Ah, but ideally the same procedure would work around a similar problem with
overlapping names in other forcefields?
On Fri, Dec 9, 2011 at 8:28 PM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
> Doesn't necessarily mean that.
>
>
> On Fri, Dec 9, 2011 at 8:26 PM, Aron Broom <broomsday.gmail.com> wrote:
> > Thank you for the information. Does this mean that such an overlap is
> not
> > an issue in other versions of the amber forcefield, for instance ff03?
> >
> > ~Aron
> >
> > On Fri, Dec 9, 2011 at 7:50 PM, Jodi Ann Hadden <jodih.uga.edu> wrote:
> >
> >> Currently there is an issue with the CY atom type which overlaps in
> ff99SB
> >> and GLYCAM.
> >>
> >> This issue is in the process of being resolved, but in the mean time,
> >> please use the following work around to ensure your prmtops contain the
> >> correct information and your ring geometries are not distorted when
> >> building a sugar that contains a CY atom (e.g. sialic acid, 0SA).
> >>
> >> - Go to www.glycam.org/params and download the most up-to-date version
> of
> >> the parameters.
> >> - If you are building a system that contains only a protein, load only
> >> ff99SB into leap, do not load GLYCAM.
> >> - If you are building a system that contains a carbohydrate, load
> GLYCAM,
> >> ff99SB, then GLYCAM again.
> >>
> >> source leaprc.GLYCAM_06
> >> source leaprc.ff99SB
> >> source leaprc.GLYCAM_06
> >>
> >> This should ensure your input files contain correct information.
> >>
> >>
> >>
> >> _______________________________________________
> >> 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
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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>
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Received on Fri Dec 09 2011 - 18:00:02 PST
