Hello Charles and other members of Xplor-NIH,
I am trying to refine a cyana output structure against RDC and NOE data
using xplor. This cyana pdb has already been converted into xplor format
using pdbstat. I am using modified version of refine.py script that has
floating Da and Rh while running the structure calculation.
The output error message that I am getting is :
Pin1RDC_highT.py(73): protocol.loadPDB("4xplor.pdb")
loading pdb file: 4xplor.pdb [psf]PDBTool:read: atom not found in
structure: A MET 1 H
PDBTool:read: atom not found in structure: A MET 1 HB3(name converted from
3HB)
PDBTool:read: atom not found in structure: A MET 1 HG3(name converted from
3HG)
PDBTool:read: atom not found in structure: A ALA 2 H
PDBTool:read: atom not found in structure: A ASP 3 H
PDBTool:read: atom not found in structure: A ASP 3 HB3(name converted from
3HB)
PDBTool:read: atom not found in structure: A GLU 4 H
PDBTool:read: atom not found in structure: A GLU 4 HB3(name converted from
3HB)
PDBTool:read: atom not found in structure: A GLU 4 HG3(name converted from
3HG)
PDBTool:read: atom not found in structure: A GLU 5 H..............
matchInexactAtomEntry: matching entry A 1 H to atom A 1 HT1 [rule 2]
matchInexactAtomEntry: found no match for entry A 1 3HB
matchInexactAtomEntry: found no match for entry A 1 3HG
matchInexactAtomEntry: matching entry A 2 H to atom A 2 HN [rule 1]
matchInexactAtomEntry: matching entry A 3 H to atom A 3 HN [rule 1]
matchInexactAtomEntry: matching entry A 3 3HB to atom A 3 HB1 [rule
12]
matchInexactAtomEntry: matching entry A 4 H to atom A 4 HN [rule 1]
matchInexactAtomEntry: matching entry A 4 3HB to atom A 4 HB1 [rule
12]
matchInexactAtomEntry: matching entry A 4 3HG to atom A 4 HG1 [rule
12]
matchInexactAtomEntry: matching entry A 5 H to atom A 5 HN [rule
1]..................
initCoords: Warning: unable to read 2 pdb ATOM entries (nonpseudoatom)
initCoords: still 9 unknown atomic coordinates
[coords]
Pin1RDC_highT.py(74): xplor.simulation.deleteAtoms("not known")
MAPIC: Atom numbers being modified
Pin1RDC_highT.py(77): protocol.fixupCovalentGeom(maxIters=100,useVDW=1)
Pin1RDC_highT.py(83): from potList import PotList
Pin1RDC_highT.py(84): potList = PotList()
Pin1RDC_highT.py(88): from simulationTools import MultRamp, StaticRamp,
InitialParams
Pin1RDC_highT.py(90): rampedParams=[]
Pin1RDC_highT.py(91): highTempParams=[]
Pin1RDC_highT.py(106): from varTensorTools import create_VarTensor
Pin1RDC_highT.py(107): media={}
Pin1RDC_highT.py(109): for (medium,Da,Rh) in [
Pin1RDC_highT.py(110): ('s', -10.4, 0.46),
Pin1RDC_highT.py(113): oTensor = create_VarTensor(medium)
Pin1RDC_highT.py(114): oTensor.setDa(Da)
Pin1RDC_highT.py(115): oTensor.setRh(Rh)
Pin1RDC_highT.py(116): media[medium] = oTensor
Pin1RDC_highT.py(117): pass
Pin1RDC_highT.py(110): ('s', -10.4, 0.46),
Pin1RDC_highT.py(136): from rdcPotTools import create_RDCPot, scale_toNH
Pin1RDC_highT.py(137): rdcs_rig = PotList('rdc_rig')
Pin1RDC_highT.py(138): for (medium,expt,file, scale) in \
Pin1RDC_highT.py(139): [('s','NHN','nh_rdc_Pin1_Pf1.tbl',1),
Pin1RDC_highT.py(146): rdc_rig =
create_RDCPot("%s_%s"%(medium,expt),file,media[medium])
Pin1RDC_highT.py(151): scale_toNH(rdc_rig) #
needed for these datasets
Pin1RDC_highT.py(155): rdc_rig.setScale(scale)
Pin1RDC_highT.py(156): rdc_rig.setShowAllRestraints(1) #all restraints
are printed during analysis
Pin1RDC_highT.py(157): rdc_rig.setThreshold(3) # in Hz
Pin1RDC_highT.py(158): rdcs_rig.append(rdc_rig)
Pin1RDC_highT.py(159): pass
Pin1RDC_highT.py(139): [('s','NHN','nh_rdc_Pin1_Pf1.tbl',1),
Pin1RDC_highT.py(160): potList.append(rdcs_rig)
