Hi Prof Case,
I have used Prof William Jorgensen’s parameters for C3N (it’s 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
