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标题: 求助:准备拓扑文件及坐标文件出错 [打印本页]

作者
Author:
caroline    时间: 2020-7-18 13:12
标题: 求助:准备拓扑文件及坐标文件出错
使用AMBER模拟绿色荧光蛋白,在准备准备拓扑文件及坐标文件时出现如下错误:


Warning: There is a bond of 9.047713 angstroms between:


Warning: There is a bond of 4.746564 angstroms between:


Warning: There is a bond of 4.181516 angstroms between:


Warning: There is a bond of 4.704681 angstroms between:


Warning: There is a bond of 4.666477 angstroms between:


Warning: There is a bond of 4.083635 angstroms between:


Warning: There is a bond of 7.175441 angstroms between:


Warning: There is a bond of 3.032060 angstroms between:


Warning: There is a bond of 4.329275 angstroms between:


Warning: There is a bond of 3.076905 angstroms between:


Warning: There is a bond of 7.620519 angstroms between:


Warning: There is a bond of 4.933300 angstroms between:


Warning: There is a bond of 5.736748 angstroms between:


Warning: There is a bond of 4.497794 angstroms between:


Warning: There is a bond of 3.046111 angstroms between:


Warning: There is a bond of 5.293748 angstroms between:


Warning: There is a bond of 3.212249 angstroms between:


Warning: The unperturbed charge of the unit (-6.000003) is not zero.
FATAL:  Atom .R<VAL 65>.A<H3 17> does not have a type.
FATAL:  Atom .R<ET 76>.A<S 1> does not have a type.
FATAL:  Atom .R<NMET 77>.A<H 20> does not have a type.
FATAL:  Atom .R<ET 88>.A<S 1> does not have a type.
FATAL:  Atom .R<NMET 89>.A<H 20> does not have a type.
FATAL:  Atom .R<ET 155>.A<S 1> does not have a type.
FATAL:  Atom .R<NMET 156>.A<H 20> does not have a type.
FATAL:  Atom .R<ET 222>.A<S 1> does not have a type.
FATAL:  Atom .R<NMET 223>.A<H 20> does not have a type.


Error: Failed to generate parameters


Warning: Parameter file was not saved.
输入文件如下所示:
source leaprc.protein.ff14SB
set default PBRadii mbondi3
loadAmberPrep cro.prepin
loadAmberParams frcmod2.cro
loadAmberParams frcmod1.cro
x = loadPDB gfp.pdb
saveAmberParm x gfp.parm7 gfp.rst7
quit
这个该如何解决呢?



作者
Author:
DoubeeTwT    时间: 2020-7-23 11:32
将PDB文件中的H全部删除让amber自己补H
或者用pdb4amber对原子名进行修改
作者
Author:
caroline    时间: 2020-7-23 15:45
DoubeeTwT 发表于 2020-7-23 11:32
将PDB文件中的H全部删除让amber自己补H
或者用pdb4amber对原子名进行修改

谢谢,已解决
作者
Author:
try    时间: 2021-9-17 21:10
caroline 发表于 2020-7-23 15:45
谢谢,已解决

您好,请问是怎样解决的Warning: There is a bond of 9.047713 angstroms between: 这个问题呢?感谢回复~




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