http://blog.gmane.org/gmane.science.biology.xplor-nih.general hourly 1 1901-01-01T00:00+00:00 http://gmane.org/img/gmane-25t.png http://gmane.org http://permalink.gmane.org/gmane.science.biology.xplor-nih.general/1749 <pre> Hello-- When using the Python interface, deviations and numbers of violations are printed out in the REMARKs section of each calculated structure. The identity of the violations is printed in a .viols file, and statistics on most commonly violated restraints are listed in a .stats file. I hope this answers your question. best regards-- Charles -- Charles Schwieters email: Charles&lt; at &gt;Schwieters.org www: http://schwieters.org/cds phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> Charles Schwieters 2013-05-21T14:22:42 http://permalink.gmane.org/gmane.science.biology.xplor-nih.general/1748 <pre>Hi All, how to generate deviation from idealized geomtry in xplor(such as bond)? should we compare with an X-ray structure as an idealized geomtry? Many thanks. _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> wangtian780< at >hotmail.com 2013-05-21T03:42:23 http://permalink.gmane.org/gmane.science.biology.xplor-nih.general/1747 <pre> Hello Santhosh-- You specified that only one structure be calculated. The message menas that there wasn't enough work for a second structure (ensemble). You can parallelize over ensemble member by specifying -num_threads 2. Anyway, there should be a pdb written for each ensemble member. best regards-- Charles -- Charles Schwieters email: Charles&lt; at &gt;Schwieters.org www: http://schwieters.org/cds phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> Charles Schwieters 2013-05-13T23:52:03 http://permalink.gmane.org/gmane.science.biology.xplor-nih.general/1746 <pre>Hello Charles, I have written a script for ensemble refinement based on dna_ensembe/ensemble.py and gb1_rdc/refine.py. The script is along with the mail below. When running the simulation, one of the child process stops working and in the log files I found this line : barrier: error reading from process 1 The simulation proceeds with computing only one structure. While the killed process has : StructureLoop: this process has no work. Exiting... Can you tell me where am I going wrong ? The below script is executed this way: xplor -smp 2 -py -o refine.out 5050.py xplor.requireVersion("2.17") numberOfStructures=1 ensembleSize=2 # number of ensemble members outFilename = "SCRIPT_%d_STRUCTURE_MEMBER.sa" % ensembleSize import protocol protocol.initRandomSeed() command = xplor.command protocol.initParams("protein") #load pdb and covalently minimize the protein protocol.loadPDB("model.pdb") xplor.simulation.deleteAtoms("not known") protocol.fixupCovalentGeom(maxIters=1000,useVDW=1) #initilize ensemble simulations from ensembleSimulation import EnsembleSimulation esim = EnsembleSimulation("ensemble",ensembleSize) # # a PotList contains a list of potential terms. This is used to specify which # terms are active during refinement. # from potList import PotList potList = PotList() # parameters to ramp up during the simulated annealing protocol # from simulationTools import MultRamp, StaticRamp, InitialParams rampedParams=[] highTempParams=[] # orientation Tensor - used with the dipolar coupling term # one for each medium # For each medium, specify a name, and initial values of Da, Rh. # from varTensorTools import create_VarTensor media={} expdatadir = 'xplor5050/' import os,re mediaList = open(expdatadir+'mediaList.txt').readlines() #media[medium] = create_VarTensor(medium) for mediaName in mediaList: mediaName = mediaName.strip() if not mediaName in media.keys(): media[mediaName] = create_VarTensor(mediaName) from rdcPotTools import create_RDCPot, scale_toNH,correctGyromagneticSigns correctGyromagneticSigns() bondTypes = ['NH','CAC','CAHA','CN','CHN'] #xplorBondTypes = {'NH':'NH','CN':'NCO','HNC':'CHN','CAHA':'CAHA', 'CAC':'CACO'} #bondTypeScales = {'NH':15, 'CAHA':3, 'CN':100, 'CAC':100, 'CHN':3} bondTypeScales = {'NH':1, 'CAHA':1, 'CN':1, 'CAC':1, 'CHN':1} rdcs = PotList('rdc') for medium in media.keys(): #rdc = create_RDCPot("%s_%s"%(medium,expt),file,media[medium]) for btype in bondTypes: if os.path.isfile(expdatadir+medium+'_'+btype+'.tbl'): rdc = create_RDCPot("%s_%s"%(medium,btype),expdatadir+medium+'_'+btype+'.tbl',media[medium]) rdc.setScale(bondTypeScales[btype]) rdc.setAveType("sum") # its set to be average by default rdc.setShowAllRestraints(1) rdcs.append(rdc) potList.append(rdcs) rampedParams.append( MultRamp(0.05,5.0, "rdcs.setScale( VALUE )") ) # calc. initial tensor orientation # and setup tensor calculation during simulated annealing # from varTensorTools import calcTensorOrientation, calcTensor for medium in media.keys(): calcTensor(media[medium]) rampedParams.append( StaticRamp("calcTensor(media['%s'])" % medium) ) pass #add other things about NOE later from avePot import AvePot from xplorPot import XplorPot potList.append( AvePot(XplorPot,'VDW') ) rampedParams.append( StaticRamp("protocol.initNBond()") ) rampedParams.append( MultRamp(0.9,0.8, "command('param nbonds repel VALUE end end')") ) rampedParams.append( MultRamp(.004,4, "command('param nbonds rcon VALUE end end')") ) potList.append( AvePot(XplorPot,"BOND") ) potList.append( AvePot(XplorPot,"ANGL") ) potList['ANGL'].setThreshold( 5 ) rampedParams.append( MultRamp(0.4,1,"potList['ANGL'].setScale(VALUE)") ) potList.append( AvePot(XplorPot,"IMPR") ) potList['IMPR'].setThreshold( 5 ) rampedParams.append( MultRamp(0.1,1,"potList['IMPR'].setScale(VALUE)") ) # Give atoms uniform weights, except for the anisotropy axis # protocol.massSetup() # IVM setup # the IVM is used for performing dynamics and minimization in torsion-angle # space, and in Cartesian space. # from ivm import IVM dyn = IVM() dyn.reset() for m in media.values(): m.setFreedom("varyDa, varyRh") #vary tensor Rh, Da, vary orientation protocol.torsionTopology(dyn) #for ending with cartesian minimzation minc = IVM() protocol.initMinimize(minc) for m in media.values(): m.setFreedom("varyDa, varyRh") #allow all tensor parameters float here pass protocol.cartesianTopology(minc) # object which performs simulated annealing # from simulationTools import AnnealIVM init_t = 3000. # Need high temp and slow annealing to converge cool = AnnealIVM(initTemp =init_t, finalTemp=25, tempStep =12.5, ivm=dyn, rampedParams = rampedParams) #criteria to accept a structure def accept(potList): """ return True if current structure meets acceptance criteria """ #if potList['noe'].violations()&gt;0: # return False if potList['rdc'].rms()&gt;1.2: #this might be tightened some return False #if potList['CDIH'].violations()&gt;0: # return False if potList['BOND'].violations()&gt;0: return False if potList['ANGL'].violations()&gt;0: return False if potList['IMPR'].violations()&gt;1: return False return True def calcOneStructure(loopInfo): """ this function calculates a single structure, performs analysis on the structure, and then writes out a pdb file, with remarks. """ # initialize parameters for high temp dynamics. InitialParams( rampedParams ) # high-temp dynamics setup - only need to specify parameters which # differfrom initial values in rampedParams InitialParams( highTempParams ) # high temp dynamics # protocol.initDynamics(dyn, potList=potList, # potential terms to use bathTemp=init_t, initVelocities=1, finalTime=10, # stops at 10ps or 5000 steps numSteps=5000, # whichever comes first printInterval=100) dyn.setETolerance( init_t/100 ) #used to det. stepsize. default: t/1000 dyn.run() # initialize parameters for cooling loop InitialParams( rampedParams ) # initialize integrator for simulated annealing # protocol.initDynamics(dyn, potList=potList, numSteps=100, #at each temp: 100 steps or finalTime=.2 , # .2ps, whichever is less printInterval=100) # perform simulated annealing # cool.run() # final torsion angle minimization # protocol.initMinimize(dyn, printInterval=50) dyn.run() # final all- atom minimization # protocol.initMinimize(minc, potList=potList, dEPred=10) minc.run() #do analysis and write structure loopInfo.writeStructure(potList) pass from simulationTools import StructureLoop, FinalParams StructureLoop(numStructures=numberOfStructures, pdbTemplate=outFilename, structLoopAction=calcOneStructure, genViolationStats=1, averagePotList=potList, averageTopFraction=0.5, #report only on best 50% of structs averageAccept=accept, #only use structures which pass accept() averageContext=FinalParams(rampedParams), averageFilename="SCRIPT_ave.pdb", #generate regularized ave structure