关于amber中parmchk2的问题

sun666

初学Amber，请教各位老师parmchk2的功能。以有机分子分子为例，个人认为是检查有机分子的键长，键角，二面角等参数是否在Amber自带默认力场（有机分子为GAFF）中是否包含。但是我在自己做的时候发现，对于一个有机分子用parmchk2产生的frcmod文件与，含有两个有机分子的结构（有机分子结构一样）产生的frcmod文件不同。两个有机分子产生的frcmod文件明显缺失的参数很多。按我的理解两个分子的键长，键角等参数一样产生的frcmod文件内容应该一样，是哪里的问题呢
两个结构文件及frcmod文件见附件

另外对于缺失的参数该如何获取呢。从MCPB.py的参考文献“MCPB.py: A Python Based Metal Center Parameter Builder”的附件中[size=10.0001pt]Examples2的输入文件中[size=13.3335px]FAJYAR01_mcpbpy.frcmod文件中看到了“Created by Seminario method using MCPB.py [size=13.3335px]”
不知道MCPB.py是否还有创建参数的功能，该如何使用呢。

rpestana94

Be aware that the two files are not the same, for the 1507.mol2 you don't have the bonds information inside the file, meanwhile the 2507.mol2 has it. If you are using vmd to check your structure I suggest using something different like chimerax or maestro, vmd connects the dots for you so this kind of things you can't see it.

Try with a mol2 file with all the information

sun666

rpestana94 发表于 2021-7-5 06:05
Be aware that the two files are not the same, for the 1507.mol2 you don't have the bonds information ...

Thank you very much for your answer，I have understood my mistake.  I  would like to ask you the problem of using parmchk2 to generate  FRCMOD file contained the "ATTN, need revision" item how to solve.

sun666

遇到一个奇怪的问题，对于同一个有机分子（如一楼附件），用parmchk2检出很多缺失。但是使用acpype.py进行生产GAFF力场的itp文件却丝毫没有问题（生成用于GMX的itp文件与用amber的parmchk2生产的FRCMOD文件见附件）。这我感觉很奇怪，acpype.py是调用的Antechamber，按理来说这两种区别的只是分别用于GMX和amber的格式，但是参数等应该一样。现在的这个问题该如何解释呢。我该信哪个呢

rpestana94

sun666 发表于 2021-7-4 22:01
Thank you very much for your answer，I have understood my mistake.  I  would like to ask you the p ...

The way to solve this is doing QM calculation to get the parameters you need or look for them in paper or website, for example here are some parameters: http://amber.manchester.ac.uk/

rpestana94

sun666 发表于 2021-7-5 10:12
遇到一个奇怪的问题，对于同一个有机分子（如一楼附件），用parmchk2检出很多缺失。但是使用acpype.py进行 ...

For this I'm not sure, I think that should be the same but I don't know how gromacs treats the parameters for the force field and how it actually estimates it.