[AMBER] Rigid body simulation of Nitrogenase's FeMo cluster

From: Sadra Aghajani <aghajanisadra.gmail.com>
Date: Tue, 9 Oct 2018 02:32:17 -0500

Dear all,

I want to simulate a truncated version of the FeMo cluster in Nitrogenase (PDB of the truncated model is attached).
I will be using GAFF for His, Cys and the homocitrate moieties and I want to keep the structure of the FeMo cluster frozen to the crystal structure.
I have made .mol2 and .frcmod files for the cluster where I manually made atom types and made the bonds and angles between the atoms in the cluster very stiff (force constant of 500 for bonds and 200 for angles).
When I use Leap to make .prmtop and .inpcrd files, Leap gives me errors on the missing torsion parameters and doesn’t make the .prmtop and .inpcrd files.
Any idea how to fix that? Is there a way for Leap to ignore the missing parameters?

Thanks,
Sadra



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Received on Tue Oct 09 2018 - 01:00:02 PDT
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