residue: .R

Created a new atom named: H2'' within residue: .R

Added missing heavy atom: .R

.A
Added missing heavy atom: .R

.A
Created a new atom named: OP1 within residue: .R

Created a new atom named: OP2 within residue: .R

Created a new atom named: H5' within residue: .R

Created a new atom named: H5'' within residue: .R

Created a new atom named: H2' within residue: .R

Created a new atom named: H2'' within residue: .R

Added missing heavy atom: .R

.A
Added missing heavy atom: .R

.A
Created a new atom named: OP1 within residue: .R

Created a new atom named: OP2 within residue: .R

Created a new atom named: H5' within residue: .R

Created a new atom named: H5'' within residue: .R

Created a new atom named: H2' within residue: .R

Created a new atom named: H2'' within residue: .R

Added missing heavy atom: .R

.A
Added missing heavy atom: .R

.A
Created a new atom named: OP1 within residue: .R

Created a new atom named: OP2 within residue: .R

Created a new atom named: H5' within residue: .R

Created a new atom named: H5'' within residue: .R

Created a new atom named: H2' within residue: .R

Created a new atom named: H2'' within residue: .R

Added missing heavy atom: .R

.A
Added missing heavy atom: .R

.A
Created a new atom named: OP1 within residue: .R

Created a new atom named: OP2 within residue: .R

Created a new atom named: H5' within residue: .R

Created a new atom named: H5'' within residue: .R

Created a new atom named: H2' within residue: .R

Created a new atom named: H2'' within residue: .R

Added missing heavy atom: .R

.A
Added missing heavy atom: .R

.A
Created a new atom named: OP1 within residue: .R

Created a new atom named: OP2 within residue: .R

Created a new atom named: H5' within residue: .R

Created a new atom named: H5'' within residue: .R

Created a new atom named: H2' within residue: .R

Created a new atom named: H2'' within residue: .R

Added missing heavy atom: .R

.A
Added missing heavy atom: .R

.A
Created a new atom named: OP1 within residue: .R

Created a new atom named: OP2 within residue: .R

Created a new atom named: H5' within residue: .R

Created a new atom named: H5'' within residue: .R

Created a new atom named: H2' within residue: .R

Created a new atom named: H2'' within residue: .R

Created a new atom named: HO3' within residue: .R

Added missing heavy atom: .R

.A
Added missing heavy atom: .R

.A
  total atoms in file: 638
  Leap added 122 missing atoms according to residue templates:
   42 Heavy
   80 H / lone pairs
  The file contained 120 atoms not in residue templates
这个文件怎么处理呢？

回复此楼

» 猜你喜欢

» 本主题相关价值贴推荐，对您同样有帮助:

如何做动力学模拟pdb文件已经有4人回复
把一个pdb的蛋白质复合物保存成prmtop 和inpcrd 文件已经有3人回复
如何从下载的PDB文件中提取酶的活性中心已经有6人回复
如何制作简单的化学分子的pdb文件已经有11人回复
pdb蛋白的处理已经有7人回复
pdb文件的处理已经有5人回复
pdb文件的处理已经有4人回复
pdb文件中加入氢原子已经有7人回复
AutoDock产生的结果dlg文件转化成pdb文件已经有13人回复
【求助】如何合并文件 pdb psf 已经有4人回复
【求助】psf文件的生成已经有19人回复
【求助】用于ligplot的pdb文件究竟应如何准备? 已经有3人回复

1楼 2010-04-26 15:21:04

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

licaiqin

铜虫 (小有名气)

应助: 0 (幼儿园)
金币: 135.7
散金: 24
红花: 1
帖子: 112
在线: 19.1小时
虫号: 966779
注册: 2010-03-10
专业: 理论和计算化学

引用回帖:

Originally posted by wujiangjie at 2010-05-31 09:08:05:
应该是某些定义在Amber里面和你现在的pdb文件中定义不同导致的，那时我做DNA时就遇到过这种情况，然后按照要求稍加修改就好了

谢谢哈！

回复此楼

10楼2010-05-31 10:55:53

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

查看全部 14 个回答

wujiangjie

木虫 (正式写手)

应助: 0 (幼儿园)
金币: 7947.1
散金: 34
红花: 2
帖子: 444
在线: 72.9小时
虫号: 578671
注册: 2008-07-04
专业: 生物化工与食品化工

★
小木虫(金币+0.5):给个红包，谢谢回帖交流

楼主，你这个是处理什么物质的pdb文件？

赞一下(1人)

