[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
Charmm (as well as Gromacs) does contain improper dihedrals to maintain
"Racemization" is definitely a misatke if you want to realistically simulate
itself but if you want to predict a structure (eg. by running
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.
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