[gmx-users] charge assignment for the anomeric carbon in 53a6 ff

[Justin A. Lemkul]

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.

-Justin

> Regards,
> 
> 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
> 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 <http://vt.edu/> | (540) 231-9080 
> <tel:%28540%29%20231-9080>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/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

========================================