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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
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licaiqin

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[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？
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1楼2010-04-26 15:21:04
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gaoqunqunl

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lei0736:请勿多次无意义顶贴 2010-05-14 20:05:01
群主好难啊
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2楼2010-05-14 17:10:13
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wujiangjie

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楼主，你这个是处理什么物质的pdb文件？
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3楼2010-05-27 09:29:36
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张军帅

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你用的什么软件啊
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人生若只如初见
4楼2010-05-27 09:32:53
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licaiqin

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是一种酶
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5楼2010-05-27 15:42:05
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licaiqin

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是Amber9
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6楼2010-05-27 15:42:28
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gcl600754

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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
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7楼2010-05-30 09:15:44
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wujiangjie

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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
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8楼2010-05-31 09:08:05
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licaiqin

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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！
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9楼2010-05-31 10:55:31
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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！
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10楼2010-05-31 10:55:53
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