回复此楼

3楼2010-05-27 09:29:36

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

张军帅

木虫 (正式写手)

应助: 0 (幼儿园)
贵宾: 0.005
金币: 1037.1
散金: 800
红花: 1
帖子: 551
在线: 79小时
虫号: 985303
注册: 2010-03-29
性别: MM
专业: 天然药物化学

★
小木虫(金币+0.5):给个红包，谢谢回帖交流

你用的什么软件啊

赞一下(1人)

回复此楼

人生若只如初见

4楼2010-05-27 09:32:53

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

gcl600754

应助: (幼儿园)
在线:
虫号: 833652

★ ★
小木虫(金币+0.5):给个红包，谢谢回帖交流
lei0736(金币+1):谢谢 2010-05-30 09:45:50

是不是因为你的有些原子定义在Amber力场没有，你试试对比看看，再稍作修改，应该就可以了

赞一下(2人)

回复此楼

7楼2010-05-30 09:15:44

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

查看全部 14 个回答

最具人气热帖推荐 [查看全部]		作者	回/看	最后发表

[基金申请] 长年满屏的广告，版主太不责任了。基金也等的急 +4	gltch 2026-08-12	4/200	2026-08-12 16:08 by eulota
[基金申请] filecode +13	documentary 2026-08-10	15/750	2026-08-12 15:56 by 云上清扬
[论文投稿] 职称评审，求友友推荐见刊最快的期刊 +4	工厂打螺丝 2026-08-08	4/200	2026-08-12 09:18 by hansi2025
[基金申请] 综述论文作为代表作会不会影响评审专家的印象分？ +11	yufeiwaner 2026-08-09	13/650	2026-08-12 08:17 by yufeiwaner
[基金申请] 是这周出结果还是下周出结果？ +3	yuleib84 2026-08-11	3/150	2026-08-11 21:53 by jnhyjjm
[基金申请] 小木虫上这么多卖论文的，真有人买论文么？感觉没必要啊 +8	Tide man 2026-08-10	9/450	2026-08-11 20:39 by beefly
[基金申请] 帮忙看看fileCode +7	wwncly 2026-08-10	13/650	2026-08-11 19:36 by 冰心玉壶晴
[基金申请] 什么时候出结果，有咨询渠道？？？ +3	Tide man 2026-08-11	3/150	2026-08-11 17:54 by kudofaye
[基金申请] 听说今天filecode变了 +26	布布和一二 2026-08-06	49/2450	2026-08-11 13:18 by WH3796
[基金申请] 确定了，国自然21号放榜 +6	布布和一二 2026-08-10	7/350	2026-08-10 19:15 by 2000zf36392
[基金申请] 静等基金结果 +5	gjjjzhong 2026-08-10	16/800	2026-08-10 17:19 by Tide man
[基金申请] 据悉今年马上要出结果了 +7	瞬息宇宙 2026-08-10	8/400	2026-08-10 12:42 by Vivilian
[基金申请] 这样的filecode谁见过 +11	布布和一二 2026-08-08	22/1100	2026-08-10 11:10 by wmfsnow
[基金申请] 面上项目filecode邪修 +5	西山十月 2026-08-09	7/350	2026-08-10 07:32 by 仁砚薪传
[基金申请] fileCode有新解读？ +10	Tide man 2026-08-08	18/900	2026-08-09 12:55 by 仁砚薪传
[基金申请] 关于豆爷回答的JTJC与%2F数量 +5	yang182083 2026-08-06	7/350	2026-08-08 18:29 by zhanghaozhu
[基金申请] 国基金的申报应该改成非等额制，评价高的钱多评价低的钱少，但是增加资助率 +7	a089 2026-08-07	7/350	2026-08-08 18:05 by gltch
[基金申请] 固定端突然变了，今天 +6	archvillain 2026-08-06	10/500	2026-08-07 16:03 by 医学老男孩
[基金申请] 大家散了吧，后缀研究没有意义，别浪费时间了，过好目前的每一天，不要焦虑 +5	Tide man 2026-08-06	7/350	2026-08-07 13:11 by 医学老男孩
[基金申请] filecode +14	等待解的谜 2026-08-06	19/950	2026-08-07 12:20 by wlwhappy

24小时热门版块排行榜

licaiqin

[交流] 【求助】PDB文件的处理 已有7人参与

» 猜你喜欢

» 本主题相关价值贴推荐，对您同样有帮助:

licaiqin

wujiangjie

张军帅

gcl600754

[交流] 【求助】PDB文件的处理已有7人参与