Hello, Charles,
Thank you for your advice! I wrote a script as you suggest, but it
does not work! I append it at the the end of this email, and put some
comments in it. Can you help me to check what's wrong with it?
Thanks!
Xiaogang
xplor.parseArguments()
seq= " ACE ASP ALA ALA DAP ALA ALA "
import psfGen
psfGen.residueTypes['protein'].append("DAP")
import protocol
protocol.initTopology("protein")
protocol.initParams("protein")
psfGen.seq2PSF(seq, amidate_cterm=True)
# xplor always report some error like: AttributeError: 'module' object has
no attribute 'seq2PSF'
xplor.command("""
residue DAP
group
atom N type=NH1 charge=-0.360 end
atom HN type=H charge= 0.260 end
group
atom CA type=CT charge= 0.000 end
atom HA type=HA charge= 0.100 end
group
atom CB type=CT charge=-0.200 end
atom HB1 type=HA charge= 0.100 end
atom HB2 type=HA charge= 0.100 end
group
atom NZ type=NH3 charge=-0.810 end
atom HZ type=HC charge= 0.435 end
group
atom C type=C charge= 0.480 end
atom O type=O charge=-0.480 end
bond N HN
bond N CA bond CA HA
bond CA CB bond CB HB1 bond CB HB2
bond CE NZ bond NZ HZ
bond CA C
bond C O
improper HA N C CB !stereo CA
improper HB1 HB2 CA NZ !stereo CB
dihedral NZ CB CA N
end
presidue CLOS
delete atom +OD2 end
add bond -NZ +CG
add angle +CB +CG -NZ
add angle +OD2 +CG -NZ
add angle +CG -NZ -CB
add angle +CG -NZ -HZ
end
""")
# xplor stop here with: %X-PLOR-ERR: unrecognized command:
xplor.command("""
patch CLOS reference=-=(resid 5) reference=+=(resid 2) end
patch LTOD reference==(resid 2) end
""")
# in my last email, I forgot I need change ASP from L to D. I found it can
be achieved by LTOD, can I write like this?
xplor.command("write psf output=isodd.psf end")
import protocol
protocol.initRandomSeed()
protocol.addUnknownAtoms(dyn_stepsize=0.012,dyn_numStepMul=2)
for i in range(4):
try:
protocol.fixupCovalentGeom(useVDW=1,maxIters=400)
break
except Exception, e:
if e.args[0].startswith("Covalent geometry still violated"):
continue
raise
pass
from pdbTool import PDBTool
PDBTool("isodd.pdb").write()
On Fri, May 15, 2015 at 11:58 PM, Charles Schwieters <[email protected]
> wrote:
>
> 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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