Cristian, Please send us a ticket at [email protected]. The lts (“long term support”) VMs are very light on resources and I expect any calculation you start will take a long time to run compared to our production VMs.
-- Gerard Weatherby | Application Architect NMRbox | NAN | Department of Molecular Biology and Biophysics | UConn Health 263 Farmington Avenue, Farmington, CT 06030-6406 uchc.edu<http://uchc.edu> On Jul 5, 2022, 9:25 PM -0400, Scott Robson <[email protected]>, wrote: *** Attention: This is an external email. Use caution responding, opening attachments or clicking on links. *** Hi Cristian, I've had some issues recently too with software on nmrbox. In my case cyana... (am I allowed to say cyana on this list? ;)) Anyway I've noticed that the more newly updated nmrbox servers will not run certain aspects of cyana while the old servers still work ok. So I suggest you try an old server and see if your problem goes away. Try lts2021-33.nmrbox.org<https://urldefense.com/v3/__http://lts2021-33.nmrbox.org__;!!Cn_UX_p3!nY__NFBCmuRSP7E2B2mI_dqLK2wC6SQLgiA2cq1rC53GPtLxDo0KLPf3pSl3ZiohD3fi8l9-Va_PYA0MRqr_kNARgyL5iQ$>? If the problem goes away but persists on the newer system you have the error on you can contact the nmrbox people about it. Or let me know and I can help you elevate it to their attention - I need to do this for cyana anyway. My guess is a legacy library that got updated and no longer works the way the old compiled versions of these software expect. Scott On Tue, Jul 5, 2022 at 6:49 PM Cristian E. <[email protected]<mailto:[email protected]>> wrote: Hi, I have been using a script to refine a NMR structure using NOEs, RDCs, SAXS and other data without problems until recently. Now, the same script results in a Segmentation fault (core dumped) error. After doing some trouble shooting, I noticed that the program runs fine when I remove the RDC part in the script, but I don't know what the issue is. I use Xplor-NIH in NMRBOX. Here is the code and the last lines in the output. Thanks for the help, Cristian ########################################################################### import psfGen outfilename = 'SCRIPT_STRUCTURE.pdb' import protocol protocol.initRandomSeed(3422) # by specific seed number # Load paramaters. protocol.initParams(files=['nucleic']) psfGen.pdbToPSF(pdb_filename) protocol.initCoords(pdb_filename) xplor.simulation.deleteAtoms("not known") from potList import PotList potList = PotList() crossTerms = PotList() from simulationTools import StaticRamp, MultRamp, InitialParams, AnnealIVM highTempParams = [] rampedParams = [] # # Set up distance restraint potential # import noePotTools noe = PotList('noe') for (name, scale, table) in [('all', 1, noe_tbl), ]: pot = noePotTools.create_NOEPot(name, table) pot.setScale(scale) noe.append(pot) potList.append(noe) rampedParams.append(MultRamp(2, 50, "noe.setScale( VALUE )")) import xplorPot # Set up dihedral angles protocol.initDihedrals(dihedral_tbl, #useDefaults=False # by default, symmetric sidechain # restraints are included ) potList.append( xplorPot.XplorPot('CDIH') ) highTempParams.append( StaticRamp("potList['CDIH'].setScale(10)") ) rampedParams.append( StaticRamp("potList['CDIH'].setScale(200)") ) # # Set up potential for base-pair planarity restraints. # protocol.initPlanarity(plane_tbl) potList.append(xplorPot.XplorPot('PLAN')) # Set up statistical torsion angle potential (torsionDB). # import torsionDBPotTools torsiondb = torsionDBPotTools.create_TorsionDBPot(name='torsiondb',system='rna') potList.append(torsiondb) rampedParams.append(MultRamp(0.5, 