Hello everyone,
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.
I also attached the definition of ACD and DAP I wrote for
protein.top file. I hope someone can check whether it is correct.
Thanks!
Xiaogang
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
residue ACD
group
atom N type=NH1 charge=-0.36 end
atom HN type=H charge= 0.26 end
group
atom CA type=CT charge= 0.00 end
atom HA type=HA charge= 0.10 end
group
atom CB type=CT charge=-0.45 end
atom HB1 type=HA charge= 0.10 end
atom HB2 type=HA charge= 0.10 end
group
atom CG type=C charge= 0.49 end
atom OD1 type=OC charge=-0.62 end
atom OD2 type=OC charge=-0.62 end
group
atom C type=C charge= 0.48 end
atom O type=O charge=-0.48 end
group
atom CE type=C charge= 0.48 end
atom OE type=OC charge=-0.48 end
group
atom CZ type=C charge=-0.3 end
atom HZ1 type=HA charge=0.1 excl = (HZ) end
atom HZ2 type=HA charge=0.1 excl = (HZ) end
atom HZ2 type=HA charge=0.1 excl = (HZ) end
bond N HN
bond N CA bond CA HA
bond CA CB bond CB HB1 bond CB HB2
bond CB CG
bond CG OD1
bond CG OD2
bond CA C
bond C O
bond N CE
bond CE OE
bond CE CZ
bond CZ HZ1 bond CZ HZ2 bond CZ HZ3
improper HA N C CB !stereo CA
improper CG CB OD1 OD2
improper HB1 HB2 CA CG !stereo CB
dihedral CG CB CA N
dihedral OD1 CG CB CA
end
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