Re: [AMBER] Error while using Parmchk2

From: David A Case <>
Date: Wed, 17 Jun 2020 08:12:38 -0400

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

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.


AMBER mailing list
Received on Wed Jun 17 2020 - 05:30:03 PDT
Custom Search