averageFitSel="name CA", averageCompSel="not resname ANI and not name H*" ).run() Thanks for your support, Santhosh _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> santhu kumar 2013-05-13T21:38:59 http://permalink.gmane.org/gmane.science.biology.xplor-nih.general/1745 <pre> Hello Marie-- The DIHE term is required during water refinement to act as the normal dihedral portion of the force field during that calculation. The DIHE force constants are low, so violations are more likely. In general, I would evaluate the dihedral quality with a tool like molprobity or whatcheck, rather than the fit of this term. best regards-- Charles -- Charles Schwieters email: Charles&lt; at &gt;Schwieters.org www: http://schwieters.org/cds phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> Charles Schwieters 2013-05-13T17:02:39 http://permalink.gmane.org/gmane.science.biology.xplor-nih.general/1744 <pre>Hello, I've been doing some water refinements using the script from the gb1_rdc example in eginput and I get this term DIHE (it wasn't present while running the annealing script) that has rather large energies comparatively to noes or CDIH. How do I output those violations or how do I know what's creating this term. Shouldn't it be part of the IMPR term? Thanks, Marie </pre> Marie-Laurence Tremblay 2013-05-13T14:45:03 http://permalink.gmane.org/gmane.science.biology.xplor-nih.general/1743 <pre> Hello Santhosh-- Those coordinates are cruft written long ago, and the Python scripts do not actually read these. In the Python interface, the first four atom selections are actually ignored, and the alignment tensor is specified separately, and usually you need not be concerned with the pseudo atoms. The table format remains the same as that read by the old XPLOR RDC terms (dipo and sani) for backward compatibility. Like I said the pseudo atom coordinates are not read in, and axis-orthogonality is maintained by the IVM in the Python scripts. I hope this clears things up a bit. Charles -- Charles Schwieters email: Charles&lt; at &gt;Schwieters.org www: http://schwieters.org/cds phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> Charles Schwieters 2013-05-11T17:43:01 http://permalink.gmane.org/gmane.science.biology.xplor-nih.general/1742 <pre>Hello Charles, Thanks for the clarification. But I am confused from the 7 pseudo atoms. ATOM 856 X ANI 500 322.383 -47.025 154.522 1.00 3.06 ATOM 857 Y ANI 500 322.080 -50.957 156.088 1.00 4.37 ATOM 858 Z ANI 500 323.128 -50.368 152.019 1.00 4.35 ATOM 859 OO ANI 500 324.205 -49.405 154.647 1.00 4.04 These 4 should define the tensor axis. And the RDC definition is done : assign ( resid 500 and name OO ) ( resid 500 and name Z ) ( resid 500 and name X ) ( resid 500 and name Y ) ( resid 2 and name N ) ( resid 2 and name HN ) -3.7330 0.2000 Out of which the first 4 lines are the axes and the remaning 2 are the actual atoms. Am I wrong ? And about the perpendicularity : Do you mean that I need not manually maintain perpendicularity in the model.pdb? Sorry if I am overlooking something. Thanks Santhosh On Sat, May 11, 2013 at 11:16 AM, Charles Schwieters &lt;charles&lt; at &gt;schwieters.org _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> santhu kumar 2013-05-11T16:40:23 http://permalink.gmane.org/gmane.science.biology.xplor-nih.general/1741 <pre> Hello Santhosh-- If you use the Python interface (suggested) then there are 7 pseudo atoms per alignment tensor. The axes must be perpendicular, or you will get nonphysical results. In a proper Xplor-NIH Python script, you don't have to manually configure any pseudo atoms, and the axes will remain perpendicular irrespective of force constants. No- overlap of pseudo atoms corresponding to different alignment tensors is no problem, and with standard parameters there should be no VDW energy calculated. best regards-- Charles -- Charles Schwieters email: Charles&lt; at &gt;Schwieters.org www: http://schwieters.org/cds phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> Charles Schwieters 2013-05-11T16:16:52 http://permalink.gmane.org/gmane.science.biology.xplor-nih.general/1740 <pre>Hello Charles, I think I know the answer for these questions but just want to confirm with you. In refinement of structures using RDC's, we use 4 pseudo-atoms to define an axis and these are part of the PDB also. For more than one RDC dataset, we should have more than such 4 pseudo-atoms. Now the questions are : 1). Should the four atoms be created as a axis? I mean should O-XX be perpendicular to O-YY and so on? Or could it be any four atoms far away from the protein? In the examples, they are mostly perpendicular. 