[gmx-users] D-L conversion!
Ing. Vojtěch Spiwok
Vojtech.Spiwok at vscht.cz
Thu Aug 28 15:38:01 CEST 2003
> Swetha Vijayakrishan wrote:
> > hi all,
> > I had run a 2 nanosecond MD using Charmm.
> > Now i find a few of the residues having their chirality changed from L
> > 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
> > again??
> One could argue whether doing MD with Charmm is a mistake ;-)
> I would not expect L-D transitions in Prolines, these are known to be very
> slow (experimentally, that is) and can be e.g. rate limiting for folding.
> Don't know about the parameterization of the Charmm forcefield, however.
> As for re-running, I know from other people that Charmm can be about 10
> times slower than Amber, and I know from own experience that Gromacs can
> be about 5-10 times faster than Amber. You do the maths...
> We have a choice variety of forcefields: Gromos, OPLS (and Amber coming).
Level of D-aminoacids in dental proteins could be used for estimation of age
as it raises with age, so nothing for molecular dynamics (even with Gromacs
As I know in vivo L-D transition is two-step covalent reaction, anyway.
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