- modeller_usage - salilab.org

Re: Bad template?--log ali. and top files.
by Lei Wang 02 May '02

02 May '02

log file: ####################################### MODELLER 6v1, 17 Jan 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux master.cl.mssm.edu 2.4.9-13smp i686 Date and time of compilation : 01/24/2002 16:28:15 Job starting time (YY/MM/DD HH:MM:SS): 2002/05/02 11:04:08.230 getprog_531W> ROUTINE redefined: getnames check_ali___> Checking the sequence-structure alignment. Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- END OF TABLE ############################################ Top file: ********************************* INCLUDE SET ATOM_FILES_DIRECTORY = './' SET ALNFILE = '1gh0B-3-1eyxK.ali' SET KNOWNS = '1eyxK' SET SEQUENCE = '1gh0B' SET STARTING_MODEL = 1 SET ENDING_MODEL = 5 CALL ROUTINE = 'model' SUBROUTINE ROUTINE = 'getnames' STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION = 'EQ', THEN = ; 'STRING_OPERATE OPERATION = CONCATENATE, STRING_ARGUMENTS = 1gh0B-3-1eyxK .ini, RESULT = MODEL' STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATION = 'EQ', THEN = ; 'STRING_OPERATE OPERATION = CONCATENATE, STRING_ARGUMENTS = 1gh0B-3-1eyxK .rsr, RESULT = CSRFILE' STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = '1gh0B-3-1eyxK' '.sch', RESULT = SCHFILE STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = '1gh0B-3-1eyxK' '.mat', RESULT = MATRIX_FILE SET ROOT_NAME = '1gh0B-3-1eyxK' RETURN END_SUBROUTINE ************************************* >P1;1gh0B structureX:1gh0B: 1 :B: 172 :B:undefined:undefined:-1.00:-1.00 MFDAFTKVVSQADTRGEMLSTAQIDALSQMVAESNKRLDVVNRITSNASTIVSNAARSLFAEQPQLIAPGG-AYT SRRMAACLRDMEIILRYVTYAVFAGDASVLEDRCLNGLRETYLALGTPGSSVAVGVGKMKEAALA---IVNDPAG ITPGDCSALASEIAGYFDRAAAAVS* >P1;1eyxK structureX:1eyxK: 1 : : 164 : :undefined:undefined:-1.00:-1.00 MKSVITTVISAADSAGRFPSSSDLESVQGNIQRASARLEAAEKLASNHEAVVKEAGDACFGKYGYLKNPGEAGEN QEKINKCYRDIDHYMRLVNYSLVIGGTGPLDEWGIAGAREVYRTLNLPTSAYIAAFAFTRDR-LCGPRDMS---- -----AQ-AGVEYSTALDYIINSLS*

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Bad template?
by Lei Wang 02 May '02

