http://ambermd.org/formats.html
On Thu, 6 Apr 2017 10:13:23 +0200
Andreas Tosstorff <andreas.tosstorff.cup.uni-muenchen.de> wrote:
> Hi all,
>
> I am trying to write an frcmod file for acetonitrile to use
> parameters from the literature. I could only find little information
> on frcmod files, neither in the manual nor online so I have a few
> questions.
>
> I attached an frcmod file I generated with parmchk2 below in order to
> facilitate the discussion.
>
> Here go my questions:
>
> * In the MASS card, I have four columns. What are the third and
> fourth columns? Is the third one the charge?
> * In the NONBON card, are those the same Lennard Jones Parameters A
> and B as in the topology files?
> * If I specify e.g. NONBON parameters, do I have to do this for all
> atom types in my molecule or only for those I actually want to
> change? e.g. my molecule has 5 different atom types, but I only
> want to change parameters for 2 of them
> * Assuming I have to different ligands in my system, that include
> the same atom type. Can I assign different parameters to the same atom
> type for each ligand? Or do I need to define a new atom type? e.g.
> Ligand1 has an atom of charge 0.5 and ligand2 has an atom of the
> same type but with a charge of 0.6
>
> I would really appreciate your help!
>
> Best,
> Andy
>
> Remark line goes here
> MASS
> CT 12.010 0.878 same as c3
> HC 1.008 0.135 same as hc
> ...
>
> BOND
> CT-HC 330.60 1.097 same as c3-hc, penalty score= 0.0
> C -CT 313.00 1.524 same as c-c3, penalty score= 0.0
> ...
>
> ANGLE
> CT-C -O 67.400 123.200 same as c3-c -o , penalty score= 0.0
> CT-C -N 66.790 115.180 same as c3-c -n , penalty score= 0.0
> ...
>
> DIHE
> CT-C -N -H 4 10.000 180.000 2.000 same as X
> -c -n -X , penalty score= 0.0
> CT-C -N -CT 1 0.000 0.000 -2.000 same as
> c3-c -n -c3
> CT-C -N -CT 1 1.500 180.000 1.000 same as
> c3-c -n -c3, penalty score= 0.0
> ...
>
> IMPROPER
> CT-N -C -O 1.1 180.0 2.0 Using the
> default value
> C -CT-N -H 1.1 180.0 2.0 Using the
> default value
> C -H -N -H 1.1 180.0 2.0 Same as X
> -X -n -hn, penalty score= 6.0 (use general term))
>
> ...
>
> NONBON
> CT 1.9080 0.1094 same as c3
>
>
>
>
>
>
>
>
> On 04/05/2017 06:08 PM, Andreas Tosstorff 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
> >
> >
> >
> > _______________________________________________
> > 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 Thu Apr 06 2017 - 02:30:02 PDT
