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    

小木虫论坛-学术科研互动平台 » 计算模拟区 » 分子模拟 » Gromacs/Amber/NAMD » 【求助】PDB文件的处理
141/2返回列表12下一页
查看: 2990  |  回复: 13
只看楼主 @他人 存档 新回复提醒 (忽略) 收藏    在APP中查看

licaiqin

铜虫 (小有名气)

[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
  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:
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)
★
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)
★
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)
★
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)
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)
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

★ ★
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)
★ ★ ★
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)
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)
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
相关版块跳转 我要订阅楼主 licaiqin 的主题更新
141/2返回列表12下一页
普通表情 龙 兔 虎 猫 高级回复 (可上传附件)
信息提示
关闭
请填处理意见
关闭