4, "torsiondb.setScale(VALUE)")) # Setup parameters for atom-atom repulsive term (van der Waals-like term). # from repelPotTools import create_RepelPot,initRepel repel = create_RepelPot('repel') potList.append(repel) rampedParams.append( StaticRamp("initRepel(repel,use14=False)") ) rampedParams.append( MultRamp(.004, 4, "repel.setScale( VALUE)") ) # nonbonded interaction only between C1' atoms highTempParams.append( StaticRamp("""initRepel(repel, use14=True, scale=0.004, repel=1.2, moveTol=45, interactingAtoms="name C1'" )""") ) # Selected 1-4 interactions. import torsionDBPotTools repel14 = torsionDBPotTools.create_Terminal14Pot('repel14') potList.append(repel14) highTempParams.append(StaticRamp("repel14.setScale(0)")) rampedParams.append(MultRamp(0.004, 4, "repel14.setScale(VALUE)")) # Set up bond length potential. potList.append(xplorPot.XplorPot('BOND')) # (The setup of this term remains unchanged throughout; no need to involve # highTempParams and/or rampedParams.) # # Set up bond angle potential. potList.append(xplorPot.XplorPot('ANGL')) rampedParams.append(MultRamp(0.4, 1.0, "potList['ANGL'].setScale(VALUE)")) # # Set up improper dihedral angle potential. potList.append(xplorPot.XplorPot('IMPR')) rampedParams.append(MultRamp(0.1, 1.0, "potList['IMPR'].setScale(VALUE)")) ###RDC from varTensorTools import create_VarTensor from rdcPotTools import create_RDCPot, scale_toNH from varTensorTools import calcTensorOrientation, calcTensor media={} for medium, Da, Rh in tensor_list: #print(medium,Da, Rh, tensor_list) oTensor = create_VarTensor(medium) oTensor.setDa(Da) oTensor.setRh(Rh) oTensor.setFreedom ("varyDa, varyRh" ) #oTensor.setFreedom ("fixDa, fixRh" ) media[medium] = oTensor highTempParams.append(StaticRamp(""" for medium in media.values(): calcTensorOrientation(medium) """) ) rdcs = PotList('rdc') for medium, expt, rdc_file, scale in rdc_exp_list: #print(experiments_list, medium, expt, rdc_file, scale, media_dictionary) rdc = create_RDCPot("%s_%s"%(medium,expt), file=rdc_file, oTensor=media[medium]) #rdc.setScale(scale) scale_toNH(rdc) rdc.setShowAllRestraints(1) #all restraints are printed during analysis rdc.setThreshold(1.5) # in Hz rdcs.append(rdc) potList.append(rdcs) rampedParams.append( MultRamp(0.01,1, "rdcs.setScale( VALUE )") ) ### SAXS term ########### #from solnXRayPotTools import create_solnXRayPot import solnXRayPotTools xray=solnXRayPotTools.create_solnXRayPot('xray', experiment=saxs_data, #data file with columns q, I, err numPoints=100, #specifies the number of datapoints to sample normalizeIndex=-3, #specifies which grid point to use to normalize data. -3 specifies normalization which minimizes the Chi^2 value. preweighted=False) xrayCorrect=solnXRayPotTools.create_solnXRayPot('xray-c', experiment=saxs_data, numPoints=100, #should be the same as 'xray' normalizeIndex=-3, preweighted=False) solnXRayPotTools.useGlobs(xray) #uses atom globbing aproximation xray.setNumAngles(100) #number of angles in solid angle averaging xrayCorrect.setNumAngles(500) # use a large number for correction term xray.setScale(50) #restrint weight value xray.setCmpType("plain") #'plain' potList.append(xray) #add to potlist energy terms crossTerms.append(xrayCorrect) from solnScatPotTools import fitParams rampedParams.append( StaticRamp( "fitParams(xrayCorrect);xray.calcGlobCorrect(xrayCorrect.calcd())", stride=100)) # Give atoms uniform weights, except for anisotropy axes (if any). # protocol.massSetup() # # Set up IVM object(s). # # IVM object for torsion-angle dynamics/minimization. import ivm dyn = ivm.IVM() protocol.torsionTopology(dyn, flexRiboseRing='resid 