Doesn't necessarily mean that.
On Fri, Dec 9, 2011 at 8:26 PM, Aron Broom <broomsday.gmail.com> wrote:
> 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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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> http://lists.ambermd.org/mailman/listinfo/amber
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Fri Dec 09 2011 - 17:30:03 PST
