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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Received on Fri Dec 09 2011 - 17:00:02 PST
