[AMBER] How to minimize average structure (pdb) using Amber 16

From: priya murugan <priyajenny712.gmail.com>
Date: Thu, 14 Oct 2021 00:23:48 +0800

Hi everyone,

I have been using Amber 16 for months to run MD simulations and do the
analysis for MD trajectories. Everything goes fine with Amber 16. After
simulation, I was required to extract the average PDB structure from the
2drms plot of MD simulation trajectories.

So, I used CPPTRAJ to run the script and successfully extracted the average
PDB structure from the trajectories. But, now the problem is I need to
minimise these average structures in PDB format to eliminate the bad
contacts and optimised them as well as to prepare these structures for
further docking steps.

Hence, suggest how to run minimisation for PDB structure using Amber 16. I
had the experience of running minimization of topology files in (parm7,
promtop) format as per following the Amber Tutorial. However, I'm clueless
about how to run minimization using the structure in PDB format. I have
almost 40 average PDB structures. So, suggest the most efficient method to
conduct minimization in Amber 16.

I'll be highly grateful if you can help me to sort this out.

Thanks & Regards

*Doctor of Philosophy*
Theoretical and Computational Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400, Selangor, Malaysia

E-mail: GS60358.student.upm.edu.my
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Received on Wed Oct 13 2021 - 09:30:02 PDT
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