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

From: David A Case <>
Date: Tue, 9 Oct 2018 08:17:47 -0400

On Tue, Oct 09, 2018, Sadra Aghajani wrote:
> 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?

There is no way for leap to ignore the missing parameters, as far as I
know. You can use generic "X -a1-a2-X " entries in your frcmod file,
with zero force constants.


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Received on Tue Oct 09 2018 - 05:30:02 PDT
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