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

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Fri, 27 Dec 2019 16:07:29 +0000

I have received the prepi files and frcmod files from a collegue.
These are the contents of acetonitrile.prepi

    0 0 2

Acetonitrile from Kollman and co authors with HF 6-311G* derived charges, modified NY
molecule.res
C3N INT 0
CORRECT OMIT DU BEG
  0.0000
   1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
   2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
   3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
   4 N1 NY M 3 2 1 1.540 111.208 180.000 -0.533000
   5 C2 CY M 4 3 2 1.116 62.875 154.931 0.481000
   6 C3 CT M 5 4 3 1.435 173.934 -165.471 -0.479000
   7 H4 HC E 6 5 4 1.038 112.476 54.290 0.177000
  8 H5 HC E 6 5 4 1.087 112.347 170.861 0.177000
   9 H6 HC E 6 5 4 1.097 107.907 -67.912 0.177000


LOOP

IMPROPER

DONE
STOP

Acetonitrile.frcmod

remark goes here
MASS

BOND

ANGLE
CY-CT-HC 35.000 110.000 from Kollman

DIHE

IMPROPER

NONBON

Thanks sir,












Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

From: Carlos Simmerling<mailto:carlos.simmerling.gmail.com>
Sent: 25 December 2019 17:21
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] Minimization equilibration of protein+ligand prior to TI setup

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 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.
>
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 27 2019 - 08:30:02 PST
Custom Search