Hello Xiaogang--
>
> I want use xplor-nih to calculate a special cyclic peptide. The
> sequence of this peptide is 'Ac-AspAlaAlaDapAlaAla-NH2', where Dap is a
> unnatural
> amino acid similar to Lys without CG and CE groups. The N terminal of Asp
> connect
> to a CH3-CO- group, and the C terminal of Ala connect to a -NH2 group.The side
> chain -CO-OH group of Asp and the side chain -NH3 group of DAP make a cyclic
> peptide connection by "Asp-CO-NH-DAP".
>
> I want to generate a PSF file about this peptide. I think it may be
> good to define Ac-Asp part as one unnatural amino acid which I named ACD, thus
> the peptide can be wrote as "ACD ALA ALA DAP ALA ALA" in Xplor-NIH formate. So
> the question is how to generate a cyclic connection between ACD and DAP side
> chain in the protocol? I read the example file in eginput, but it looks like
> no
> case like this.
>
It seems that you are on the right track. The closest example in
eginputs is probably eginput/PSF_generation/genModCircPep.py, but it
is not exactly the same. Usually, N-terminal acetylation is achieved
by specifying the ACE residue- this might make things a bit simpler
for you. Amidation of the C-terminal domain can be achieved by
specifying amidate_cterm=True to psfGen.seqToPSF.
So the simplest generation script would be something like:
seq="ACE ASP ALA ALA DAP ALA ALA"
import psfGen
psfGen.residueTypes['protein'].append("DAP")
import protocol
protocol.initTopology("protein")
protocol.initParams("protein")
xplor.command("""
load DAP topology
load DAP parameters
""")
psfGen.seq2PSF(seq,amidate_cterm=True)
xplor.command("""
load patch definition for presidue CLOS - for loop closure
load any required parameters for this
""")
xplor.command("patch CLOS reference=-=(resid 5) reference+=(resid 1) end")
Please let me know if you need help with this, or with generating the
required parameters.
best regards--
Charles
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