From: Angelo Rossi (angelo.raymond.rossi_at_gmail.com)
Date: Tue Aug 23 2022 - 12:58:38 CDT
Jeff Comer is correct that the CHARMM carbohydrate force field is much more
accurate for Dextran 70.
What I thought is that one could begin by running a series of small
simulations with different size dextran oligomers replicated to provide the
idea of crowding. One could ramp up the number of dextran oligomers to
observe property differences. The longer the polymer, correspondingly
longer equilibration times are needed. The 389 glucose monomers per
polymer *times* the total number of polymer chains could begin to be quite
significant for gleaning property evaluation. The number of Dextran 70
polymer chains required for crowding isn't mentioned.
Kind regards,
Angelo
On Tue, Aug 23, 2022 at 1:13 PM Jeff Comer <jeffcomer_at_gmail.com> wrote:
> Dextran is not a well defined species, but a polymer of glucose with
> mainly alpha 1,3 and alpha 1,6 linkages (
>
> https://urldefense.com/v3/__https://en.wikipedia.org/wiki/Dextran__;!!DZ3fjg!4oN-m8V3HtruppgcFZ88vebTiMLK6mk3PqoPXYmlNn_fOsjqEyGcSJG-L1VAH7JvVFYvXRZROy35RL3gGb4$
> ). If you don't know what that
> means, I recommend studying a bit about carbohydrate structure.
> Dextran 70 refers to Dextran polymers with molecular masses of about
> 70 kDa. So we are talking about 70000/180.156 ~ 389 glucose units.
>
> CGenFF, as suggested by Angelo Rossi, is probably the easiest
> solution, but not a very correct one for carbohydrates like dextran
> and ficoll. The CHARMM carbohydrate force field would likely do a
> better job than CGenFF and be the preferred solution.
>
> To make an accurate model of dextran 70, you'll need to connect ~300
> glucose units. Alpha glucose is resname AGLC in the official CHARMM
> carbohydrate force field topology file top_all36_carb.rtf. You then
> will patch them together using the α1->6 linkage and α1->3 linkage
> patches in the same file (16AT and 13aa, I think).
>
> There are several different patches that are actually the same in
> topology (13aa, 13ab, 13ba, 13bb) or (16at, 16bt). The only difference
> is the automatically generated coordinates. It does not matter which
> you use if you set the coordinates correctly yourself.
>
> Regards,
> Jeff
>
> –––––––––––––––––––––––––––––––––––———————
> Jeffrey Comer, PhD
> Associate Professor
> Department of Anatomy and Physiology
> Kansas State University
> Office: 334 Coles Hall
> Phone: 785-532-6311
> Website:
> https://urldefense.com/v3/__http://jeffcomer.us__;!!DZ3fjg!4oN-m8V3HtruppgcFZ88vebTiMLK6mk3PqoPXYmlNn_fOsjqEyGcSJG-L1VAH7JvVFYvXRZROy35VKmES0Y$
>
>
> On Mon, Aug 22, 2022 at 2:19 PM Polly Ren <pollyren_at_uchicago.edu> wrote:
> >
> > Hello!
> >
> > I was wondering whether anyone has the CHARMM force field for the Ficoll
> 70 or Dextran 70 molecules? We are trying to perform a macromolecule
> crowding simulation but we are unable to find the force field for either
> polymer. Any guidance on where they could be found or how they can be
> constructed would be greatly appreciated!
> >
> > Thank you,
> > Polly Ren
>
>
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