[AMBER] Error while using Parmchk2

From: Sodiq Waheed <sowaheed.mtu.edu>
Date: Tue, 16 Jun 2020 12:51:22 -0400


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

The warning message is:
"Warning: Atom type (SI) is not in PARMCHK.DAT; using default values
         for improper_flag [0], group_id [0], and equivalent_flag [0].
Warning: No mass information for atom type (SI); set to 0.0.
         It is recommended to add the new atom type (SI) to PARMCHK.DAT."
Thank you!

Kind regards,

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Received on Tue Jun 16 2020 - 10:00:03 PDT
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