Re: [AMBER] Minimization equilibration of protein+ligand prior to TI setup

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Tue, 24 Dec 2019 14:44:24 +0000

Hi Prof Case,
I have used Prof William Jorgensenís parameters for C3N (itís a acetonitrile molecule).
I m setting up my protein in water simulation today in absence of the ligand to see what is the scenario.

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From: David Case<mailto:david.case.rutgers.edu>
Sent: Monday, December 23, 2019 9:37 PM
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] Minimization equilibration of protein+ligand prior to TI setup

On Mon, Dec 23, 2019, Debarati DasGupta wrote:

>I am trying to equilibrate my system (protein =286 residues, ligand is C3N (6 atoms)287-RES_ID) and I am providing the input files I used.

It's unlikley to be a problem with the input files. How did you make
the C3N residue library? Have you tried a test heating simulation
without the ligand? Or with just something like water there?

....dac


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Received on Tue Dec 24 2019 - 07:00:02 PST
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