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标题: 求助：构建环状DNA拓扑结构时发生'Atom have no type' [打印本页]

作者
Author: 不知去向的小狼 时间: 2021-6-24 01:17
标题: 求助：构建环状DNA拓扑结构时发生'Atom have no type'
使用oxDNA制作了一个环状DNA结构，现在用ambertools20 leap构建amber拓扑文件
命令如下：

pdb4amber -i 45e.pdb -o 45e-amber.pdb
tleap
>source leaprc.DNA.bsc1
>loadamberparams frcmod.ionsjc_tip3p
>dna = loadpdb 45e-amber.pdb
>check dna

这个时候提醒：

-- residue 23: duplicate [ O] atoms (total 2)
-- residue 23: duplicate [ P] atoms (total 2)

Warning: Atom names in each residue should be unique.
   (Same-name atoms are handled by using the first
   occurrence and by ignoring the rest.
   Many instances of duplicate atom names usually come
   from alternate conformations in the PDB file.)

Created a new atom named: O within residue: .R<DG3 23>
  total atoms in file: 748
  Leap added 2 missing atoms according to residue templates:
   2 H / lone pairs
  The file contained 1 atoms not in residue templates

FATAL:  Atom .R<DG3 23>.A<O 35> does not have a type.

如图片所示为pdb的DG3上原子信息

请问各位大神，问题该如何破解

作者
Author: HZW 时间: 2021-7-5 15:41
oxDNA构建的核酸结构就算转换成PDB后还是考虑比较精细的CG模型，用amber的全原子力场来准备肯定不对罗，还是回归到用oxDNA模拟吧

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