Re: [AMBER] Acetonitrile Water Mix

From: Marcos Serrou do Amaral <marcossamaral.gmail.com>
Date: Fri, 7 Apr 2017 09:44:44 -0400

Hi,

I got them from Tables I (BOND, ANGLE, DIHEDRAL), II (column C for charges
in mol2 file), and III (NONBON).
I need to double check everything carefully. But, I just got some
preliminar results of ACN:WAT 60:40 v/v system and they look better when
compared with my previous gaff ACN simulation.


Best,

---
Marcos S.A.
On Fri, Apr 7, 2017 at 9:32 AM, Andreas Tosstorff <
andreas.tosstorff.cup.uni-muenchen.de> wrote:
> Thank you so much Marcos!
>
>
> Can you please tell me how you obtained the BOND, ANGLE and DIHEDRAL
> parameters and also the NONBON for CT and HC?
>
>
> Best,
>
> Andy
>
>
> On 04/07/2017 02:58 PM, Marcos Serrou do Amaral wrote:
> > Hi Andy,
> >
> > I am sending to you ACN parameter files for this new 6-site model.
> > In leap, you should use these lines:
> > source leaprc.water.tip3p
> > loadamberparams ACN_model.prm
> > ACN = loadmol2 acn-model.mol2
> >
> > Please, double check all parameters.
> >
> > HTH,
> >
> >
> > ---
> > Marcos S.A.
> >
> >
> > On Wed, Apr 5, 2017 at 12:08 PM, Andreas Tosstorff <
> > andreas.tosstorff.cup.uni-muenchen.de> wrote:
> >
> >> Dear all,
> >>
> >>
> >> thank you for your replies! As David pointed out, setting up the
> >> simulation was not the problem, but it's the separation of the two
> >> solvents, as seen in the attached pictures.
> >>
> >> After the suggested google search I came across a paper titled "New
> >> Six-site Acetonitrile Model for Simulations of Liquid Acetonitrile and
> its
> >> Aqueous Mixtures" by NIKITIN and LYUBARTSEV from 2007 (attached to this
> >> mail).
> >>
> >> They report that they were able to succesfully simulate
> water-acetonitrile
> >> mixtures with their acetonitrile model. They furthermore state that
> their
> >> model can easily be included into AMBER.
> >>
> >> So how do I do this?
> >>
> >> Do I write an .frcmod and .lib file for acetonitrile using the
> parameters
> >> (Lennard-Jones parameters, charge, what else?) they published and then
> >> rebuild my system in tleap?
> >>
> >>
> >> This is completely new to me so I would really appreciate your help!
> >>
> >>
> >> Best,
> >>
> >> Andy
> >>
> >>
> >>
> >> On 04/05/2017 05:00 PM, David Cerutti wrote:
> >>
> >>> You will not have an extra time with this if you want your simulation
> to
> >>> go
> >>> a long time.  For starters you can use the AddToBox utility in
> amber/bin
> >>> (run with no arguments to see the list of things you can do).  That
> will
> >>> help you randomly mix acetonitrile and water initially (make sure to
> >>> minimize before starting dynamics).
> >>>
> >>> But if you simulate just a few hundred acetonitriles and a thousand
> waters
> >>> (or whatever the ratio needs to be), then check after 50ns or so, and
> find
> >>> that they separate (which appears likely) you have as DAC said an
> >>> imbalance
> >>> in your FF and a parameter development problem.
> >>>
> >>> Once you get your solvents to stay mixed, round II: protein in solvent
> >>> mixture.  You could very well find that the protein gets coated in
> >>> acetonitrile and that the acetonitrile gets leached out of solution in
> the
> >>> process.  To determine whether THAT is realistic or not you will need
> the
> >>> right kind of experimental data.
> >>>
> >>> Dave
> >>>
> >>> On Apr 5, 2017 10:48 AM, "Sowmya Indrakumar" <soemya.kemi.dtu.dk>
> wrote:
> >>>
> >>> Hi Andreas,
> >>>> I am not sure if this is feasible.
> >>>> Since you already know the ratio, you can do the following
> >>>> 1.solvate you protein
> >>>> 2.replace some of the water with the other molecule. For instance,
> >>>> *addions* randomly replaces water with the ion you give.
> >>>> Regards
> >>>> Sowmya
> >>>> ________________________________________
> >>>> From: David A Case [david.case.rutgers.edu]
> >>>> Sent: Wednesday, April 05, 2017 4:37 PM
> >>>> To: AMBER Mailing List
> >>>> Subject: Re: [AMBER] Acetonitrile Water Mix
> >>>>
> >>>> On Wed, Apr 05, 2017, Andreas Tosstorff wrote:
> >>>>
> >>>>> I am trying to simulate a protein in a 60% acetonitrile, 40% water
> >>>>>
> >>>> mixture.
> >>>>
> >>>>> I observed that the two solvents arrange in layers rather than to
> form a
> >>>>> homogeneous mix. See the attached pictures and input files.
> >>>>> Any advice on how to perform simulations with solvent mixtures?
> >>>>>
> >>>> Sounds like you already know how to perform the simulations.  If these
> >>>> two
> >>>> liquids are supposed to be miscible, then there is likely an
> inbalance in
> >>>> your
> >>>> force field.  Try a Google search on something like "acetonitrile
> water
> >>>> force
> >>>> field" to see what others have done in simulating this sort of
> mixture.
> >>>>
> >>>> ....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
> >>>
> >> --
> >> M.Sc. Andreas Tosstorff
> >> Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
> >> Department Pharmazie
> >> LMU München
> >> Butenandtstr. 5-13 ( Haus B)
> >> 81377 München
> >> Germany
> >> Tel.: +49 89 2180 77059
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> M.Sc. Andreas Tosstorff
> Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
> Department Pharmazie
> LMU München
> Butenandtstr. 5-13 ( Haus B)
> 81377 München
> Germany
> Tel.: +49 89 2180 77059
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Apr 07 2017 - 07:00:03 PDT
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