Re: [AMBER] Problem in installing AMBER 20 Ubantu ; configuring molecules from own data obtained from Gaussian

From: David A Case <>
Date: Wed, 29 Sep 2021 08:58:51 -0400

On Wed, Sep 29, 2021, Satya Pal Singh wrote:

>1: The installation instructions when followed exactly on ubantu is
>asking for installation of more files; showing messages as Unable to
>locate package zlib1g-dev etc.(See Screenshots) There were others but I
>have removed or updated as required with the help of answer available on
>websites. I have installed zlib1g-dev but not working yet.

Are you working from these instructions: ?

I don't see any mention of zlib1g-dev there. It would be great if you could
provide details of what changes you needed to make, to help us update the
web page as needed.

>3: pthon-mathplotlib is not available...

I would recommend using the run_cmake script that is provided, which will
download a miniconda version of python with all of the needed components.
>4: Please guide us stepwise exactly how to complete the installation in
>perfect manner. The documented commands do not appear to work.

Can you say more than "do not appear to work"? What did you try, and what
was the result?

>5: Further we shall study liquid crystal molecule properties of which we
>have already obtained optimized structures using Gaussian09. We want to
>provide/fetch the optimized coordinates into Amber Input data and want to
>add some other guest atoms or group of atoms to observe the reorganization
>process at molecular scale. Kindly guide us how to do that?

Amber is probably not the program you want for this part of the task. You
will want to create a PDB-format file that has all the components that you
wish to simulate. People on the list may have suggestions here, but
something that permits interactive model-building seems required.

Having said that, please note that Amber is a molecular mechanics program,
primarily devoted to biomolecules. If you wish to simulate liquid crystals,
you will need to generate force field descriptions for all your components.
Tutorial 2.1 can help you get started on this procedure. A good
recommendation is to find a published paper that uses Amber to do
simulations similar to the ones you want to carry out, and see how things
were done there.

....good luck....dac

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Received on Wed Sep 29 2021 - 06:00:02 PDT
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