1:24') ### Optional IVM object for final Cartesian minimization. minc = ivm.IVM() protocol.cartesianTopology(minc) # # Temperature set up. # temp_ini = 3000.0 # initial temperature temp_fin = 25.0 # final temperature def calcOneStructure(loopInfo): """Calculate a structure. """ # Fix up covalent geometry. # (The torsion restraints may include ring torsions and distort geometry.) while True: try: protocol.fixupCovalentGeom(maxIters=100, useVDW=1) break except protocol.CovalentViolation: pass # # High Temperature Dynamics Stage. # # Initialize parameters for high temperature dynamics. InitialParams(rampedParams) InitialParams(highTempParams) # purposedly overides some # setups in rampedParams # Set up IVM object and run. protocol.initDynamics(dyn, potList=potList, bathTemp=temp_ini, initVelocities=1, finalTime=15, # run for finalTime or numSteps=15001, # numSteps * 0.001, whichever is less printInterval=100) dyn.setETolerance(temp_ini/100) # used to find stepsize (default: temp/1000) dyn.run() # # Simulated Annealing Stage. # # Initialize parameters for annealing. InitialParams(rampedParams) # Set up IVM object for annealing. protocol.initDynamics(dyn, potList=potList, finalTime=0.63, # run for finalTime or numSteps=631, # numSteps * 0.001, whichever is less printInterval=100) # Set up cooling loop and run. AnnealIVM(initTemp=temp_ini, finalTemp=temp_fin, tempStep=12.5, ivm=dyn, rampedParams=rampedParams).run() # # Torsion angle minimization. # protocol.initMinimize(dyn, potList=potList, printInterval=50) dyn.run() # # Cartesian minimization (optional). # protocol.initMinimize(minc, potList=potList, dEPred=10) minc.run() from simulationTools import StructureLoop StructureLoop(numStructures=nstructures, #pdbFilesIn=infilename, pdbTemplate=outfilename, doWriteStructures=True, structLoopAction=calcOneStructure, # Arguments for generating structure statistics: genViolationStats=True, averageSortPots=[potList['noe'], # terms for structure sorting potList['PLAN'], potList['xray'], potList['CDIH'], potList['rdc']], averageTopFraction=FRACTION, # top fraction of structs. to report on averageFilename="SCRIPT_ave.pdb", averagePotList=potList, # terms analyzed averageFitSel='not (name H* or resname ANI)', # selection to fit ).run() # to average struct. # and report precision ################################################################# Log: GU12_ref_RDC_SAXS.py(373): StructureLoop(numStructures=nstructures, StructureLoop: calculating structure 0 GU12_ref_RDC_SAXS.py(306): try: GU12_ref_RDC_SAXS.py(307): protocol.fixupCovalentGeom(maxIters=100, useVDW=1) [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') GU12_ref_RDC_SAXS.py(308): break GU12_ref_RDC_SAXS.py(317): InitialParams(rampedParams) [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') [stdin](1): xplor.execfile('GU12_ref_RDC_SAXS.py') Segmentation fault (core dumped) ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: Bad URL Removed - see why - https://ees.sps.nih.gov/services/Pages/Anti-Virus.aspx?SUBED1=XPLOR-NIH&A=1<Bad%20URL%20Removed%20-%20see%20why%20-%20https://ees.sps.nih.gov/services/Pages/Anti-Virus.aspx?SUBED1=XPLOR-NIH&A=1> -- ------------------------ Scott A. Robson ________________________________ To unsubscribe from the XPLOR-NIH list, click the following link: Bad URL Removed - see why - https://ees.sps.nih.gov/services/Pages/Anti-Virus.aspx?SUBED1=XPLOR-NIH&A=1__;!!Cn_UX_p3!nY__NFBCmuRSP7E2B2mI_dqLK2wC6SQLgiA2cq1rC53GPtLxDo0KLPf3pSl3ZiohD3fi8l9-Va_PYA0MRqr_kNAzHa7h7Q$> ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
