[gmx-users] AMBER ff10 with Gromacs

[gromacs query]

Hi,

both links helped:
http://www.gromacs.org/Downloads/User_contributions/Force_fields (for
ff99sb and parmbsc0 but need to check for double stranded dna)

and improved ions here:
http://pubs.rsc.org/en/Content/ArticlePDF/2013/CP/c2cp44100d (they used
Cheatham ions with Gromacs, may need to modify itp file)
Taken from above paper "The potassium (radius 1.705 Å and well depth
0.1936829 kcal mol) parameters optimized by Cheatham and co-workers"

(I should have done homework rather! sorry)

thanks
JIo


On Thu, Nov 28, 2013 at 4:05 PM, Szilárd Páll <pall.szilard at gmail.com>wrote:

> PS: googling AMBER FF10 + GROMACS does give (at least) one relevant
> result: http://pubs.rsc.org/en/Content/ArticlePDF/2013/CP/c2cp44100d
>
> They may have something useful and may be willing to share (and it
> would certainly be useful to have it in the contrib FF section as
> well).
>
> Cheers,
> --
> Szilárd
>
>
> On Thu, Nov 28, 2013 at 4:26 PM, Thomas Piggot <t.piggot at soton.ac.uk>
> wrote:
> > In addition to where Szilard said to look, you can also try looking for
> > force fields on the user contributions part of the GROMACS website:
> >
> > http://www.gromacs.org/Downloads/User_contributions/Force_fields
> >
> > If you need to use AMBER99SB force field with the ParmBSC0 nucleic acid
> > parameters, this combination can be found there.
> >
> > Cheers
> >
> > Tom
> >
> >
> > On 11/27/2013 02:06 PM, Szilárd Páll wrote:
> >>
> >> Hi,
> >>
> >> If you look at share/gromacs/top/ in the GROMACS installation
> >> directory you can see which FF-s are included and amberff10 is not
> >> there, so the answer is no.
> >>
> >> Cheers,
> >> --
> >> Szilárd
> >>
> >>
> >> On Wed, Nov 27, 2013 at 12:33 AM, gromacs query <gromacsquery at gmail.com
> >
> >> wrote:
> >>>
> >>> Dear All
> >>>
> >>> I never used Gromacs for nucleic acids. In AMBER there is ff10
> >>> (ff99SB+parmbasco+ also one needs to add ions according to water used
> by
> >>> Thomas Cheatham et al.)
> >>>
> >>> does gromacs include this force field (AMBER ff implemented in
> gromacs)?
> >>>
> >>> regards
> >>> JIo
> >>> --
> >>> Gromacs Users mailing list
> >>>
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> >
> > --
> > Dr Thomas Piggot
> > University of Southampton, UK.
> >
> >
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