Thanks a lot!
Gustavo Seabra.
Em 20/02/2015 15:39, "Lachele Foley" <lf.list.gmail.com> escreveu:
> The best detail that exists can be found in: (a) the top of the .dat
> param file, and (b) by chemical analogy to existing entries in the
> .prep file. Since guluronic acid would differ from, say, galacturonic
> acid, only by stereochemisty, it should be simple enough to determine
> the atom types by analogy to the prep entry for galacturonic acid (0OB
> or 0OA). If you have a reducing-terminal OH, see entry ROH. If it is
> an -OMe, use OME, etc.
>
>
>
> On Thu, Feb 19, 2015 at 6:42 AM, Gustavo Seabra
> <gustavo.seabra.gmail.com> wrote:
> > Hi Lachele,
> >
> > Thank you very much for your answer.
> >
> > Yes, I’m aware of the uppercase-lowercase atom types, and those are the
> ones I’m trying to use. I have identified most of the atom types. However,
> some types are still not clear to me. (Do you know of any source that
> describes the available atom types in detail?)
> >
> > As for the GLYCAM-web files, I just noticed that I was looking at atom
> names instead of types. I just located the atom types in the generated
> prmtop file. Sorry!
> >
> > Thank you very much,
> > Gustavo Seabra
> >
> >
> >
> >> Em 19/02/2015, à(s) 00:16, Lachele Foley <lf.list.gmail.com> escreveu:
> >>
> >> You need to use the uppercase-lowercase atom types in the current parm
> >> files, and use the current parm files. Set the types in your unit by
> >> the chemical type defined in the parm file. It might be simplest to
> >> try to match those in a similar prep file. For example, you might see
> >> the prep entry for 0OB (zero capital-O capital=B), for galacturonic
> >> acid.
> >>
> >> I don't know what you mean by a unit created by GLYCAM-Web that uses
> >> all uppercase atom type names. From which URL did you generate or
> >> download this unit?
> >>
> >>
> >>
> >> On Wed, Feb 18, 2015 at 1:54 PM, Gustavo Seabra
> >> <gustavo.seabra.gmail.com> wrote:
> >>> Dear all,
> >>>
> >>> We are trying to create a custom monosaccharide unit using GLYCAM
> force field, but we are having a bit of trouble choosing the atom types to
> use.
> >>>
> >>> To understand more about the atom types to use, we have tried creating
> a related unit in Glycam-web, but the unit created seems to use different
> atom types than the ones available in the force field. Specifically, in the
> GLYCAM_06j.dat file, all atoms have uppercase first letters and lowercase
> second letters, while the unit created by GLYCAM-Web has all uppercase
> letters.
> >>>
> >>> Could anyone help us identifying the correct atom types in Glycam
> force field to use? (BTW, the unit we're trying to build is guluronic acid,
> as preset in alginate.)
> >>>
> >>> Thank you,
> >>> Gustavo Seabra
> >>>
> >>>
> >>>
> >>>
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> >>
> >>
> >>
> >> --
> >> :-) Lachele
> >> Lachele Foley
> >> CCRC/UGA
> >> Athens, GA USA
> >>
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> >> AMBER.ambermd.org
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> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
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>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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Received on Fri Feb 20 2015 - 11:30:06 PST