02 May '02

1 0

starting with 6v1
by Laurent Troxler 02 May '02

02 May '02

Hi, I am new user of Modeller and as a test I took input files (see bellow) from a friend which were successfully run with version 5. After a few minutes of computing here is the message I get in the logfile: ------------------------------------------------------------------------------------ Initial value of energy before optimization : 15011.7158 Current energy : 14658.3125 Symmetry term within energy : 0.0000 Optimizer exit status : 0 Number of iterations : 67 Number of calls to energy function : 139 Number of updates of dynamic contacts : 8 Number of non-updates of dynamic contacts : 132 Final maximal atomic shift : 0.007 act10___551E> No such routine: recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 17362145 16955.219 16.558 Starting time : 2002/05/02 10:09:43.976 Closing time : 2002/05/02 10:14:02.653 Total CPU time [seconds] : 0.00 ------------------------------------------------------------------------------------ The PDB files come from the PDB server. Is there any problem in the input file ? Thanks for any help or suggestion Laurent ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, @ Laurent TROXLER @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@/\@@/\@@/\@@@@ UPR 9022 CNRS, Réponse Immunitaire et / \/ \/ \ Développement chez les Insectes / /\/ /\/ /\ \ Institut de Biologie Moléculaire et Cellulaire\ \/ /\/ /\/ / 15 rue René Descartes \ \/\ \/\ \/ 67084 Strasbourg Cedex - FRANCE /\ \/\ \/\ \ E-mail: L.Troxler(a)ibmc.u-strasbg.fr / /\/ /\/ /\ \ Tel : (33) 03 88 41 70 07 \ \/ /\/ /\/ / @ Fax : (33) 03 88 60 69 22 @@@@@@@@@@@@@@@@@@@\@@/\@@/\@@/@@@ """"""""""""""""""""""""""""""""""""""""""""""""""\/""\/""\/"""" -- input.top: ------------------------------------------------------------------------------------ INCLUDE #SET OUTPUT_CONTROL = 1 1 1 1 2 SET DIRECTORY = 'model2_dir' SET ATOM_FILES_DIRECTORY = 'model2_dir' SET OUTPUT_DIRECTORY = 'model2_dir' SET PDB_EXT = '.pdb' SET ALNFILE = 'easter2.pir' SET KNOWNS = '1QRZ' '1DST' '1FIW' '1AUT' SET SEQUENCE = 'east' SET MD_LEVEL = 'refine1' SET OUTPUT = 'long' CALL ROUTINE = 'model' ------------------------------------------------------------------------------------ input.pir ------------------------------------------------------------------------------------ >P1;1QRZ structureX:1QRZ : 546:A: 791:A:undefined:undefined:-1.00:-1.00 -----------------------FDCGKPQVE-----------------------PKKCP GRVVGGCV----AHPHSWP-W----------QVSLRTRFG----QHFCGGTLISPEWVLT AAHCLEK---------SPRPSSYKVILGAHQEV--------------------------- ----NL------------EPHVQEIEVS---RLFLEPTR-----------KDIALLKLSS PAVITD------KVIPACLP---SPNYMVA-DRTECFITGWGETQGTFGAG------LLK EAQLPVIENKVCNR--------YEFLNGRVQSTELCAGHL-AGGTDSCQGDSGGPLVCFE KDK----YILQGVTSWG-LGCARPNKPGVYVRVSRFVTWIEGVLR-NN------------ --------------------------* >P1;1DST structureX:1DST : 16: : 243: :undefined:undefined:-1.00:-1.00 ------------------------------------------------------------ --ILGGRE----AEAHARP------------YMASVQLNG----AHLCGGVLVAEQWVLS AAHCLE----------DAADGKVQVLLGAHSLS--------------------------- ----QP------------EPSKRLYDVL---RAVPHPDYQPDTI-----DHDLLLLQLSE KATLGP------AVRPLPWQ---RVDRDVA-PGTLCDVAGWGIVNHAGRRPD-----SLQ HVLLPVLDRATCNR--------RTHHDGAITERLMCAE---SNRRDSCKGDSGGPLVCG- -------GVLEGVVSWGSRVCGNRKKPGIYTRVASYAAWIDSVLA--------------- --------------------------* >P1;1FIW structureX:1FIW : 16:A: 254:A:undefined:undefined:-1.00:-1.00 ------------------------------------------------------------ --IIGGQD----AAHGAWPWM-------VSLQIFTYHNNR---RYHVCGGSLLNSQWLLT AAHCFRI---------KKKVTDWRLIFGAKEVEWG------------------------- --TNKPV-----------KPPLQERYVE---KIIIHEKYSASSE-----ANDIALMKITP PVTCGH------FIGPGCLP---QFRAGPPRVPQTCWVAGWGFLQENARRTSP----MLQ EARVDLIDLGLCNS--------TRWYNGRIRSTNVCAGYP-EGKIDTCQGDSGGPLMCKD SAEN--SYVVVGITSWG-VGCARAKRPGVYTSTWSYLNWIASKIGSTAVHMIQLPT* >P1;1AUT structureX:1AUT : 17:C: 244:C:undefined:undefined:-1.00:-1.00 ------------------------------------------------------------ ---IDGKM----TRRGDSP-W----------QVVLLDSKK----KLACGAVLIHPSWVLT AAHCMD------------ESKKLLVRLGEYDLR--------------------------- ----RW------------EKWELDLDIK---EVFVHPNYSKSTT-----DNDIALLHLAQ PATLSQ------TIVPICLPDSGLAERELNQAGQETLVTGWGYHSSREKEAKRNRTFVLN FIKIPVVPHNECSE----------VMSNMVSENMLCAGIL-GDRQDACEGDSGGPMVASF HG----TWFLVGLVSWG-EGCGLLHNYGVYTKVSRYLDWIHGHIRD-------------- ----------------* >P1;east sequence::::::::0.00: 0.00 ------------------------------------------------------------ ---YGGMK----TKIDEFPWM----------ALIEYTKSQG-KKGHHCGGSLISTRYVIT ASHCVNG------KALPTDWRLSGVRLGEWDT---------------------------- --NTNPDCEVDVRGMKDCAPPHLDVPVE---RTIPHPDYIPASK---NQVNDIALLRLAQ QVEYTD------FVRPICLP-LDVNLRSATFDGITMDVAGWGKTEQLSASN------LKL KAAVEGSRMDECQN-------VYSSQDILLEDTQMCAG-G-KEGVDSCRGDSGGPLIGLD TNKVNTYYFLAGVVSFGPTPCGLAGWPGVYTLVGKYVDWIQNTIES-------------- --------------------------* ------------------------------------------------------------------------------------

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Re: Running MODELLER
by Bozidar Jerkovic 26 Apr '02

26 Apr '02

Hi, It looks like you : 1. didn't installed MODELLER correctly 2. didn't source .cshrc after installation Please, email me a copy of your .cshrc and all input files. Thanks, Bozidar PS. I implore everybody to email all the questions to the modeller_usage list first, because some other people might have the same problems and they could help or learn how to solve similar problems when they encounter them ;-) On Sat, 27 Apr 2002, [ISO-2022-JP] $BLpLn!!2mM5(J wrote: > I have vety basic questions about modeller6v0. > I have installed it in my PC(Linux RedHat 7). > > I tried to run modeller according to manual(Tutorial on using MODELLER for > comparative modeling). > I can make sure Atom file,Alignment file, Script file and so on. > > There is a sample script file model-default.top as follows > (examples/tutorial-model/model-default.top). > > # Homology modelling by the MODELLER TOP routine 'model'. > > INCLUDE # Include the > predefined TOP routines > > SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file > SET ALNFILE = 'alignment.ali' # alignment filename > SET KNOWNS = '5fd1' # codes of the templates > SET SEQUENCE = '1fdx' # code of the target > SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom > files > SET STARTING_MODEL= 1 # index of the first model > SET ENDING_MODEL = 1 # index of the last model > # (determines how > many models to calculate) > > CALL ROUTINE = 'model' # do homology modelling > > > > According to manual > > "To run MODELLER with the script file model-default.top, execute the > following command: > > mod model-default" > > So I tried to input mod model-default as follows. > > [root(a)fox08.tutorial-model] # mod model-default > > But,the answer is no directory. > > I can't run modeller .I tried other command too. > > Maybe, I don't understand very basci method. > > What should I do to run modeller? > >

1 0

MODELLER & XPLOR
by Mensur Dlakic 26 Apr '02

26 Apr '02

Hello, Is there any script/program to convert MODELLER-like restraints files into XPLOR/CNS NMR-like restraints files? I suspect that QUANTA might have this but don't have access to it. I am interested in comparing MODELLER's most rigorous refinement with XPLOR procedures using the same set of restraints. Has anyone tried this already? All the best, Mensur =========================================================================== | Mensur Dlakic, PhD | Tel: (734) 764-3554 | | Department of Biological Chemistry | Fax: (734) 615-3397 | | University of Michigan Medical School | http://www.umich.edu/~mensur/ | | 5416 Medical Science I | http://myprofile.cos.com/mensur | | Ann Arbor, MI 48109-0606 | E-mail: mensur(a)umich.edu | ===========================================================================

