Re: [AMBER] how to check if bad contacts exsist after min heat jobs

From: David Case <>
Date: Thu, 27 Jun 2019 02:11:11 +0000

On Wed, Jun 26, 2019, Vaibhav Dixit wrote:

>The min.rst7 still has close contacts (when I created a pdb and loaded back
>in leap).
>Is there a faster way to check structures after min, heat jobs to ensure if
>they are ok for the next steps in MD simulations?

The "checkstructure" command in cpptraj is pretty fast, and can take an rst7
file (no need to convert to PDB).

If minimization doesn't remove close contacts, there may be something wrong,
such as bonds going through rings. Take a visual look at regions that still
have bad contacts to see if there is something that is preventing the contacts
from being relieved.


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Received on Wed Jun 26 2019 - 19:30:02 PDT
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