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

From: Liao <>
Date: Wed, 13 Oct 2021 13:05:27 -0500

Hello Priya,

I’ve done that before, what I did was that each structure was treated as a starting frame in a new MD simulation. So you will have 40 new short trajectories. In your case you should use the rst7 format files to start, and not PDB format. cpptraj will give you that.
From the new rst7 files, run the minimization first (gradually releasing restraints), and then the standard short equilibration at room temp if that’s desired.
Hope it is helpful.


> On Oct 13, 2021, at 11:24 AM, priya murugan <> wrote:
> 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:
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Received on Wed Oct 13 2021 - 11:30:02 PDT
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