1 0

Re: Memory leak / kernel crash / missing chain_ID
by Bozidar Jerkovic 25 Apr '02

25 Apr '02

Hi, Loop routine doesn't use coordinates for the loop residues from the pdb file anyway. All atoms in the residues selected for the loop modeling are aligned on the line that spans two ancoring residues before the loop modeling begins. Good luck, Bozidar On Thu, 25 Apr 2002 AA_Canutescu(a)fccc.edu wrote: > Dear Bozidar, > > Thank you for help. Your hint(to put '' instead of '0') looks to work so far. > Regarding the fact that coordinates for the loop were zeroed, I did this in > order to get a de novo loop prediction. > > Adrian > > Quoting Bozidar Jerkovic <bozidar(a)oboe.rockefeller.edu>: > > > > > Dear Adrian, > > > > A simple answer to your question is: you specified a non-existing > > segment of the protein for the loop optimization: > > SELECTION_SEGMENT = '151:0' '154:0', SELECTION_STATUS = 'initialize' > > > > In your pdb file there is no '0' chain: > > ATOM 1165 CD2 LEU 150 44.348 42.655 43.046 1.00 15.23 C > > ATOM 1166 N GLY 151 0.000 0.000 0.000 1.00 16.38 N > > ATOM 1167 CA GLY 15 0.000 0.000 0.000 1.00 15.57 C > > > > This results in MODELLER selecting the whole protein to perform 'loop' > > routine on it: > > Number of all, selected real atoms : 1480 1480 > > > > Another thing I noticed is that you have compresses all the residues you > > are selecting into one point? Is there any specific reason for this? > > ATOM 1166 N GLY 151 0.000 0.000 0.000 1.00 16.38 N > > ATOM 1167 CA GLY 151 0.000 0.000 0.000 1.00 15.57 C > > ATOM 1168 C GLY 151 0.000 0.000 0.000 1.00 16.31 C > > > > MODELLER complains about this though, but it keeps on: > > serious non-bonded atom clash: 1143 1148 0.000 > > serious non-bonded atom clash: 1143 1149 0.000 > > serious non-bonded atom clash: 1143 1150 0.000 > > > > Energies are way off the charts: > > Initial value of energy before optimization : 477452.2400 > > Current energy : 476905.9000 > > Maximal energy, step : 525495.1200 > > 28 > > Minimal energy, step : 449273.2100 > > 81 > > Average energy, stand.dev. : 506870.8100 > > 15563.8500 > > > > What causes MODELLER to become a memory hog is the fact that you > > unintentionally tried to perform an ab initio calculation of the whole > > protein. I myself almost crashed our main Linux machine in the group, > > running your top file. A job used up 92% of the available memory at one > > point. > > > > After I corrected the .top file: > > SELECTION_SEGMENT = '151:' '154:', SELECTION_STATUS = 'initialize' > > > > Energy returned to normal: > > Initial value of energy before optimization : 27.4512 > > Current energy : 4.5270 > > Maximal energy, step : 67.8339 > > 34 > > Minimal energy, step : 25.2391 > > 363 > > Average energy, stand.dev. : 43.2928 > > 10.7857 > > > > ... and MODELLER produced a beautiful model ;-) > > > > Summa sumarum: > > One has to make sure that when s/he selects a segment of the protein, > > using 'res_ID:chain_ID' convention (which is updated for the 6v2 > > release), that there is an existing chain_ID there. This is actually > > quite a common mistake many users do: their pdb has a chain_ID, and they > > omit it in their top file (just opposite of what you did). > > > > I am still curious why you have compressed all the loop residues into a > > single point (why those residues have all the coordinates equal to > > zero)? It worked, because those resides were brought back into the > > protein in the model MODELLER calculated, which is obviously good, and > > their energy is also fine. If this is some empirical finding, and not > > missing coordinates, I would certainly like to learn more about it. > > > > ...and there is no memory leak, thankfully ;-) > > > > All the best and happy modeling, > > Bozidar > > > > > > > > -----Original Message----- > > From: AA_Canutescu(a)fccc.edu [mailto:AA_Canutescu@fccc.edu] > > Sent: Wednesday, April 17, 2002 6:49 PM > > To: Bozidar Jerkovic > > Subject: Re: MODELLER > > > > > > Dear Bozidar, > > > > > > > > Yes I am aware of this one. I think it may have to do with static vs. > > > dynamic linking. > > > > It's not obvious to me why could be a linking problem, but anyway it's > > interesting this happens only for certain input files. For the input > > data sets that generate this bug, the bug is repro(reproducible -all the > > time). There is no situation(as far as I tested) in which for the same > > input data to get the software working sometime and not working other > > time. It just doesn't work -all the time - for that input data. > > > > > > > What did you mean by "repro"? > > > > An error that is exactly reproducible under any circumstances. It's used > > in programers' jargon. > > > > > > The other problem, that is actually the most serious one is also repro. > > For certain input data sets, modeller starts allocating huge amounts of > > memory (about 1GB/min on my machine). This indicates a serious memory > > leak. I got my kernal crashed twice today because