To 'make it work with GLYCAM', first you have to change the atom types
in the GLYCAM amino libs that aren't glycam types. They need to match
the types in your ff. Then, you need to come up with parameters for
the linkages using those new atom types. The simple option there is
merely to copy the relevant entries for the other ff and change the
atom type names. But, you need to choose where to use the ff03 params
and where to use glycam, and there's no guarantee things will work
properly. As Jason said, you really must validate.
On Sat, Mar 14, 2015 at 11:56 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Sat, Mar 14, 2015 at 11:04 AM, Pedro Swagger <pedrito.swagger.gmail.com>
> wrote:
>
>> Thanks dor your reply.
>>
>> I still want to use the ff03.r1 I was wondering which glycam version FF is
>> recommended for it?
>>
>
> Based on the link that Lachele sent you; none of them.
>
> Note that ff03 has a completely different charge derivation scheme compared
> to the 'standard' Amber force fields (ff94, ff99, ff99SB, ff12SB, and
> ff14SB), so parameters are generally not transferrable between those two
> families of force fields (especially the torsions). There might also be
> atom type-based conflicts... I'm just not sure (and I don't know if anybody
> has rigorously checked that).
>
> So unless somebody knows of a study that I'm unfamiliar with that you can
> cite for justification, you will have to either switch to ff12SB or figure
> out how to make one of the GLYCAM force fields compatible with ff03 *and*
> validate it somehow.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Sat Mar 14 2015 - 13:00:02 PDT
