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

Ing. Vojtěch Spiwok Vojtech.Spiwok at vscht.cz
Wed Aug 27 12:30:01 CEST 2003

> 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
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
in final structure by some programs (I think Sybyl or Insight) and than
with optimization and evaluation.

Vojtech Spiwok
ICT Prague

More information about the gromacs.org_gmx-users mailing list