Re: [AMBER] Separate forcefield for oligosaccharide residues?

From: FyD <>
Date: Mon, 31 Oct 2016 17:22:48 +0100

Dear Lachele,

Please, no need to write me that You did not read that paper (+ You
are so busy, personally I am not).
   This is not my concern...

> The AMBER manual also contains lots of good information on the topic.

  (y) :-))

> GLYCAM is made to treat most oligosaccharides well in most
> biologically-relevant contexts. We are constantly tweaking the behavior of
> the force field and adding functionality. If you develop a new force field
> for a specific molecule in a specific situation, you will get better
> results for that molecule in that situation. The results will not
> necessarily apply anywhere else. It is also necessary to be careful how
> you validate any new force field.

My feeling is that the association of different scaling factors for
1-4 interactions + different charge models in different force fields
(FF) to be used together is all but natural (but this is just my
personal opinion). This is what we tried to demonstrate in that
paper... Yes, FF specificity vs generality: but just an evidence...
and I do not think that Glc a(1,4) is that a new residue ;-) Anyway,
all FFs have their limitations...

regards, Francois

> On Sat, Oct 29, 2016 at 6:27 AM, FyD <> wrote:
>> > I'm going to conduct MD simulation for protein molecule
>> > which has some covalently bound oligosaccharide residues.
>> > Should I treat these residues separately by the specially designed
>> > forcefield (e.g. GLYCAM) ?
>> You might be interested in a work about glicoconjugates reported in
>> REDDB...
>> In my opinion the approach to follow to design your FF is highly
>> related to the oligosaccharide structure itself...

           F.-Y. Dupradeau

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Received on Mon Oct 31 2016 - 18:00:03 PDT
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