You can use the "numbering system" in this case: Although the article
(
https://doi.org/10.1080/07391102.2023.2283812 ) explains it based
on Pd, you can apply it to similar molecules. For this, you only need
to introduce the Zn parameters to the assignv2.py program. The program
will then automatically assign the parameters.
For the program to work properly with Zn:
Change the line METAL=Pd to METAL=Zn in the GitHub repository program
(
https://github.com/bkurt00/palladiumFF2/blob/main/assign_v2/assign_v2.py).
Introduce the relevant atoms to parmchk2.
Add the Zn parameters to the following databases:
database_mass=[]
database_bond= []
database_angle= []
database_dihedral= []
database_improper= []
database_nonbond= []
The program uses this section as a database. Then, load your mol2
file, and it will prepare your frcmod file compatible with gaff. Once
you perform this one-time setup, you can convert all Zn mol2 files
with a single click.
saverio lemme via AMBER <amber.ambermd.org>, 29 May 2024 Çar, 14:01
tarihinde şunu yazdı:
>
> Hi,
> It is possible to use the Center ID 4 - Metal Center Type
> Zn-CCHH in the case one H is a HID and the other H is
> a HIE.
> In this case I receive many errors.
>
> Thanks in advance.
>
> Saverio Lemme
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed May 29 2024 - 04:30:02 PDT
