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.
>
>
>
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>
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Received on Fri Dec 09 2011 - 17:30:02 PST
