Yun Shi wrote:
Hi Justin,
Thanks a lot for the replies.
I wonder what are the "newer versions" you indicated, but I find one as:
/A reoptimized GROMOS force field for hexopyranose-based carbohydrates
accounting for the relative free energies of ring conformers, anomers,
epimers, hydroxymethyl rotamers, and glycosidic linkage conformers/
. This new version 56A_CARBO is claimed to be "nearly equivalent to
53A6 for non-carbohydrate systems", and I find, at least, atomic charges
for C1 and C5 look more chemically reasonable.
But changes for a couple of 1-4 van der Waals parameter C12 were made to
53a6 force field, and additional atom types were added. So could you
tell me which file contain those LJ parameters with respect to different
atom types?
New atom types need to be added to atomtypes.atp and their parameters defined in
ffnonbonded.itp.
Alternatively, would it be reasonably good enough to use your
Lysozyme-JZ4 strategy, i.e., to build initial topology of carbohydrate
molecules by PRODRG, and then modify the atomic charges according to the
56A_CARBO paper?
Maybe, but check the bonded parameters carefully. Sugars are particularly
sensitive to incorrect angle and dihedral parameters, especially.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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