I want to clarify this statement:
- If you are building a system that contains only a protein, load only
ff99SB into leap, do not load GLYCAM.
This applies if your system only contains a protein and will not be
compared to a system requiring use of the GLYCAM force field. If you
are comparing two systems, for example, one with and one without a
glycan, it is safest to use exactly the same set and sequence of
parameter loads for each. For example, if one parameter file contains
a parameter "1.23" and the other has, for the same parameter "1.232",
then you can get differing topology files. Most differences will be
minor in terms of overall effect on a simulation, but if one is
comparing energies between the two, you will get better results if the
starting parameters match exactly.
We are working on updated parameter sets that will make it easier to
mix force fields without worrying about details like this.
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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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu Dec 15 2011 - 08:00:03 PST
