[gmx-users] Re: D-L conversion! (Swetha Vijayakrishan)

[Ing. Vojtěch Spiwok]

> I had run a 2 nanosecond MD using Charmm.
> Now i find a few of the residues having their chirality changed from L to
> D especially the Prolines.
> Is this very common in MD? Or have i made some mistake.
> Does anybody know how i can rectify this problem without rerunning the MD
> again??
>
> thanks
>
> swetha

Charmm (as well as Gromacs) does contain improper dihedrals to maintain
correct chiralities.
"Racemization" is definitely a misatke if you want to realistically simulate
dynamics
itself but if you want to predict a structure (eg. by running
high-temperature MD
with NMR-derived restraints, simulated annealing etc.) you can change
chiralities
in final structure by some programs (I think Sybyl or Insight) and than
continue
with optimization and evaluation.

Vojtech Spiwok
ICT Prague