of this, so I have to > > wait for your patch before using again modeller. > > > > I will attach again an input data set that leads to this memory leak. > > > > Everything is run on RedHat 7.2 on x86 architecture. > > > > Thanks, > > Adrian > > > > > > > > > > Thanks for these reports. It's sometimes hard for us to catch > > > everything. > > > > > > Best, > > > Bozidar > > > > > > > > > On 17/4/02 5:33 PM, "AA_Canutescu(a)fccc.edu" <AA_Canutescu(a)fccc.edu> > > > wrote: > > > > > > > Dear Bozidar, > > > > > > > > I have another problem to report, besides the memory leak one. For > > > some > > > > reasons, I got in certain situations the following error: > > > > > > > > ? FORTRAN Runtime Error: > > > > ? Illegal character in numeric input > > > > ? READ(UNIT=INTERNAL,... > > > > > > > > I wasn't able to track down any cause, and the error message is not > > > very > > > > explanatory to me. I would appreciate if you could give me a hint > > > about this > > > > sitation. This situation is a repro one, like also the memory leak > > > one. I run > > > > everything > > > > > > > > > > > > > > > > Thank you, > > > > > > > > Adrian > > > > > > > > > > > > Quoting Bozidar Jerkovic <bozidar(a)salilab.org>: > > > > > > > >> > > > >> Hi, > > > >> > > > >> Loop is definitely supported ;-). I'll see what's going on. > > > >> > > > >> Best, > > > >> Bozidar > > > >> > > > >> > > > >> On 10/4/02 1:18 PM, "AA_Canutescu(a)fccc.edu" <AA_Canutescu(a)fccc.edu> > > > >> wrote: > > > >> > > > >>> Hi, > > > >>> > > > >>> I attached a tar.gz that contains top, log and pdb input file. In > > > >> case 'loop' > > > >>> routine is not anymore supported in mod6v1, what would be a get > > > around > > > >> for my > > > >>> problem? > > > >>> > > > >>> Thanks for your help. > > > >>> > > > >>> Adrian > > > >>> > > > >>> > > > >>> Quoting Bozidar Jerkovic <bozidar(a)salilab.org>: > > > >>> > > > >>>> > > > >>>> Hi, > > > >>>> > > > >>>> Can you please send me your .top and .log and all input files and > > > >> I'll > > > >>>> run > > > >>>> it here. I can't actually see which part of .top fails. I presume > > > >> it's > > > >>>> "CALL > > > >>>> ROUTINE = 'loop' # do loop modeling", but I don't wanna > > guess. > > > >>>> > > > >>>> Best, > > > >>>> Bozidar > > > >>>> > > > >>>> > > > >>>> > > > >>>> On 8/4/02 3:24 PM, "AA_Canutescu(a)fccc.edu" > > > >>>> <AA_Canutescu(a)fccc.edu> > > > >>>> wrote: > > > >>>> > > > >>>>> Dear Bozidar, > > > >>>>> > > > >>>>> > > > >>>>> I downloaded the last version of MODELLER and I am running into > > > >> some > > > >>>>> problems. For the time being, I use MODELLER mostly for loop > > > >> modeling. > > > >>>> Using > > > >>>>> the > > > >>>>> previous version(mod6a), I used to create a top file like this, > > > and > > > >>>> everything > > > >>>>> worked ok: > > > >>>>> > > > >>>>> INCLUDE > > > >>>>> SET OUTPUT_CONTROL = 1 0 0 1 0 # Set to 1 1 1 1 0 for > > > >> debugging. > > > >>>>> SET SEQUENCE = '1dysA_47-50' > > > >>>>> SET LOOP_MODEL = '1dysA_47-50.pdb' > > > >>>>> SET LOOP_MD_LEVEL = 'refine2' # refine3 - fastest > > > >>>>> # refine2 - medium > > > >>>>> # refine1 - most thorough SET > > > >>>>> LOOP_STARTING_MODEL = 1 SET LOOP_ENDING_MODEL = 3 # number of > > > >>>>> loop models > > > >>>>> SET RAND_SEED = -38901 # change for different starting models > > > >>>>> CALL ROUTINE = 'loop' # do loop modeling > > > >>>>> > > > >>>>> # Pick model residues that need to be refined. > > > >>>>> > > > >>>>> SUBROUTINE ROUTINE = 'select_loop_atoms' # Uncomment if you > > > >>>>> also > > > >> want > > > >>>> to > > > >>>>> optimize the environment: > > > >>>>> # SET SELECTION_SEARCH = 'SPHERE_SEGMENT', SPHERE_RADIUS = 6 > > > >>>>> PICK_ATOMS SELECTION_SEGMENT = '47:A' '50:A', SELECTION_STATUS = > > > >>>> 'initialize' > > > >>>>> RETURN > > > >>>>> END_SUBROUTINE > > > >>>>> > > > >>>>> > > > >>>>> With the newest version of MODELLER that I downloaded last > > > >>>>> week, > > > >>>> doesn't work > > > >>>>> anymore. I receive an error message in the end of.log file like > > > >> this: > > > >>>>> > > > >>>>> act10___551E> No such routine: > > > >>>>> recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > > >>>>> > > > >>>>> Dynamically allocated memory at finish [B,kB,MB]: > > > >>>> 28478873 > > > >>>>> 27811.400 27.160 > > > >>>>> Starting time : > > > >> 2002/04/08 > > > >>>>> 14:20:40.274 > > > >>>>> Closing time : > > > >> 2002/04/08 > > > >>>>> 14:20:51.421 > > > >>>>> Total CPU time [seconds] : > > > >> 11.00 > > > >>>>> > > > >>>>> > > > >>>>> Could you help me please regarding this matter? Could you also > > > tell > > > >> me > > > >>>> if > > > >>>>> there is any dependency needed(some libraries, fortran, etc)? I > > > >>>>> am > > > >>>> using > > > >>>>> RedHat > > > >>>>> 7.2 with kernal 2.4.7-10 > > > >>>>> > > > >>>>> > > > >>>>> > > > >>>>> Thanks, > > > >>>>> > > > >>>>> Adrian Canutescu > > > >>>> > > > >>>> > > > >>> > > > >> > > > >> > > > > > > > > > > > > > > >

