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] 303求调剂 +3	睿08 2026-03-17	3/150	2026-03-17 15:24 by 哦哦123
[考研] 278求调剂 +3	Yy7400 2026-03-13	3/150	2026-03-17 08:24 by laoshidan
[考研] [导师推荐]西南科技大学国防/材料导师推荐 +3	尖角小荷 2026-03-16	6/300	2026-03-16 23:21 by 尖角小荷
[考研] 一志愿985，本科211，0817化学工程与技术319求调剂 +5	Liwangman 2026-03-15	5/250	2026-03-16 17:10 by 我的船我的海
[考研] 304求调剂 +5	素年祭语 2026-03-15	5/250	2026-03-16 17:00 by 我的船我的海
[考研] 304求调剂 +3	曼殊2266 2026-03-14	3/150	2026-03-16 16:39 by houyaoxu
[考研] 311求调剂 +5	26研0 2026-03-15	5/250	2026-03-16 16:21 by a不易
[考研] 0703化学调剂，求各位老师收留 +8	秋有木北 2026-03-14	8/400	2026-03-16 15:21 by 哦哦123
[考研] 285求调剂 +6	ytter 2026-03-12	6/300	2026-03-16 15:05 by njzyff
[教师之家] 焦虑 +7	水冰月月野兔 2026-03-13	9/450	2026-03-16 10:00 by Quakerbird
[基金申请] NSFC申报书里申请人简历中代表性论著还需要在申报书最后的附件里面再上传一遍吗 20+5	NSFC2026我来了 2026-03-10	14/700	2026-03-15 23:53 by 不负韶华的虎
[考研] 331求调剂（0703有机化学 +5	ZY-05 2026-03-13	6/300	2026-03-14 10:51 by Jy?
[考研] 332求调剂 +3	zjy101327 2026-03-11	6/300	2026-03-13 22:48 by JourneyLucky
[考研] 0703，333分求调剂一志愿郑州大学-物理化学 +3	李魔女斗篷 2026-03-11	3/150	2026-03-13 22:24 by JourneyLucky
[考研] 336求调剂 +6	Iuruoh 2026-03-11	6/300	2026-03-13 22:06 by JourneyLucky
[考研] 333求调剂 +3	球球古力 2026-03-11	3/150	2026-03-13 21:27 by JourneyLucky
[考研] 328化工专硕求调剂 +4	。，。，。，。i 2026-03-12	4/200	2026-03-13 14:44 by JourneyLucky
[考博] 福州大学杨黄浩课题组招收2026年专业学位博士研究生，2026.03.20截止 +3	Xiangyu_ou 2026-03-12	3/150	2026-03-13 09:36 by duanwu655
[考研] 283求调剂，材料、化工皆可 +8	苏打水7777 2026-03-11	10/500	2026-03-13 09:06 by Linda Hu
[考研] 420求调剂 +4	莫向外求11 2026-03-10	6/300	2026-03-12 14:41 by ruiyingmiao

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