Dear xplor users,
I would like to calculate an oligomeric structure based on the KFFE
tetrapeptide. I have reasons to believe that the peptide is all
neutral i.e. I would like to define patch residues for H2N-R
N-terminal and R-COOH C-terminal and neutral Lysine side chain ~NH2
and neutral Glu side chain ~COOH.
I generate two KFFE segments:
'''
segment
name="A "
SETUP=TRUE
chain
@TOPPAR:toph11.pep
sequence
LYS PHE PHE GLU
end
end
end
segment
name="B "
SETUP=TRUE
chain
@TOPPAR:toph11.pep
sequence
LYS PHE PHE GLU
end
end
end
'''
I define the presidues and apply the patches:
'''
topology
presidue KNDD
!Deprotonated N-terminal (NH2) and deprotonated Lysine
group
delete atom HT3 END
!modify atom N type=NH2 charge= -0.3 END
modify atom N charge= -0.3 END
!modify atom HT2 type=H charge= 0.15 END
!modify atom HT1 type=H charge= 0.15 END
modify atom HT2 charge= 0.15 END
modify atom HT1 charge= 0.15 END
modify atom CA charge= -0.1 END
! HA charge= 0.1 (still)
group
modify atom CE charge= -0.2 END
modify atom HE1 charge= 0.1 END
modify atom HE2 charge= 0.1 END
group
delete atom HZ3 END
!modify atom NZ type=NH2 charge= -0.3 END
modify atom NZ charge= -0.3 END
!modify atom HZ2 type=H charge= 0.15 END
!modify atom HZ1 type=H charge= 0.15 END
modify atom HZ2 charge= 0.15 END
modify atom HZ1 charge= 0.15 END
end
presidue ECPP
!protonated C-terminal (COOH) and protonated GLU
group
modify atom C charge= 0.78 END
modify atom OT1 type=O charge= -0.61 END
!modify atom OT1 charge= -0.61 END
modify atom OT2 type=OH charge= -0.67 END
add atom HCT type=H charge= 0.46 END
modify atom CA charge= 0.14 END
group
modify atom CG charge= -0.2 END
modify atom HG1 charge= 0.1 END
modify atom HG2 charge= 0.1 END
group
modify atom CD charge= 0.75 END
modify atom OE1 type=O charge= -0.55 END
!modify atom OE1 charge= -0.55 END
modify atom OE2 type=OH charge= -0.61 END
add atom HE2 type=H charge= 0.44 END
add bond HCT OT2
add angle HCT OT2 C
add bond HE2 OE2
add angle HE2 OE2 CD
end
end
patch KNDD
reference=nil=( segid A and resid 1 )
end
patch ECPP
reference=nil=( segid A and resid 4 )
end
patch KNDD
reference=nil=( segid B and resid 1 )
end
patch ECPP
reference=nil=( segid B and resid 4 )
end
'''
The psf is produced without errors. However, generating an extended
structure from the psf-file fails:
'''
protocol.initParams("protein")
protocol.initStruct('kffe2.psf')
for i in range(3):
protocol.genExtendedStructure("kffe_extended"+str(9099+i*100)+".pdb")
'''
output:
X-PLOR>end
genExt.py(16): for i in range(3):
genExt.py(17):
protocol.genExtendedStructure("kffe_extended"+str(9099+i*100)+".pdb")
%ATMCHK-ERR: Unknown coordinates
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
BOMLEV= 0 reached. Program execution will be terminated.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Subroutine DIE called . Terminating
------------
The whole procedure runs succesful using the same procedure but with
only one segment! Hope someone can help me on what is going wrong with
two segments.
best regards,
Jakob
--
Jakob Toudahl Nielsen, post doc
Laboratory for Biomolecular NMR Spectroscopy
inSPIN, Center for Insoluble Protein Structures
Department of Chemistry, University of Aarhus
Langelandsgade 140, DK-8000 Aarhus C, Denmark
Phone: +458942 5528 or +452993 8502 (cell)
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