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Re: Memory leak / kernel crash / missing chain_ID (fwd)
by Bozidar Jerkovic 25 Apr '02

25 Apr '02

Dear Bozidar, Thank you for help. Your hint(to put '' instead of '0') looks to work so far. Regarding the fact that coordinates for the loop were zeroed, I did this in order to get a de novo loop prediction. Adrian Quoting Bozidar Jerkovic <bozidar(a)oboe.rockefeller.edu>: > > Dear Adrian, > > A simple answer to your question is: you specified a non-existing > segment of the protein for the loop optimization: > SELECTION_SEGMENT = '151:0' '154:0', SELECTION_STATUS = 'initialize' > > In your pdb file there is no '0' chain: > ATOM 1165 CD2 LEU 150 44.348 42.655 43.046 1.00 15.23 C > ATOM 1166 N GLY 151 0.000 0.000 0.000 1.00 16.38 N > ATOM 1167 CA GLY 15 0.000 0.000 0.000 1.00 15.57 C > > This results in MODELLER selecting the whole protein to perform 'loop' > routine on it: > Number of all, selected real atoms : 1480 1480 > > Another thing I noticed is that you have compresses all the residues you > are selecting into one point? Is there any specific reason for this? > ATOM 1166 N GLY 151 0.000 0.000 0.000 1.00 16.38 N > ATOM 1167 CA GLY 151 0.000 0.000 0.000 1.00 15.57 C > ATOM 1168 C GLY 151 0.000 0.000 0.000 1.00 16.31 C > > MODELLER complains about this though, but it keeps on: > serious non-bonded atom clash: 1143 1148 0.000 > serious non-bonded atom clash: 1143 1149 0.000 > serious non-bonded atom clash: 1143 1150 0.000 > > Energies are way off the charts: > Initial value of energy before optimization : 477452.2400 > Current energy : 476905.9000 > Maximal energy, step : 525495.1200 > 28 > Minimal energy, step : 449273.2100 > 81 > Average energy, stand.dev. : 506870.8100 > 15563.8500 > > What causes MODELLER to become a memory hog is the fact that you > unintentionally tried to perform an ab initio calculation of the whole > protein. I myself almost crashed our main Linux machine in the group, > running your top file. A job used up 92% of the available memory at one > point. > > After I corrected the .top file: > SELECTION_SEGMENT = '151:' '154:', SELECTION_STATUS = 'initialize' > > Energy returned to normal: > Initial value of energy before optimization : 27.4512 > Current energy : 4.5270 > Maximal energy, step : 67.8339 > 34 > Minimal energy, step : 25.2391 > 363 > Average energy, stand.dev. : 43.2928 > 10.7857 > > ... and MODELLER produced a beautiful model ;-) > > Summa sumarum: > One has to make sure that when s/he selects a segment of the protein, > using 'res_ID:chain_ID' convention (which is updated for the 6v2 > release), that there is an existing chain_ID there. This is actually > quite a common mistake many users do: their pdb has a chain_ID, and they > omit it in their top file (just opposite of what you did). > > I am still curious why you have compressed all the loop residues into a > single point (why those residues have all the coordinates equal to > zero)? It worked, because those resides were brought back into the > protein in the model MODELLER calculated, which is obviously good, and > their energy is also fine. If this is some empirical finding, and not > missing coordinates, I would certainly like to learn more about it. > > ...and there is no memory leak, thankfully ;-) > > All the best and happy modeling, > Bozidar > > > > -----Original Message----- > From: AA_Canutescu(a)fccc.edu [mailto:AA_Canutescu@fccc.edu] > Sent: Wednesday, April 17, 2002 6:49 PM > To: Bozidar Jerkovic > Subject: Re: MODELLER > > > Dear Bozidar, > > > > > Yes I am aware of this one. I think it may have to do with static vs. > > dynamic linking. > > It's not obvious to me why could be a linking problem, but anyway it's > interesting this happens only for certain input files. For the input > data sets that generate this bug, the bug is repro(reproducible -all the > time). There is no situation(as far as I tested) in which for the same > input data to get the software working sometime and not working other > time. It just doesn't work -all the time - for that input data. > > > > What did you mean by "repro"? > > An error that is exactly reproducible under any circumstances. It's used > in programers' jargon. > > > The other problem, that is actually the most serious one is also repro. > For certain input data sets, modeller starts allocating huge amounts of > memory (about 1GB/min on my machine). This indicates a serious memory > leak. I got my kernal crashed twice today because of this, so I have to > wait for your patch before using