2). In case of multiple RDC constraints, would there be a problem if I overlap many such pseudo-atoms on top of each other? eg : ATOM 856 X ANI 500 322.383 -47.025 154.522 1.00 3.06 ATOM 857 Y ANI 500 322.080 -50.957 156.088 1.00 4.37 ATOM 858 Z ANI 500 323.128 -50.368 152.019 1.00 4.35 ATOM 859 OO ANI 500 324.205 -49.405 154.647 1.00 4.04 ATOM 860 X ANI 600 322.383 -47.025 154.522 1.00 3.06 ATOM 861 Y ANI 600 322.080 -50.957 156.088 1.00 4.37 ATOM 862 Z ANI 600 323.128 -50.368 152.019 1.00 4.35 ATOM 863 OO ANI 600 324.205 -49.405 154.647 1.00 4.04 Would this be fine as per VDW calculations or anything. I am hoping that they could overlap as I have many RDC datasets and it would be tricky to create many such random points. Thanks a lot, Santhosh _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> santhu kumar 2013-05-10T22:08:35 http://permalink.gmane.org/gmane.science.biology.xplor-nih.general/1739 <pre> Hello Jonesy-- It looks like you specified a pdb file where a psf file should be. You might want to try the Python interface instead of the old XPLOR interface. However, you will still need a psf file because you are using nonstandard residues. Please let me know if you have further issues. best regards-- Charles -- Charles Schwieters email: Charles&lt; at &gt;Schwieters.org www: http://schwieters.org/cds phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> Charles Schwieters 2013-05-09T01:04:29 http://permalink.gmane.org/gmane.science.biology.xplor-nih.general/1738 <pre>Hi all, I am trying to generate initial .pdb structures for a peptide RNA complex. My peptide contains nonstandard amino acids; I have already added their topology data to protein.top. When I try to run my script in xplor, I keep getting the following errors (see attached). I have checked to see that my NOE table assignments match what I have put into the topology file, but I am not sure what else to check from here. Any help? Jonesy _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> Alisha Nicole Jones 2013-05-08T22:04:32 http://permalink.gmane.org/gmane.science.biology.xplor-nih.general/1737 <pre> Hello Santhosh-- If you are refining a structure, it does indeed make sense to obtain initial guesses from the starting structure. The script eginput/gb1_rdc/refine.py expects reasonable initial Da and rhombicity values, but can be easily changed to just calculate them from the intial structure, by changing the calcTensorOrientation to calcTensor. The helper script calcTensor will do this for you. calcTensor rdc.tbl structure files... Then these values could be input to a refinement script, as you suggest. hope this helps-- Charles -- Charles Schwieters email: Charles&lt; at &gt;Schwieters.org www: http://schwieters.org/cds phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> Charles Schwieters 2013-04-30T14:59:29 http://permalink.gmane.org/gmane.science.biology.xplor-nih.general/1736 <pre>Hello I am new to Xplor-NIH and have done cartesian coordinate refinements using gromacs before. I have been through the relevant code and tutorials. The striking difference I have seen is that Xplor requires initial Da and Rh values to be provided. This makes sense when we are annealing from a completely unfolded chain but when refining from a good start point [structurally], and letting Da and Rh float [change], would it make a difference if we provide or not provide these initial estimates? And is there an easy way to compute Da and Rh values within xplor framework, given ensemble, RDC data without creating RDCpot ? [ for the initial estimate]. I could write a script in python which does the computation but if it could be done within xplor, it would be more convenient. Thanks Santhosh _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> santhu kumar 2013-04-30T14:11:15 http://permalink.gmane.org/gmane.science.biology.xplor-nih.general/1735 <pre> Hello Jakob-- ok. It's also possible