From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Tue Aug 23 2022 - 12:08:07 CDT
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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