Thank you so much it worked. Thank you for all your support.
On Wed, Jun 11, 2014 at 12:34 PM, Lachele Foley <lf.list.gmail.com> wrote:
> To use the GLYCAM force fields, you need to ensure that the residue
> and atom names are consistent with GLYCAM residues. Assuming it is a
> standard cyclodextrin, with alpha-D glucopyranoses 1-4 linked, then
> the proper residue name is 4GA.
>
> To learn more about residue naming in GLYCAM: http://glycam.org/naming
>
> If leap complains of incorrect atom names, check out the 4GA entry in
> the file $AMBERHOME/dat/leap/prep/GLYCAM_06j-1.prep . If you are
> using an older AMBER, see the next paragraph.
>
> If you are using AmberTpools14, then you should be able to source
> leaprc.GLYCAM_06j-1, which is the most recent set of GLYCAM
> parameters. To learn more about GLYCAM Parameters, see
> glycam.org/params . To download an archive of the current params for
> use with other versions of AMBER (starting with 10), see
> glycam.org/currentparams .
>
> If your AMBER is older than 10, you need different information. Or,
> even better, you need to upgrade.
>
>
> On Wed, Jun 11, 2014 at 2:54 PM, Soumendranath Bhakat
> <bhakatsoumendranath.gmail.com> wrote:
> > Hii All;
> >
> > We are just testing with some gamma cyclodextrins to set up a system. The
> > file is attached herewith. This is a glucose 1-4 linked cyclic moiety.
> >
> > We wished to generate parameters for this system using GLYCAM force
> field.
> > We uploaded glycam library in the tleap but leads to a fatal error
> saying "
> > GLC atom type not found. As GLC is denoted the cyclodextrin in this case.
> >
> > Could anybody help which we should edit instead of GLC so that tleap
> > recognise it as glucose and atom types should be recognizable by tleap.
> >
> > And which glycam ff we should use for this type of cyclodextrin unit.
> >
> > Help will be highly appreciated.
> >
> > Thank you all in advance.
> >
> > --
> > Thanks & Regards;
> > Soumendranath Bhakat
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Thu Jun 12 2014 - 02:00:02 PDT
