I think DAC also wanted to know how you made the ligand files - did
Jorgensen provide Amber libraries? Or did you do the conversion of their
parameters to Amber? Many things can go wrong when creating library
files....
On Tue, Dec 24, 2019, 10:44 AM Debarati DasGupta <
debarati_dasgupta.hotmail.com> wrote:
> 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.
>
> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
> 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 Wed Dec 25 2019 - 04:00:02 PST
