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

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

085600材料与化工求调剂已经有3人回复
311求调剂已经有7人回复
303求调剂已经有3人回复
有没有道铁/土木的想调剂南林，给自己招师弟中～已经有7人回复
梁成伟老师课题组欢迎你的加入已经有10人回复
一志愿苏州大学材料工程（085601）专硕有科研经历三项国奖两个实用型专利一项省级立项已经有8人回复
070300化学319求调剂已经有3人回复
一志愿天津大学化学工艺专业（081702）315分求调剂已经有4人回复
268求调剂已经有7人回复
290求调剂已经有11人回复

» 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

[考研] 材料工程专硕274一志愿211求调剂 +6	薛云鹏 2026-03-15	6/300	2026-03-17 11:05 by 学员h26Tkc
[考研] 本人考085602 化学工程专硕 +15	不知道叫什么！ 2026-03-15	17/850	2026-03-17 10:13 by Sammy2
[考研] 0703化学336分求调剂 +3	zbzihdhd 2026-03-15	4/200	2026-03-16 23:52 by zbzihdhd
[考研] 328求调剂，英语六级551，有科研经历 +3	生物工程调剂 2026-03-16	4/200	2026-03-16 20:13 by Wangjingyue
[考研] 0703化学调剂 290分有科研经历，论文在投 +7	腻腻gk 2026-03-14	7/350	2026-03-16 10:12 by houyaoxu
[考研] 326求调剂 +3	mlpqaz03 2026-03-15	3/150	2026-03-16 07:33 by Iveryant
[考博] 东华理工大学化材专业26届硕士博士申请 +6	zlingli 2026-03-13	6/300	2026-03-15 20:00 by ryzcf
[考研] 070305求调剂 +3	mlpqaz03 2026-03-14	4/200	2026-03-15 11:04 by peike
[考研] 材料与化工 323 英一+数二+物化，一志愿：哈工大本人本科双一流 +4	自由的_飞翔 2026-03-13	5/250	2026-03-14 19:39 by hmn_wj
[考研] 中科大材料专硕319求调剂 +3	孟鑫材料 2026-03-13	3/150	2026-03-14 18:10 by houyaoxu
[考研] 308 085701 四六级已过求调剂 +7	温乔乔乔乔 2026-03-12	14/700	2026-03-14 10:49 by JourneyLucky
[基金申请] 有必要更换申报口吗 20+3	fannyamoy 2026-03-11	3/150	2026-03-14 00:52 by zhanghaozhu
[考研] 279求调剂 +3	抓着星星的女孩 2026-03-10	3/150	2026-03-13 23:47 by userper
[考研] 0805，333求调剂 +3	112253525 2026-03-10	3/150	2026-03-13 23:42 by JourneyLucky
[考研] 求材料调剂 +5	隔壁陈先生 2026-03-12	5/250	2026-03-13 22:03 by 星空星月
[考研] 290求调剂 +9	ADT 2026-03-11	9/450	2026-03-13 21:55 by JourneyLucky
[考研] 315求调剂 +9	小羊小羊_ 2026-03-11	10/500	2026-03-13 21:13 by SXNU李老师
[考研] 【0856】化学工程（085602）313 分，本科学科评估A类院校化学工程与工艺，诚求调剂 +7	小刘快快上岸 2026-03-11	7/350	2026-03-13 16:06 by ruiyingmiao
[考研] 08食品或轻工求调剂，本科发表3篇sci一区top论文，一志愿南师大食品科学与工程 +3	我是一个兵， 2026-03-10	3/150	2026-03-13 10:21 by Yuyi.
[考研] 290求调剂 +3	ADT 2026-03-13	3/150	2026-03-13 10:19 by peike

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