Hello Kirthi--
>
> Hope this mail finds you well. I want to use Xplor for the structure
> calculation of seven residue peptides which has a combination of D- and L-
> amino acid residues (for eg. L-His D-Tyr L-His D-Tyr L-His D-Phe D-Phe), Does
> Xplor have a database for D-amino acids? If not, is there a way to incorporate
> information of D-amino acids in the existing topalhdg.pro file of L-amino
> acids
> and use it for structure calculations?
>
Currently, you will need to generate and consistently use a PSF file
when handling peptides which include D-amino acids. To generate the
PSF for your example peptide, you will need something like:
seq="HIS TYR HIS TYR HIS PHE PHE"
import psfGen
psfGen.seqToPSF(seq)
for resid in (2,4,6,7):
psfGen.dAmino(resid)
pass
xplor.command("write psf output=new.nsf end")
import protocol
protocol.genExtendedStructure()
protocol.writePDB("new.pdb")
Please let me know if you have difficulties.
Charles
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