[gmx-users] charge assignment for the anomeric carbon in 53a6 ff
Justin A. Lemkul
jalemkul at vt.edu
Sun Aug 7 21:07:30 CEST 2011
Yun Shi wrote:
> Thanks again.
> Since I am running MD simulation on a public cluster, I cannot modify
> atomtypes.atp and ffnonbonded.itp on that cluster.
You can make local copies in your working directory and call that force field
when running grompp.
> But I could get every parameter ready and prepare the xxx.tpr files
> locally, and pass them to the cluster. So the practical question is,
> does the tpr file contain all those C12 and C6 LJ parameters already? Or
> mdrun need to retrieve these parameters according to the atom types from
> corresponding files within the gromos53a6.ff folder?
All the necessary information is contained in the .tpr file.
> Yun Shi
> 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
> > 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 A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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