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Hello Lixin--
> Thank you for your quick response. I added in the improper parameter as
> you suggested. This part is working. Now I run into another error
> message: Some bond angles are missing in the topology and parameter file
> that involve this donor atom (-C).
>
You might just use the little Python script I attach here. The solution
to your problem may be as simple as preceeding the PRESidue statement
with
auto angle=false dihe=false end
best regards--
Charles
import psfGen
psfGen.seqToPSF("GLY THR")
for atom in AtomSel("resid 2 and name HT*"):
print atom.string()
xplor.command(r"""
topo
auto angle=false dihe=false end
presidue CTOH ! C-terminal for all, CH2OH at end * -CTOH
delete atom -OT2 end
delete atom -OT1 end
group
modify atom -C type=CT charge= 0.08 end
add atom -H1 type=HA charge= 0.10 end
add atom -H2 type=HA charge= 0.10 end
group
add atom -OH type=OH charge=-0.68 end
add atom -H3 type=H charge= 0.40 end
add bond -C -H1
add bond -C -H2
add bond -C -OH
add bond -OH -H3
add angle -CA -C -OH
add angle -H1 -C -H2
add angle -H3 -OH -C
add angle -H1 -C -OH
add angle -H2 -C -OH
add improper -H1 -H2 -CA -OH !stereo CH2
add dihedral -OH -C -CA -CB
end
end
patch CTOH reference=-=(resid 2) end
param
improper HA NH1 CT CT $kchi 0 65.977 ! CA chirality
end
""")
import protocol
protocol.genExtendedStructure()
protocol.fixupCovalentGeom()
from pdbTool import PDBTool
PDBTool('t.pdb').write()
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