again modeller. > > I will attach again an input data set that leads to this memory leak. > > Everything is run on RedHat 7.2 on x86 architecture. > > Thanks, > Adrian > > > > > > Thanks for these reports. It's sometimes hard for us to catch > > everything. > > > > Best, > > Bozidar > > > > > > On 17/4/02 5:33 PM, "AA_Canutescu(a)fccc.edu" <AA_Canutescu(a)fccc.edu> > > wrote: > > > > > Dear Bozidar, > > > > > > I have another problem to report, besides the memory leak one. For > > some > > > reasons, I got in certain situations the following error: > > > > > > ? FORTRAN Runtime Error: > > > ? Illegal character in numeric input > > > ? READ(UNIT=INTERNAL,... > > > > > > I wasn't able to track down any cause, and the error message is not > > very > > > explanatory to me. I would appreciate if you could give me a hint > > about this > > > sitation. This situation is a repro one, like also the memory leak > > one. I run > > > everything > > > > > > > > > > > > Thank you, > > > > > > Adrian > > > > > > > > > Quoting Bozidar Jerkovic <bozidar(a)salilab.org>: > > > > > >> > > >> Hi, > > >> > > >> Loop is definitely supported ;-). I'll see what's going on. > > >> > > >> Best, > > >> Bozidar > > >> > > >> > > >> On 10/4/02 1:18 PM, "AA_Canutescu(a)fccc.edu" <AA_Canutescu(a)fccc.edu> > > >> wrote: > > >> > > >>> Hi, > > >>> > > >>> I attached a tar.gz that contains top, log and pdb input file. In > > >> case 'loop' > > >>> routine is not anymore supported in mod6v1, what would be a get > > around > > >> for my > > >>> problem? > > >>> > > >>> Thanks for your help. > > >>> > > >>> Adrian > > >>> > > >>> > > >>> Quoting Bozidar Jerkovic <bozidar(a)salilab.org>: > > >>> > > >>>> > > >>>> Hi, > > >>>> > > >>>> Can you please send me your .top and .log and all input files and > > >> I'll > > >>>> run > > >>>> it here. I can't actually see which part of .top fails. I presume > > >> it's > > >>>> "CALL > > >>>> ROUTINE = 'loop' # do loop modeling", but I don't wanna > guess. > > >>>> > > >>>> Best, > > >>>> Bozidar > > >>>> > > >>>> > > >>>> > > >>>> On 8/4/02 3:24 PM, "AA_Canutescu(a)fccc.edu" > > >>>> <AA_Canutescu(a)fccc.edu> > > >>>> wrote: > > >>>> > > >>>>> Dear Bozidar, > > >>>>> > > >>>>> > > >>>>> I downloaded the last version of MODELLER and I am running into > > >> some > > >>>>> problems. For the time being, I use MODELLER mostly for loop > > >> modeling. > > >>>> Using > > >>>>> the > > >>>>> previous version(mod6a), I used to create a top file like this, > > and > > >>>> everything > > >>>>> worked ok: > > >>>>> > > >>>>> INCLUDE > > >>>>> SET OUTPUT_CONTROL = 1 0 0 1 0 # Set to 1 1 1 1 0 for > > >> debugging. > > >>>>> SET SEQUENCE = '1dysA_47-50' > > >>>>> SET LOOP_MODEL = '1dysA_47-50.pdb' > > >>>>> SET LOOP_MD_LEVEL = 'refine2' # refine3 - fastest > > >>>>> # refine2 - medium > > >>>>> # refine1 - most thorough SET > > >>>>> LOOP_STARTING_MODEL = 1 SET LOOP_ENDING_MODEL = 3 # number of > > >>>>> loop models > > >>>>> SET RAND_SEED = -38901 # change for different starting models > > >>>>> CALL ROUTINE = 'loop' # do loop modeling > > >>>>> > > >>>>> # Pick model residues that need to be refined. > > >>>>> > > >>>>> SUBROUTINE ROUTINE = 'select_loop_atoms' # Uncomment if you > > >>>>> also > > >> want > > >>>> to > > >>>>> optimize the environment: > > >>>>> # SET SELECTION_SEARCH = 'SPHERE_SEGMENT', SPHERE_RADIUS = 6 > > >>>>> PICK_ATOMS SELECTION_SEGMENT = '47:A' '50:A', SELECTION_STATUS = > > >>>> 'initialize' > > >>>>> RETURN > > >>>>> END_SUBROUTINE > > >>>>> > > >>>>> > > >>>>> With the newest version of MODELLER that I downloaded last > > >>>>> week, > > >>>> doesn't work > > >>>>> anymore. I receive an error message in the end of.log file like > > >> this: > > >>>>> > > >>>>> act10___551E> No such routine: > > >>>>> recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > >>>>> > > >>>>> Dynamically allocated memory at finish [B,kB,MB]: > > >>>> 28478873 > > >>>>> 27811.400 27.160 > > >>>>> Starting time : > > >> 2002/04/08 > > >>>>> 14:20:40.274 > > >>>>> Closing time : > > >> 2002/04/08 > > >>>>> 14:20:51.421 > > >>>>> Total CPU time [seconds] : > > >> 11.00 > > >>>>> > > >>>>> > > >>>>> Could you help me please regarding this matter? Could you also > > tell > > >> me > > >>>> if > > >>>>> there is any dependency needed(some libraries, fortran, etc)? I > > >>>>> am > > >>>> using > > >>>>> RedHat > > >>>>> 7.2 with kernal 2.4.7-10 > > >>>>> > > >>>>> > > >>>>> > > >>>>> Thanks, > > >>>>> > > >>>>> Adrian Canutescu > > >>>> > > >>>> > > >>> > > >> > > >> > > > > > > > > >

