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licaiqin

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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？

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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

ope123456789

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小木虫(金币+0.5):给个红包，谢谢回帖交流
ghcacj(金币+3):谢谢 2010-07-08 14:12:06

因为你的pdb文件里有非正常残基DA,amber是无法识别的，所以它自动的将这些原子加入库里面，要为这个非正常残基重新定义一套力场，然后加入库中，才能做下去，这要做很多的前期工作啊.依我的观察，你这个应该是一个DNA分子片段的pdb，你的力场没选对，你tleap或xleap后用source leaprc.ff99SB,应该就不会出问题了