Kinda depends. Good chance it will. Best to check carefully. If in
doubt, pester us. We can figure it out.
On Fri, Dec 9, 2011 at 8:34 PM, Aron Broom <broomsday.gmail.com> wrote:
> Ah, but ideally the same procedure would work around a similar problem with
> overlapping names in other forcefields?
>
> On Fri, Dec 9, 2011 at 8:28 PM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
>
>> 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
>> >>
>> > _______________________________________________
>> > 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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>> 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 - 18:00:03 PST
