How to resolve the atom type and/or the parameter missing problems in a QM/MM job?

[Dl Li]

Hi everyone,

 

I am trying the QM/MM simulations on an ion channel by the NEB method in NWCHEM-7.0. I have already got the topology and restart files for both reactants and products (required for NEB) with the aid of the “prepare” module. Next, I made the input file (*.nw) for QM/MM computation based on the document of NWCHEM. The error occurred once I start the job, which indicates “Unresolved atom types in fragment ***”.

 

(1) I have read the document which tells a manual way to correct the type. However, there are more 1000 amino residues in my system, which makes it impossible to correct the fragment manually one by one. Is there a program to do the conversion, if I got the Amber format parameter-topology ( *.prmtop) and input-coordinate files (*.inpcrd) by the “tleap” module (Amber)?

 

(2) The Fortran code that performs conversion from AMBER program parameter file format to NWChem is not available on the github website at present. Could anyone please help to fix the problem or send a copy to me?

 

(3) It is not clear when the Fortran code is really needed. Does it mean that if the code is implemented, all the AMBER program parameters will be converted which in turn resolved the errors in question(1)? If NOT, could anyone please explain how to resolve the type and/or the parameter missing problems efficiently (such as by a code)? It will be better if there is a tutorial for reference.

 

Thanks a lot for your help and looking forward to your reply.

 

Best,

Dailin

[Edoardo Aprà]

The Fortran code that performs conversion from AMBER program parameter file format to NWChem can be found at the URL

https://nwchemgit.github.io/amber-helper.tgz

More details at

https://nwchemgit.github.io/QMMM_Appendix.html#conversion-of-standard-amber-program-parameter-files

[霖]

Hi Edoardo,

Thanks for your reply and the code. Actually, I have read the contents  in your reply before. The questions I posted are just from the materials on that website. It is still not clear enough how to resolve the atom type and parameter missing problems automatically.

Best,

Dailin

------------------ 原始邮件 ------------------

发件人: "nwchem-forum" <edoard...@gmail.com>;

发送时间: 2021年3月12日(星期五) 上午9:51

收件人: "NWChem Forum"<nwchem...@googlegroups.com>;

主题: [nwchem-forum] Re: How to resolve the atom type and/or the parameter missing problems in a QM/MM job?

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[Edoardo Aprà]

Did you have a look at the README file and parameter-file.pdf that are bundled in https://nwchemgit.github.io/amber-helper.tgz ?