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
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Received on Wed Jun 11 2014 - 13:00:02 PDT