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array too small error
by Marina Gimpelev 24 Apr '02

24 Apr '02

Hi, I've been trying to create a homology model using three templates. Modeller got to the point of "Restraint type to be calculated: distance", then gave me a lot of warnings that "Two basis restraints have means too far apart" and then quit altogether giving me an error "Array too small. Increase MPRMCNS, current maximum, current need: 812700 813746". What does it mean and how can I fix it? thank you very much, -- Marina Gimpelev

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RE: RE: RE: Segmentation Fault during modelling with modeller6v
by Bozidar 24 Apr '02

24 Apr '02

Hi, The problem with that one .ali file is the nature of the loops you select/create. You have to really scrutinize that alignment, making sure that one-residue gap insertion there is what really makes that alignment better then some other possible arrangement. As for the random seed: I don't think it makes any difference. Andrej might be able to add something about this? Thanks, Bozidar -----Original Message----- From: Kees-Jan.Francoijs(a)P450.BC.WAU.NL [mailto:Kees-Jan.Francoijs@P450.BC.WAU.NL] Sent: Wednesday, April 24, 2002 3:56 AM To: bozidar(a)salilab.org Subject: re: RE: RE: Segmentation Fault during modelling with modeller6v Hi, i started the job with SET GAP_EXTENSION = 0 0 yesterday with both alignments and one of the jobs has crashed againat the 100th model as well, the other job is still running 450+models. The top and pir filesof the job that crashed are attached. I will start 10 jobs with each generating 125 models. To see if in every run the 100th model crashes. As soon as i have results I let you know. One question about the seed, is it wise to take this randomly between -50000 and -2 like -44656, -35435, -9835, - 15684, -378 ... or is it oke to take in order like -32768, - 16384, - 8192, -4096, -2048... Thanks in advance Kees-Jan Francoijs - - - - - - - - - - - - - - Original Message - - - - - - - - - - - - - - On Tue Apr 23 18:03:13 2002, "Bozidar" <bozidar(a)salilab.org> wrote: > >Hi, > >These are the observations I got so far: > >1. Your OK job is OK with me also. It's still running (200+ models). > >2. Your crash job crashed at me as well at 99th model. What happened is >that energy of the 100th model (which never got written out) went >through the roof (NaN) and the system never recovered from it. > >The workaround is as follows: you can run this job in parallel. Instead >of generating 1000 models in one run, you can start maybe 5 jobs that >will generate 200 models each. All you need to do it to give a random >seed number in the top files (between -50000 to -2) to each of them: >SET RAND_SEED = -xvz > >Why this particular alignment crashes and not the other one is hard to >say. As I mentioned in my earlier email, you are selecting 50% of your >protein as loop region. Given the close similarity between two >alignments, it might be that 5 vs. 4 loops results in formation of bad >structure at some point (knots maybe), that simply collapses the >system. > > >Al least what we know is that MODELLER reports no errors and that it >runs fine. I think that you have very specific case here, which will >require careful modeling on your part, making sure you control each >step of the way. > >Still, please let me know how happens with SET GAP_EXTENSION = 0 0 > >Happy modeling, >Bozidar > > > >-----Original Message----- >From: Kees-Jan.Francoijs(a)P450.BC.WAU.NL >[mailto:Kees-Jan.Francoijs@P450.BC.WAU.NL] >Sent: Monday, April 22, 2002 3:52 AM >To: bozidar(a)oboe.rockefeller.edu >Subject: re: RE: Segmentation Fault during modelling with modeller6v1 > > >Hi, > >Sorry for the delay. I send you the requested files. (ed) > >When running this top pir and pdb file the job crashes (crash.zip). >When using another pir same top and pdb file everything goes >oke(oke.zip). The log file a >is included as zip file AVR4.zip in crash.zip. If there is anything >else you >want to know just ask. > >with regards > >Kees-Jan Francoijs >- - - - - - - - - - - - - - Original Message - - - - - - - - - - - - - >- On Thu Apr 18 19:06:31 2002, "Bozidar Jerkovic" ><bozidar(a)oboe.rockefeller.edu> wrote: >> >>Hi, >> >>1. Please send me complete set of input files plus log files and I'll >>run it on 6v2 (not public yet) to see if it happens there. >> >>2. Yes we went through this, as well. Prosa is not sensitive assessing >>loops. Please read the comment on the use of statistical profile for >>assessing loops, in Andras Fiser's Prot Sci 2000 loop modeling paper. >>People should use modeller scores to rank them. >> >>Thanks, >>Bozidar >> >> >>-----Original Message----- >>From: Kees-Jan.Francoijs(a)P450.BC.WAU.NL >>[mailto:Kees-Jan.Francoijs@P450.BC.WAU.NL] >>Sent: Tuesday, April 16, 2002 8:00 AM >>To: bozidar(a)oboe.rockefeller.edu >>Subject: Segmentation Fault during modelling with modeller6v1 >> >> >>Hi Bozidar, >> >>I have been using modeller for 2 years now . I'm using modeller since >>version 4. Recently I ran into a few problems maybe you can point me in > >>the right >>direction. >> >>Two Questions: >> >>1.) When running modeller 6V1 on a pentium III redhat 7.2 with all >>recommended patches applied. The following problem occurred. After I >>started a job doing loop modelling i generated 1000 models and every >>thing went fine. >>I changed the alignment a bit and try to run for an other 1000 models >>the job >>crashes after 198 models. So i decided to run on a other machine, >>different >>one 1.7 Ghz Dual Xeon, same problem. What can be the source of the >>problem. >>The job crashes with segmentation fault error. >> >>2.) I assessed the 1000 generated models with ProsaII to find the 20 >>best models. I also used the value from the objective function from >>modeller to >>rank them. When doing this it was easy to see if there is any >>correlation >>between the rankings and guess what, there is none actual it seems >>random. Is >>there an explanation for this and which one is right or did i do >>something >>wrong ? This surprised me since Andrej uses the ProsaII score in many >of >>his >>articles as an objective criterion for the quality of the models and >one >>would expect the objective function of Modeller to be related in >>quality. >> >> >>with regards >> >>C.J.J Francoijs >> >> > >- - - - - - - - - - - - End of Original Message - - - - - - - - - - - - > > > - - - - - - - - - - - - End of Original Message - - - - - - - - - - - -

