If you don't have a large protein a simple way is to load the peptide into pymol, pick three atoms (e.g., CB, CA, H) and use the option ctrl-E, which will invert the stereochemistry of this CA.
You can do a similar thing in leap.
Good luck,
Rami
On Jul 21, 2010, at 10:51 AM, Jason Swails wrote:
> Hello,
>
> Here's a suggestion, though some others may have reasons that it is not very good... You can make a copy of the amino acid library templates (all_amino94.lib), and go through each atom and take Dr. Case's advice and invert each x-coordinate. This will give you templates for all of the D-amino acids. You'll have to rename the D-residues though, so leap doesn't confuse them with the regular amino acids. Then, if you're using a pdb, delete all of the side chains for the amino acids that you want to change to the D-form and change their name to whatever you called it in the library file. Alternatively, you can just use the sequence command as you normally would using the D-names where you want them instead of the normal names.
>
> Hope this helps,
> Jason
>
> --
> Jason Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
> On Jul 21, 2010, at 3:39 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>> 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
Roman Osman
roman.osman.mssm.edu
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 21 2010 - 08:30:06 PDT
