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[AMBER] amber 倒入蛋白PDB生成参数时提示出错

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发表于 2016-3-19 12:14:31 | 显示全部楼层 |阅读模式

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   本人最近在学习amber遇到了一个问题一直都没有解决,自己弄了半边天也没有搞定,想请amber大神帮忙看下这个问题该怎么解决:
   > source leaprc.gaff
> a=loadpdb h2.pdb
Loading PDB file: ./h2.pdb
......
Leap added 185 missing atoms according to residue templates:
       185 H / lone pairs
  The file contained 188 atoms not in residue templates
> check a
Checking 'a'....
WARNING: The unperturbed charge of the unit: -5.000000 is not zero.
FATAL:  Atom .R<NALA 1>.A<H 13> does not have a type.
FATAL:  Atom .R<TYR 3>.A<HB1 22> does not have a type.
FATAL:  Atom .R<CYS 4>.A<HB1 12> does not have a type.
FATAL:  Atom .R<ARG 5>.A<HB1 25> does not have a type.
FATAL:  Atom .R<ARG 5>.A<HG1 26> does not have a type.
FATAL:  Atom .R<ARG 5>.A<HD1 27> does not have a type.
FATAL:  Atom .R<ASP 6>.A<HB1 13> does not have a type.
FATAL:  Atom .R<ASP 6>.A<HD2 14> does not have a type.
FATAL:  Atom .R<ARG 7>.A<HB1 25> does not have a type.
FATAL:  Atom .R<ARG 7>.A<HG1 26> does not have a type.
FATAL:  Atom .R<ARG 7>.A<HD1 27> does not have a type.
......
Warning: Close contact of 0.971473 angstroms between .R<NALA 1>.A<H3 4> and .R<N ALA 1>.A<H 13>
Warning: Close contact of 0.807217 angstroms between .R<NALA 1>.A<H1 2> and .R<N ALA 1>.A<H 13>
Warning: Close contact of 1.061144 angstroms between .R<NALA 1>.A<N 1> and .R<NA LA 1>.A<H 13>
......
Checking parameters for unit 'a'.
Checking for bond parameters.
Checking for angle parameters.
check:  Errors:  188   Warnings: 472


后面的动力学参数就没法生成了!

发表于 2016-3-22 22:51:28 | 显示全部楼层
“The file contained 188 atoms not in residue templates” 问题在于有188个原子有问题,不是标准的氨基酸残基。
发表于 2017-9-3 15:52:41 | 显示全部楼层
请问出现这种问题的时候要删除孤对电子么?
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