using the old XPLOR angle term- and probably easier in this case. Attached is an example of how to do this using model.pdb from eginput/gb1_rdc. best regards-- Charles import protocol protocol.loadPDB('model.pdb',deleteUnknownAtoms=True) import xplorPot print xplorPot.XplorPot('ANGL').calcEnergy() xplor.command(''' topo presidue ang1 add angle 1CA 2CA 3CA end end ''') #define the angle (CA 2) - (CA 4) - (CA 20) with equilibrium value of 120 degrees xplor.command(''' patch ang1 refe=1=(resid 2) refe=2=(resid 4) refe=3=(resid 20) end ''') print xplorPot.XplorPot('ANGL').calcEnergy() xplor.command(''' param ANGLE (resid 2 and name CA) (resid 4 and name CA) (resid 20 and name CA) 500.00 120 end ''') print xplorPot.XplorPot('ANGL').calcEnergy() -- Charles Schwieters email: Charles&lt; at &gt;Schwieters.org www: http://schwieters.org/cds phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> Charles Schwieters 2013-04-25T17:46:50 http://permalink.gmane.org/gmane.science.biology.xplor-nih.general/1734 <pre>Thanks Charles, I wish to use a few angle constraints to define the orientation between different monomers. I guess the bondAngle term is the better option. Do I need to write this potential myself or is it already coded in an example? best regards, Jakob Hello Jakob-- If you group three atoms together in a rigid body (using the group() method of the IVM) the angle will be preserved. Some care must be taken if you are also using torsion angle dynamics and the atoms are involved with bonds to other atoms. It is also possible to write a simple Python energy term using bondAngle.BondAngle if you'd like a few angle-only restraints If things aren't 100% clear please provide further details. best regards-- Charles </pre> Jakob Toudahl Nielsen 2013-04-25T15:06:49 http://permalink.gmane.org/gmane.science.biology.xplor-nih.general/1733 <pre> Hello Jakob-- If you group three atoms together in a rigid body (using the group() method of the IVM) the angle will be preserved. Some care must be taken if you are also using torsion angle dynamics and the atoms are involved with bonds to other atoms. It is also possible to write a simple Python energy term using bondAngle.BondAngle if you'd like a few angle-only restraints If things aren't 100% clear please provide further details. best regards-- Charles -- Charles Schwieters email: Charles&lt; at &gt;Schwieters.org www: http://schwieters.org/cds phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> Charles Schwieters 2013-04-25T14:20:38 http://permalink.gmane.org/gmane.science.biology.xplor-nih.general/1732 <pre>Dear all, sorry if there is an obvious answer to this simple question, which I could not find. I wish to use angles constaints constraining three atoms, which are not related by bonds, to a certain angle. It seems it is only possible to constrain dihedral angles, and guess adding to the parameter file is not a good option. Is there a way to go? thanks in advance, 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 and Interdisciplinary Nanoscience Center (iNANO) Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark Office: 1593-227 Phone: +45 871 56654 (office) &amp; 2993 8501 (cell) _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> Jakob Toudahl Nielsen 2013-04-25T13:47:57 http://permalink.gmane.org/gmane.science.biology.xplor-nih.general/1731 <pre>Hello Charles Thanks. That solved it and I can successfully start the docking. I had to change names for the atom types to get the addunknownatoms to recognize them. Best regards Carl 23 apr 2013 kl. 17:39 skrev "Charles Schwieters" &lt;charles&lt; at &gt;schwieters.org&gt;: </pre> Carl Diehl 2013-04-25T08:06:15 http://permalink.gmane.org/gmane.science.biology.xplor-nih.general/1730 <pre> Hello Carl-- Please see the example in eginput/PSF_generation/addAtoms.py in the Xplor-NIH distribution. From your description, it seems that you missed calling protocol.addUnknownAtoms(). best regards-- Charles -- Charles Schwieters email: Charles&lt; at &gt;Schwieters.org www: http://schwieters.org/cds phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> Charles Schwieters 2013-04-23T15:39:49 http://permalink.gmane.org/gmane.science.biology.xplor-nih.general/1729 <pre>Hello I'm in the process of setting up a docking