Hi Jorgen,
A while back I was working with a polymer with enantiomeric centers. I created two different residues files to represent two enatiomeric configurations. However, I was having difficulty getting Leap to recognize the enantiomeric center, as there was a bug in Leap (tleap and sleap) at the time when trying to connect the residues together to form a chain. I am not sure if this is corrected yet, but I know the Amber development team was working on it. I suggest that you double check Leap's output to verify that your enantiomeric centers in your peptide are what you think they are before you run a production run simulation.
Cheers,
Karl
----- Original Message -----
From: "FyD" <fyd.q4md-forcefieldtools.org>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Wednesday, July 21, 2010 9:39:32 AM
Subject: Re: [AMBER] L and D peptides
Jorgen,
> I am simulating a L-Tyr-L-Tyr-L-Tyr-L-Tyr-LTyr ect peptide and want to
> observe if the same is true for the D-isomer.
Yes, replacing x by -x in the PDB file will allow to generate
enantiomers for PDB files.
Now mixing different enantiomer units (D & L) will be more tricky and
will lead to diastereoisomers which should present different
properties... I wonder if C. Simmerling did not work on
enantiomers/diastereoisomers. But I cannot find the reference here...
regards, Francois
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 21 2010 - 03:30:03 PDT
