Sorry, let me clarify...
I am simply searching for where someone got these numbers for the 12-6
parameters of Na+ and Cl-:
| sigma (nm) epsilon (kJ/mol)
Cl 4.40104e-01 4.18400e-01
Na 2.58400e-01 4.18400e-01
This was included into a force-field set in GROMACS with parmbsc1 for the
DNA. I am digging through literature to find a source for these numbers. I
was only hoping some of the files in Amber would have hints about where to
look.
Honestly, I am starting to think that these numbers are probably incorrect
since they are not equal to the parameters used in the parmbsc1 paper (
https://www.nature.com/articles/nmeth.3658.pdf)... I'll keep looking.
On Fri, Mar 2, 2018 at 10:44 AM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> Hi Dan,
>
> I am not sure what do you mean by the "Amber force field files" ? If you
> are using Gromacs, why do you need the Amber files ?
> In Amber, there are several newer ion parameters available (Cheatham,
> Li&Merz) .. From your emails, it is not clear what are you actually
> trying to use and in which software ... Unless you are more specific, I
> guess it would be hard for anybody to give useful answers ....
>
> Vlad
>
> On 03/02/2018 04:24 PM, Dan Gil wrote:
> > Hello, I found the references for the Na+ and the Cl- LJ parameters. But
> > these are not matching with what I have in GROMACS (I am using GROMACS
> with
> > parmbsc1 force-field that someone else prepared). Is there somewhere I
> can
> > download just the Amber force-field files?
> >
> > Dan Gil
> > PhD Student
> > Department of Chemical and Biomolecular Engineering
> > Case Western Reserve University
> >
> >
> > On Thu, Mar 1, 2018 at 2:38 PM, Dan Gil <dan.gil9973.gmail.com> wrote:
> >
> >> Thank you very much everyone!
> >>
> >> Dan
> >>
> >> On Thu, Mar 1, 2018 at 11:32 AM, ABEL Stephane <Stephane.ABEL.cea.fr>
> >> wrote:
> >>
> >>> Hi Dan
> >>>
> >>> it refers to the following experimental paper
> >>>
> >>> [1] J. Applequist, J.R. Carl, K.K. Fung, An Atom Dipole Interaction
> Model
> >>> for Molecular Polarizability. Application to Polyatomic Molecules and
> >>> Determination of Atom Polarizabilities, J. Am. Chem. Soc. 94 (1972)
> 2952
> >>> –2960.
> >>> https://pubs.acs.org/doi/pdf/10.1021/ja00764a010
> >>>
> >>> HTH
> >>>
> >>> Stéphane
> >>>
> >>> ________________________________________
> >>> De : Dan Gil [dan.gil9973.gmail.com]
> >>> Envoyé : jeudi 1 mars 2018 16:09
> >>> À : amber.ambermd.org
> >>> Objet : [AMBER] Question about Parmbsc1 Force Field
> >>>
> >>> Hi,
> >>>
> >>> I am using parmbsc1 and I am looking for the original papers for the
> >>> source
> >>> of some of the force-field parameters.
> >>>
> >>> I am having trouble with finding the source for Na+ ion parameters. I
> see
> >>> "Applequist" in the files, but I have no idea what it means and where
> it
> >>> leads to.
> >>>
> >>> If you could help me find the source, that would be greatly
> appreciated!
> >>>
> >>> Best Regards,
> >>>
> >>> Dan Gil
> >>> PhD Student
> >>> Department of Chemical and Biomolecular Engineering
> >>> Case Western Reserve University
> >>> _______________________________________________
> >>> 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
>
> --
> Vlad Cojocaru, PD (Habil.), Ph.D.
> -----------------------------------------------
> Project Group Leader
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> Röntgenstrasse 20, 48149 Münster, Germany
> -----------------------------------------------
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/43241/cojocaru
>
>
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>
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Received on Fri Mar 02 2018 - 08:30:03 PST