run using chemical shifts, and are running into problems with the generation of a input structure for one of the proteins in the docking. I'm docking 2 proteins, where one of the proteins is a Zinc-finger with 2 Zn2+ atoms, one coordinated by 4 Cys and the other one coordinated by 2 Cys &amp; 2 His. One histidine is coordinated by NE2 and the other by ND1. Based on answers from the mailing list and examples, I modified a topology file and parameter file for incorporating the two Zn. Upon running the file (see below) I can successfully generate the psf-file and a pdb-file. However, in the pdb-file, the Zn2+ and some N and C-terminal residues gets coordinates -9999.9. I have tried fixing that by running fixupCovalentGeom in the script, which causes the script to fail, saying missing atoms. What have I missed when setting up the protein and how can I fix this? I also want to mutate one residue to another in order to generate my version of the protein. The topology file is based on toph19.ion, where I generated bonds and angles, based upon how Zn2+ are handled in Aria/CNS. The file is as follows: PRESidue ZNK GROUP delete atom 1HG end MODIfy ATOM 1CB CHARge= 0.19 END MODIfy ATOM 1SG TYPE=S CHARge=-0.19 END ATOM 1ZN TYPE=ZN CHARGE=+2.0 END GROUP delete atom 2HG end MODIfy ATOM 2CB CHARge= 0.19 END MODIfy ATOM 2SG TYPE=S CHARge=-0.19 END GROUP delete atom 3HG end MODIfy ATOM 3CB CHARge= 0.19 END MODIfy ATOM 3SG TYPE=S CHARge=-0.19 END GROUP delete atom 4HG end MODIfy ATOM 4CB CHARge= 0.19 END MODIfy ATOM 4SG TYPE=S CHARge=-0.19 END ADD BOND 1ZN 1SG ADD BOND 1ZN 2SG ADD BOND 1ZN 3SG ADD BOND 1ZN 4SG ADD ANGLe 1CB 1SG 1ZN ADD ANGLe 2CB 2SG 1ZN ADD ANGLe 3CB 3SG 1ZN ADD ANGLe 4CB 4SG 1ZN ADD ANGLe 1SG 2SG 1ZN ADD ANGLe 1SG 3SG 1ZN ADD ANGLe 1SG 4SG 1ZN ADD ANGLe 2SG 3SG 1ZN ADD ANGLe 2SG 4SG 1ZN ADD ANGLe 3SG 4SG 1ZN END PRESidue C2HED GROUP delete atom 1HG end MODIfy ATOM 1CB CHARge= 0.19 END MODIfy ATOM 1SG TYPE=S CHARge=-0.19 END ATOM 1ZN TYPE=ZN CHARGE=+2.0 END GROUP delete atom 2HG end MODIfy ATOM 2CB CHARge= 0.19 END MODIfy ATOM 2SG TYPE=S CHARge=-0.19 END GROUP MODIFY ATOM 3ND1 TYPE=NR CHARge=-0.40 END GROUP MODIFY ATOM 4NE2 TYPE=NR CHARge=-0.40 END add bond 1ZN 1SG add bond 1ZN 2SG add bond 1ZN 3ND1 add bond 1ZN 4NE2 add angle 1SG 1ZN 2SG add angle 1SG 1ZN 3ND1 add angle 1SG 1ZN 4NE2 add angle 2SG 1ZN 3ND1 add angle 2SG 1ZN 4NE2 add angle 3ND1 1ZN 4NE2 add angle 1ZN 1SG 1CB add angle 1ZN 2SG 2CB add angle 1ZN 3ND1 3CG add angle 1ZN 3ND1 3CE1 add angle 1ZN 4NE2 4CG add angle 1ZN 4NE2 4CD2 END RESIdue ZN {* zinc *} GROUP ATOM ZN TYPE=ZN CHARGE=+2.0 END END and the parameter file is: bonds S ZN 500.0 2.30 BOND NR ZN 500.000 2.00 angles S ZN S 500.0 109.5 angles ZN S CH2E 70.0 120.0 angles ZN S CT 70.0 120.0 angles S ZN NR 500.0 109.5 angles NR ZN NR 500 109.5 ANGLes ZN NR CR1E 500.00 120.0000 ANGLes ZN NR CRH 500.00 120.0000 ANGLes ZN NR C5 500.00 120.0000 ! eps sigma eps(1:4) sigma(1:4) ! (kcal/mol) (A) ! --------------------------------------- NONBonded ZN 0.0430 3.3676 0.0430 3.3676 ! garbage I generate the psf-file using the following python-script, where I first patch histidine residues to the correct protonation and then I add the Zn-patches: xplor.parseArguments() import protocol protocol.loadPDB("1tota_cns.pdb") import psfGen protocol.initTopology("toph19.ion") protocol.initTopology("toph19.his") protocol.initParams("param19.ion") protocol.initParams("parhcsdx.pro") xplor.command(""" topology AUTO ANGLe=False DIHEdral=False END end patch HISE reference=nil=( resid 242 ) end patch HISD reference=nil=( resid 240 ) end patch ZNK reference=1=( resid 209 ) reference=2=( resid 212 ) reference=3=( resid 231 ) reference=4=( resid 234 ) end patch C2HED reference=1=( resid 222 ) reference=2=( resid 225 ) reference=3=( resid 242 ) reference=4=( resid 240 ) end """) xplor.command("write psf output=1tota_cns_zn.psf end") from pdbTool import PDBTool PDBTool("test.pdb").write() Best Regards Carl Diehl Post-Doc NNF CPR Copenhagen university, Denmark _______________________________________________ Xplor-nih mailing list Xplor-nih&lt; at &gt;nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih </pre> Carl Diehl 2013-04-23T14:42:38 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.science.biology.xplor-nih.general