I have figured out the reason. For those who may have faced the same problem. I looked into the code and found that tinker_to_amber is looking for the line " Atom Type Definition Parameters" in analout file. But for some reason, Tinker's analyze utility generates analout file with the line "Atom Definition Parameters". So, what you need to do is just to add word Type manually. And it works.
Sorry for wasting your time.
________________________________
От: Kliuchnikov, Evgenii <Evgenii_Kliuchnikov.student.uml.edu>
Отправлено: 22 июля 2020 г. 14:37
Кому: amber.ambermd.org <amber.ambermd.org>
Тема: [AMBER] tinker_to_amber force fields
Dear Amber users,
I am trying to do MD simulation of RNA with Amoeba force filed, but I can't generate prmtop file for that. The process ends with the notification:
no success getting Atom Type Definition Parameters
when I use amoebabio09 or amoebabio18
And If I use amoebapro13 it gives:
no success finding Atoms in System!
My question is, what actual force fields are used in tinker_to_amber (I mean both, Amber and Amoeba)? And is it possible that tinker_to_amber just does not support RNA?
Thank you in advance,
Evgenii
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Received on Wed Jul 22 2020 - 12:30:05 PDT
