Hi Chinh,
Case by case:
For the the case which you have a large model which have more atoms than small model, it is hard to do that (modify large model based on QM optimized small model). This is due to the large model has more atoms than the small one and it is hard to determine how will the other atoms’ coordinates (which are not included in the small model but included in the large) will change. And under this condition, it may be OK to follow the standard procedure. Even the QM optimization of small model has a big influence on its structure, but the rigidity of the protein matrix will restrain the structure in reality. However, for the consistency purpose, you can update the generated frcmod file by replacing the metal containing equilibrium bond distances and angle values with values based on the crystal structure (and keep the corresponding force constants generated based on the QM calculation of the small model).
For the case that you have a large model and small model that have same atoms, for the large model you can perform a full geometry optimization when generating the ESP points (which will give you the same optimized structure as you obtained for the small model if they use the same level of theory and method for optimization).
Kind regards,
Pengfei
> On Sep 21, 2017, at 2:07 AM, Lê Ngọc Chính <lengocchinh2306.gmail.com> wrote:
>
> Dear Amber developer
>
> I have a question for you. In step 2 and step 3, after QM optimization of
> the small model, there were some changes in the position of the atoms.
> These changes have strong impact to perform MK charge, but QM inputs which
> were made from the step 1 did not depend on each other (the large and the
> small model). Is there a keywords or a way to regenerate the QM input for
> large model automatically after QM optimization for the small model? Or I
> must modify it by hand??
>
> --
> Best regards
> Chính
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Received on Sat Sep 23 2017 - 15:30:01 PDT
