With the word 'scan', I meant the way Antechamber identifies corresponding
parameters (bond, angle, dhedral etc.) for an molecule from the known
parameters for proteins, DNA, and others by analogy.
Is there way to make Antechamber identify parameters from INTERFACE FF
parameters in addition to protein, DNA.
Thanks,
J
On Sat, Jan 19, 2019 at 3:56 PM Pengfei Li <ambermailpengfei.gmail.com>
wrote:
> Hi Sundar,
>
> GAFF is generally designed for organic molecules. What do you mean by
> “scan”? Do mean you any specific program in the antechamber module which
> can help you to optimize the parameters?
>
> Pengfei
>
> > On Jan 14, 2019, at 9:42 AM, Sundar <jubilantsundar.gmail.com> wrote:
> >
> > Hi,
> >
> > Thanks for suggesting the tutorials.
> > I have another question on using Antechamber to find analogous parameters
> > for zeolites.
> >
> > As far as I know, antechamber scans through all the available parameters
> > within Amber FF including GAFF to find the best atomtypes, bonds, angles,
> > torsions etc for a new chemical.
> > My question is, can I call Antechamber to also scan INTERFACE FF, which
> > contains parameters for several inorganic compounds, and make the frcmod
> > file for me.
> >
> > Thanks,
> > Sundar
> >
> >
> > On Thu, Jan 10, 2019 at 9:45 AM Pengfei Li <ambermailpengfei.gmail.com
> <mailto:ambermailpengfei.gmail.com>>
> > wrote:
> >
> >> Hi Jubilant,
> >>
> >> Here is a tentative tutorial which may be helpful:
> >> http://ambermd.org/tutorials/advanced/tutorial27/index.htm <
> http://ambermd.org/tutorials/advanced/tutorial27/index.htm> <
> >> http://ambermd.org/tutorials/advanced/tutorial27/index.htm <
> http://ambermd.org/tutorials/advanced/tutorial27/index.htm>>.
> >>
> >> I don’t know any relevant papers been published. And I have no idea
> about
> >> the performance of GAFF for zeolites, or about the accuracy of
> simulating
> >> the inorganic-organic interfaces in AMBER.
> >>
> >> Hope it helps,
> >> Pengfei
> >>
> >>> On Jan 4, 2019, at 12:06 AM, Sundar <jubilantsundar.gmail.com> wrote:
> >>>
> >>> I'm trying to perform simulations on zeolites (silicates and
> aluminates).
> >>> Had anyone ever written any tutorials for them or had performed
> >> simulations
> >>> using Amber force fields and published?
> >>>
> >>> How does INTERFACE FF (https://bionanostructures.com/interface-md/)
> work
> >>> with Amber?
> >>> How good are the GAFF analogous parameters for zeolites?
> >>>
> >>> How accurate can we model inorganic-organic interfaces in Amber?
> >>>
> >>> --
> >>> Thanks,
> >>> Jubilant
> >>> _______________________________________________
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> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> >> http://lists.ambermd.org/mailman/listinfo/amber <
> http://lists.ambermd.org/mailman/listinfo/amber>
> >>
> >
> >
> > --
> > Thanks,
> > Sundar Thangapandian
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> > http://lists.ambermd.org/mailman/listinfo/amber <
> http://lists.ambermd.org/mailman/listinfo/amber>
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>
--
Thanks,
Sundar Thangapandian
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Received on Sat Jan 19 2019 - 20:00:02 PST
