On Tue, Jun 16, 2020, Sodiq Waheed wrote:
>
>I am generating parameters for a system that contains an organosilicon
>compound as the substrate. During the conversion of the mol2 file of the
>substrate to frcmod file using Parmchk2, it gave the below warning message
>and the generated frcmod file (see attachments) does not contain bonding
>information for angles, dihedral and bonds involving the silicon as well as
>the polarizability parameter of the silicon. Please, how can I fix this
>issue?
You can't: the GAFF force field does not (yet?) support silicon. Adding
a new Si atom type would require a lot of work and a deep understanding
of how antechamber works.
But you don't necessarily need to use parmchk2: there may be parameters
in the literature that can help, or you may be able to start with carbon
and then convert to silicon by analogy.
....regards...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 17 2020 - 05:30:03 PDT