Pin1RDC_highT.py(161): rampedParams.append( MultRamp(0.0005,1.0,
"rdcs_rig.setScale( VALUE )") )
Pin1RDC_highT.py(163): from rdcPotTools import create_RDCPot, scale_toNH
Pin1RDC_highT.py(164): rdcs_flx = PotList('rdc_flx')
Pin1RDC_highT.py(165): for (medium,expt,file, scale) in \
Pin1RDC_highT.py(166): [('s','NHN_flx','nh_rdc_Pin1_Pf1.tbl',1),
Pin1RDC_highT.py(173): rdc_flx =
create_RDCPot("%s_%s"%(medium,expt),file,media[medium])
Pin1RDC_highT.py(179): rdc_flx.setPotType("square")
Pin1RDC_highT.py(184): scale_toNH(rdc_flx) #
needed for these datasets
Pin1RDC_highT.py(188): rdc_flx.setScale(scale)
Pin1RDC_highT.py(189): rdc_flx.setShowAllRestraints(1) #all restraints
are printed during analysis
Pin1RDC_highT.py(190): rdc_flx.setThreshold(3) # in Hz
Pin1RDC_highT.py(191): rdcs_flx.append(rdc_flx)
Pin1RDC_highT.py(192): pass
Pin1RDC_highT.py(166): [('s','NHN_flx','nh_rdc_Pin1_Pf1.tbl',1),
Pin1RDC_highT.py(193): potList.append(rdcs_flx)
Pin1RDC_highT.py(194): rampedParams.append( MultRamp(0.0005,1.0,
"rdcs_flx.setScale( VALUE )") )
Pin1RDC_highT.py(200): from varTensorTools import calcTensorOrientation,
calcTensor
Pin1RDC_highT.py(201): for medium in media.keys():
Pin1RDC_highT.py(202): calcTensorOrientation(media[medium])
*-- POWELL ------ step= 0 --- stepsize= 0.01000 --- energy evals= 2
-*
| E(poten)= 46648.1595060 grad= 6708.3512014 s_NHN=
23622.3688735 |
| s_NHN_flx= 23025.7906325
|
*------------------------------------------------------------------------------*
*-- POWELL ------ step= 10 --- stepsize= 0.01000 --- energy evals= 27
-*
| E(poten)= 20782.3434281 grad= 3328.2872206 s_NHN=
10583.7622002 |
| s_NHN_flx= 10198.5812280
|
*------------------------------------------------------------------------------*
Powell::step: normal exit.
*-- POWELL ------ step= 16 --- stepsize= 0.01000 --- energy evals= 13
-*
| E(poten)= 20782.2260251 grad= 3329.2665131 s_NHN=
10583.6699328 |
| s_NHN_flx= 10198.5560923
|
*------------------------------------------------------------------------------*
Pin1RDC_highT.py(203): rampedParams.append(
StaticRamp("calcTensor(media['%s'])" % medium) )
Pin1RDC_highT.py(204): pass
Pin1RDC_highT.py(201): for medium in media.keys():
Pin1RDC_highT.py(207): noe=PotList('noe')
Pin1RDC_highT.py(208): potList.append(noe)
Pin1RDC_highT.py(209): from noePotTools import create_NOEPot
Pin1RDC_highT.py(210): for (name,scale,file) in [('all',1,"4xplor_noe.tbl"),
Pin1RDC_highT.py(213): pot = create_NOEPot(name,file)
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "/Users/Shared/nmrware/xplor-nih-2.48/python/trace.py", line 180, in
run
exec cmd in dict, dict
File "<string>", line 1, in <module>
File "Pin1RDC_highT.py", line 213, in <module>
pot = create_NOEPot(name,file)
File "/Users/Shared/nmrware/xplor-nih-2.48/python/noePotTools.py", line
57, in create_NOEPot
noe.addRestraints(open(file).read())
File "/Users/Shared/nmrware/xplor-nih-2.48/python/wrappers/noePot.py",
line 365, in addRestraints
return _noePot.NOEPot_addRestraints(self, *args, **kwargs)
SystemError: xplor-nih error: error reading restraint: selection string (resid
163 and name O ) selects no atoms
PyInterp::command: error executing: >execfile('Pin1RDC_highT.py')<
HEAP: maximum use= 2412447 current use= 2365677
X-PLOR: total CPU time= 5.9278 s
X-PLOR: entry time at 14:56:12 05-Jul-18
X-PLOR: exit time at 14:56:38 05-Jul-18
Looking forward to hear from you.
Thanks!
Karuna
--
Best Regards,
Karuna Dixit
Postdoctoral Research Associate
Department of Biochemistry & Biophysics
Texas A&M University
Email: [email protected]
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