求助：准备拓扑文件及坐标文件出错

caroline

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？

DoubeeTwT

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

caroline

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

try

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~