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

考研调剂-材料类-284 已经有14人回复
327求调剂已经有11人回复
08工科求调剂290分已经有11人回复
一志愿985初试354分生物调剂已经有3人回复
一志愿2110，化学学硕310分，本科重点双非求调剂已经有13人回复
353求调剂已经有8人回复
308求调剂已经有16人回复
334求调剂已经有14人回复
一志愿0807 数一英一 313 有没有二轮调剂已经有7人回复
复试调剂，一志愿郑州大学材料与化工289分已经有14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

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

[考研] 考研求调剂 +4	雯??? 2026-04-08	4/200	2026-04-08 21:44 by 土木硕士招生
[考研] 327求调剂 +12	Xxjc1107. 2026-04-06	12/600	2026-04-08 16:46 by luoyongfeng
[考研] 一志愿哈工大，初试329，求环境科学与工程调剂！ +11	余未辛 2026-04-06	11/550	2026-04-08 15:21 by screening
[硕博家园] 有没有学校材料专业收跨调(一志愿085410) +3	momo(上岸版) 2026-04-06	6/300	2026-04-08 14:53 by 化学521
[考研] 一志愿生物与医药，296分，求调剂 +14	66鹿 2026-04-03	16/800	2026-04-08 10:38 by tjzhao
[考研] 288环境专硕,求调材料方向 +35	lllllos 2026-04-04	39/1950	2026-04-07 23:24 by 一只好果子?
[考研] 363求调剂 +9	zh096 2026-04-04	9/450	2026-04-07 21:51 by 418490947
[论文投稿] Decision: Revise for Editor还会送审吗 100+3	CccccccccFD 2026-04-04	5/250	2026-04-07 10:58 by 北京莱茵润色
[考研] 信工所11408 340分本科西安交大自动化 +3	moontrek 2026-04-06	3/150	2026-04-07 09:56 by chongya
[考研] 307求调剂 +3	所念及所望 2026-04-06	3/150	2026-04-06 17:30 by 土木硕士招生
[考研] 070300化学学硕311分求调剂 +11	梁富贵险中求 2026-04-04	13/650	2026-04-06 07:24 by houyaoxu
[考研] 一志愿211，化学学硕，310分，本科重点双非，求调剂 +13	努力奋斗112 2026-04-04	13/650	2026-04-06 07:13 by jj987
[考研] 085500机械专硕初试288求调剂 +3	GZJguo666- 2026-04-05	3/150	2026-04-05 18:06 by jkddd
[考研] 313求调剂 +5	海日海日 2026-04-04	7/350	2026-04-05 13:58 by imissbao
[考研] 材料调剂 +7	dxy调剂 2026-04-04	7/350	2026-04-05 09:15 by 陌秋26
[考研] 男生，一志愿沪9生物学071000，初试308求调剂 +3	刘墨墨 2026-04-04	3/150	2026-04-05 08:26 by barlinike
[考研] 321求调剂 +6	认真求上学 2026-04-03	6/300	2026-04-04 19:51 by dongzh2009
[考研] 生物学硕341求调剂 +4	你笑起来像云朵 2026-04-03	4/200	2026-04-03 10:32 by macy2011
[考研] 一志愿安徽大学0817化学工程与技术，求调剂 +14	我不是只因 2026-04-02	15/750	2026-04-03 09:49 by 蓝云思雨
[考研] 调剂 +7	祉岷. 2026-04-02	7/350	2026-04-03 09:11 by 花呗还欠600

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