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

>论坛更新日志 (4355)
>基金申请 (433)
>虫友互识 (287)
>论文投稿 (234)
>文献求助 (128)
>导师招生 (126)
>考博 (96)
>硕博家园 (85)
>休闲灌水 (74)
>考研 (29)
>公派出国 (24)
>教师之家 (20)
>论文道贺祈福 (18)
>博后之家 (13)
>找工作 (13)
>健康生活 (12)

返回列表

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

gaoqunqunl

金虫 (小有名气)

应助: 0 (幼儿园)
金币: 936.2
散金: 14
红花: 1
帖子: 106
在线: 24.4小时
虫号: 961722
注册: 2010-03-05
专业: 生化分析及生物传感

★
小木虫(金币+0.5):给个红包，谢谢回帖交流
lei0736:请勿多次无意义顶贴 2010-05-14 20:05:01

群主好难啊

回复此楼

2楼2010-05-14 17:10:13

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

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

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

是一种酶

回复此楼

5楼2010-05-27 15:42:05

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

是Amber9

回复此楼

6楼2010-05-27 15:42:28

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

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
ghcacj(金币+2):谢谢 2010-05-31 09:22:50

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

赞一下(2人)

回复此楼

8楼2010-05-31 09:08:05

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

o 谢谢哈！

回复此楼

9楼2010-05-31 10:55:31

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:

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

相关版块跳转我要订阅楼主 licaiqin 的主题更新

返回列表

最具人气热帖推荐 [查看全部]		作者	回/看	最后发表

[基金申请] 如果此刻你正在为国基感到焦虑，不妨来听听这首《基金之外》 +8	scalable 2026-08-24	8/400	2026-08-25 12:52 by jnhyjjm
[基金申请] 人气不行了 +11	fansofjerry 2026-08-21	11/550	2026-08-25 11:04 by 孤独的英雄6
[教师之家] 导师吐槽：我怎么摊上了这么个极品研究生！ +3	苏东坡二世 2026-08-23	3/150	2026-08-25 10:35 by shisan1313
[基金申请] 2026年的国家社科基金项目通讯评审的新规则与新动向、新挑战 +5	process2012 2026-08-23	7/350	2026-08-25 09:42 by huixian257
[基金申请] 我面上完蛋了 +13	且听虎啸 2026-08-20	14/700	2026-08-25 09:10 by mrkang
[基金申请] 范进中举一文的中心思想 +7	炎黄贵胄 2026-08-22	8/400	2026-08-25 08:48 by ZJTJZ
[基金申请] 只有每年这种时候来逛逛小木虫 +25	yaoyewhu2008 2026-08-20	27/1350	2026-08-25 08:01 by Equinoxhua
[基金申请] 明天应该可查了！？ +5	chengyan1220 2026-08-23	5/250	2026-08-24 23:28 by 我4大白菜
[基金申请] 能否退出参与的面上项目解除限项 +21	koalala 2026-08-24	24/1200	2026-08-24 19:25 by 家与远方
[基金申请] filecode，4个jtjc了 +14	ziyangfang 2026-08-19	17/850	2026-08-24 18:37 by 哈哈蛤？
[基金申请] 今日不放榜？网传国自然预计 8 月 27 日可查结果 +17	医学老男孩 2026-08-20	21/1050	2026-08-24 14:21 by refreshing11
[基金申请] 让我中一个面上吧！ +13	大萍1987 2026-08-20	16/800	2026-08-24 10:23 by 太傻了
[教师之家] 跳槽后在研项目怎么办？ +5	简单化xn 2026-08-22	10/500	2026-08-23 12:38 by 简单化xn
[基金申请] 今天放榜吗？ +15	布布和一二 2026-08-19	16/800	2026-08-23 09:55 by 张春生
[基金申请] 时间戳今天，20号变了 +5	archvillain 2026-08-20	5/250	2026-08-22 06:12 by hui_daxiao
[基金申请] 看来今天不会放榜了？ +8	chengyan1220 2026-08-21	11/550	2026-08-21 17:52 by dcqxinyang
[基金申请] 时间戳又变了 +13	wuchongjun 2026-08-20	19/950	2026-08-21 17:21 by 紫杉醇
[基金申请] 应该是下周三26日公布了吧？ +4	哈哈蛤？ 2026-08-21	4/200	2026-08-21 10:58 by Vivilian
[基金申请] 今天放榜没戏了吧 +9	yuleib84 2026-08-19	11/550	2026-08-21 10:06 by gltch
[基金申请] 基金啊基金 +4	longfie172 2026-08-20	4/200	2026-08-21 08:58 by mark mao

24小时热门版块排行榜

[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:

[交流] 【求助】PDB文件的处理已有7人参与