Hi! Sorry I didn't reply. I'm a little overwhelmed lately.
Asking this question on our mailing list is a good idea. This sort of
thing has been done. You might also try a search. I just did a
search on GAFF and got several hits. Perhaps one is what you need.
Here's the link to the mailing list:
https://listserv.uga.edu/cgi-bin/wa?A0=GLYCAM-L
On Thu, May 20, 2021 at 9:10 AM David A Case <david.case.rutgers.edu> wrote:
>
> Gustaf:
>
> It's not clear if you asked this at the GLYCAM web site or not--they would
> be the best people to give advice about modified carbohydrates. I'm cc-ing
> this to Lachele Foley, just in case she's not seen it yet.
>
> ...dac
>
>
> On Tue, May 18, 2021, Gustaf Olsson wrote:
>
> >Is it possible to combine the GLYCAM forcefield for carbohydrates with AMBER/GAFF?
> >
> >I am looking at simulating a polysaccharide consisting of repeating non-standard/bacterial carbohydrates. I need to use a non-standard "derivative", which I am unable to include using glycam.org or leap.
> >
> >I suppose what I am asking is how one would proceed here, is it even possible and also preferably then reasonable, to piece together a PDB file using with atom names and types from different forcefields like when preparing a LPS/glycoprotein according to the manual/tutorials. Or, should this be treated like a “novel” molecule and parameterised using the antechamber route?
> >
> >I am a bit torn here as something close to "the base carbohydrate" can be generated pretty much as a “standard” carbohydrate. This seems beneficial as I could use FF parameters intended for this purpose.
> >
> >However, I can only add an Acetyl group at the position where I need it, I would need a modified N-acetyl group at a “non-standard” position, which I am unable to insert using GLYCAM builder/leap. Hence, I would need to insert this at the “non standard position” manually, which may be possible, and also exchange/replace the methyl group. My suspicion is that while moving the NAc group may work, the modification would break GLYCAM compatibility as the resulting derivative/substituent is not available using the builder or in the manual?
> >
> >My thought was if it was possible to maybe treat the derivative/substituent as a “protein” and just attach the sugar at the correct position. However, this would not be a standard O/N-link. Also, even if combining two different sets of parameters for the “substituent” part and the “sugar” part (gaff/amber and glycam) works, have I moved to far away from the glycam carbohydrate so that it would no longer be a reasonable representation and treating the polysaccharide as a “novel” structure would be more correct.
> >
> >Asking a lot, obviously. Summarising, is it at all possible to combine FFs in a single structure using glycam and gaff/amber using non-standard linking. Would it be reasonable to combine parameters from different FFs in some manner (manual edits, connect info, different atom-types and FFs) or would treating the entire structure as a “novel” structure a better choice?
> >
> >Best regards
> >// Gustaf
> >
>
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu May 20 2021 - 20:00:02 PDT
