Hi Xplorers,
New to xplor, I trying to incorporate RDC data in
structure refinement following examples in
eginput/gb1_rdc.
I modified the refine.py to load my data. But I got a
message about topology error. The related error
message is attached at the end of this email. The
following is the difference between the modified and
the original refine.py from gb1_rdc:
> protocol.initStruct("g_new.psf")
39c35
< seqToPSF(open('3letters.seq').read())
---
> #seqToPSF(open('protG.seq').read())
50c46
< PDBTool("Test_1.pdb").read()
---
> PDBTool("model.pdb").read()
73,75c69,70
< for (medium,Da,Rh) in [ ('g', 15.2, 0.24) ]:
---
> for (medium,Da,Rh) in [ ('t', -6.5, 0.62),
> ('b', -9.9, 0.23) ]:
101,107c96,102
< for (medium,expt,file,scale) in \
< [('g','NH','page_nh.tbl',1),
---
> for (medium,expt,file, scale) in \
> [('t','NH' ,'tmv107_nh.tbl' ,1),
> ('t','NCO','tmv107_nc.tbl' ,.05),
> ('t','HNC','tmv107_hnc.tbl' ,.108),
> ('b','NH' ,'bicelles_new_nh.tbl' ,1),
> ('b','NCO','bicelles_new_nc.tbl' ,.05),
> ('b','HNC','bicelles_new_hnc.tbl',.108)
133c128
< noe = create_NOEPot("noe","finalupl.tbl")
---
> noe = create_NOEPot("noe","noe_sum_3.tbl")
139c134
< jCoup = create_JCoupPot("jcoup","hnha.tbl",
---
> jCoup = create_JCoupPot("jcoup","jna_coup.tbl",
145c140
< protocol.initDihedrals("finalaco.tbl",
---
> protocol.initDihedrals("dihed_g_all.tbl",
154,155c149,150
< protocol.initCollapse("resid 1:122",
< Rtarget=-1)
---
> protocol.initCollapse("resid 1:56",
> Rtarget=10.16)
160c155
< protocol.initHBDA('hbond.tbl')
---
> protocol.initHBDA('hbda.tbl')
347c342
< averageCompSel="not hydro").run()
---
> averageCompSel="not hydro"
).run()
====== End of diff ================================
I tried also to use seq2psf to generate .psf file but
get the same result. I checked the Test_1.pdb file and
didn't see the coordinates of the atoms indicated in
the error message are the same. I believe the error
comes from my input file but how?
Any input?
Thanks,
Yufeng
====== Error Message ==============================
calcD_G: singular D matrix: { { 0 } }
H matrix: { { 0, 0, 0, 0, 0, 0 } }
node level: 367
number of children: 0
atoms:
1906 GLN 122 CD : { 10000, 10000, 10000 }
1909 GLN 122 HE21 : { 10000, 10000, 10000 }
1910 GLN 122 HE22 : { 10000, 10000, 10000 }
1907 GLN 122 OE1 : { 10000, 10000, 10000 }
1908 GLN 122 NE2 : { 10000, 10000, 10000 }
Traceback (most recent call last):
File "<string>", line 1, in ?
File "refine.py", line 347, in ?
averageCompSel="not hydro").run()
File "/usr/local/xplor/python/simulationTools.py",
line 149, in run
s.structLoopAction(s)
File "refine.py", line 283, in structLoopAction
dyn.run()
File "/usr/local/xplor/python/ivm.py", line 404, in
run
s.initDynamics(1)
File
"/usr/local/xplor/python/wrappers/publicIVM.py", line
167, in initDynamic
s
def initDynamics(*args): return
_publicIVM.PublicIVM_initDynamics(*args)
SystemError: InternalDynamics error: calcD_G: singular
D matrix. Bad topology?
PyInterp::command: error executing:
execfile('refine.py')
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