1 0

Memory leak / kernel crash / missing chain_ID
by Bozidar Jerkovic 23 Apr '02

23 Apr '02

Dear Adrian, A simple answer to your question is: you specified a non-existing segment of the protein for the loop optimization: SELECTION_SEGMENT = '151:0' '154:0', SELECTION_STATUS = 'initialize' In your pdb file there is no '0' chain: ATOM 1165 CD2 LEU 150 44.348 42.655 43.046 1.00 15.23 C ATOM 1166 N GLY 151 0.000 0.000 0.000 1.00 16.38 N ATOM 1167 CA GLY 15 0.000 0.000 0.000 1.00 15.57 C This results in MODELLER selecting the whole protein to perform 'loop' routine on it: Number of all, selected real atoms : 1480 1480 Another thing I noticed is that you have compresses all the residues you are selecting into one point? Is there any specific reason for this? ATOM 1166 N GLY 151 0.000 0.000 0.000 1.00 16.38 N ATOM 1167 CA GLY 151 0.000 0.000 0.000 1.00 15.57 C ATOM 1168 C GLY 151 0.000 0.000 0.000 1.00 16.31 C MODELLER complains about this though, but it keeps on: serious non-bonded atom clash: 1143 1148 0.000 serious non-bonded atom clash: 1143 1149 0.000 serious non-bonded atom clash: 1143 1150 0.000 Energies are way off the charts: Initial value of energy before optimization : 477452.2400 Current energy : 476905.9000 Maximal energy, step : 525495.1200 28 Minimal energy, step : 449273.2100 81 Average energy, stand.dev. : 506870.8100 15563.8500 What causes MODELLER to become a memory hog is the fact that you unintentionally tried to perform an ab initio calculation of the whole protein. I myself almost crashed our main Linux machine in the group, running your top file. A job used up 92% of the available memory at one point. After I corrected the .top file: SELECTION_SEGMENT = '151:' '154:', SELECTION_STATUS = 'initialize' Energy returned to normal: Initial value of energy before optimization : 27.4512 Current energy : 4.5270 Maximal energy, step : 67.8339 34 Minimal energy, step : 25.2391 363 Average energy, stand.dev. : 43.2928 10.7857 ... and MODELLER produced a beautiful model ;-) Summa sumarum: One has to make sure that when s/he selects a segment of the protein, using 'res_ID:chain_ID' convention (which is updated for the 6v2 release), that there is an existing chain_ID there. This is actually quite a common mistake many users do: their pdb has a chain_ID, and they omit it in their top file (just opposite of what you did). I am still curious why you have compressed all the loop residues into a single point (why those residues have all the coordinates equal to zero)? It worked, because those resides were brought back into the protein in the model MODELLER calculated, which is obviously good, and their energy is also fine. If this is some empirical finding, and not missing coordinates, I would certainly like to learn more about it. ...and there is no memory leak, thankfully ;-) All the best and happy modeling, Bozidar -----Original Message----- From: AA_Canutescu(a)fccc.edu [mailto:AA_Canutescu@fccc.edu] Sent: Wednesday, April 17, 2002 6:49 PM To: Bozidar Jerkovic Subject: Re: MODELLER Dear Bozidar, > > Yes I am aware of this one. I think it may have to do with static vs. > dynamic linking. It's not obvious to me why could be a linking problem, but anyway it's interesting this happens only for certain input files. For the input data sets that generate this bug, the bug is repro(reproducible -all the time). There is no situation(as far as I tested) in which for the same input data to get the software working sometime and not working other time. It just doesn't work -all the time - for that input data. > What did you mean by "repro"? An error that is exactly reproducible under any circumstances. It's used in programers' jargon. The other problem, that is actually the most serious one is also repro. For certain input data sets, modeller starts allocating huge amounts of memory (about 1GB/min on my machine). This indicates a serious memory leak. I got my kernal crashed twice today because of this, so I have to wait for your patch before using again modeller. I will attach again an input data set that leads to this memory leak. Everything is run on RedHat 7.2 on x86 architecture. Thanks, Adrian > > Thanks for these reports. It's sometimes hard for us to catch > everything. > > Best, > Bozidar > > > On 17/4/02 5:33 PM, "AA_Canutescu(a)fccc.edu" <AA_Canutescu(a)fccc.edu> > wrote: > > > Dear Bozidar, > > > > I have another problem to report, besides the memory leak one. For > some > > reasons, I got in certain situations the following error: > > > > ? FORTRAN Runtime Error: > > ? Illegal character in numeric input > > ? READ(UNIT=INTERNAL,... > > > > I wasn't able to track down any cause, and the error message is not > very > > explanatory to me. I would appreciate if you could give me a hint > about this > > sitation. This situation is a repro one, like also the memory leak > one. I run > > everything > > > > > > > > Thank you, > > > > Adrian > > > > > > Quoting Bozidar Jerkovic <bozidar(a)salilab.org>: > > > >> > >> Hi, > >> > >> Loop is definitely supported ;-). I'll see what's going on. > >> > >> Best, > >> Bozidar > >> > >> > >> On 10/4/02 1:18 PM, "AA_Canutescu(a)fccc.edu" <AA_Canutescu(a)fccc.edu> > >> wrote: > >> > >>> Hi, > >>> > >>> I attached a tar.gz that contains top, log and pdb input file. In > >> case 'loop' > >>> routine is not anymore supported in mod6v1, what would be a get > around > >> for my > >>> problem? > >>> > >>> Thanks for your help. > >>> > >>> Adrian > >>> > >>> > >>> Quoting Bozidar Jerkovic <bozidar(a)salilab.org>: > >>> > >>>> > >>>> Hi, > >>>> > >>>> Can you please send me your .top and .log and all input files and > >> I'll > >>>> run > >>>> it here. I can't actually see which part of .top fails. I presume > >> it's > >>>> "CALL > >>>> ROUTINE = 'loop' # do loop modeling", but I don't wanna guess. > >>>> > >>>> Best, > >>>> Bozidar > >>>> > >>>> > >>>> > >>>> On 8/4/02 3:24 PM, "AA_Canutescu(a)fccc.edu" > >>>> <AA_Canutescu(a)fccc.edu> > >>>> wrote: > >>>> > >>>>> Dear Bozidar, > >>>>> > >>>>> > >>>>> I downloaded the last version of MODELLER and I am running into > >> some > >>>>> problems. For the time being, I use MODELLER mostly for loop > >> modeling. > >>>> Using > >>>>> the > >>>>> previous version(mod6a), I used to create a top file like this, > and > >>>> everything > >>>>> worked ok: > >>>>> > >>>>> INCLUDE > >>>>> SET OUTPUT_CONTROL = 1 0 0 1 0 # Set to 1 1 1 1 0 for > >> debugging. > >>>>> SET SEQUENCE = '1dysA_47-50' > >>>>> SET LOOP_MODEL = '1dysA_47-50.pdb' > >>>>> SET LOOP_MD_LEVEL = 'refine2' # refine3 - fastest > >>>>> # refine2 - medium > >>>>> # refine1 - most thorough SET > >>>>> LOOP_STARTING_MODEL = 1 SET LOOP_ENDING_MODEL = 3 # number of > >>>>> loop models > >>>>> SET RAND_SEED = -38901 # change for different starting models > >>>>> CALL ROUTINE = 'loop' # do loop modeling > >>>>> > >>>>> # Pick model residues that need to be refined. > >>>>> > >>>>> SUBROUTINE ROUTINE = 'select_loop_atoms' # Uncomment if you > >>>>> also > >> want > >>>> to > >>>>> optimize the environment: > >>>>> # SET SELECTION_SEARCH = 'SPHERE_SEGMENT', SPHERE_RADIUS = 6 > >>>>> PICK_ATOMS SELECTION_SEGMENT = '47:A' '50:A', SELECTION_STATUS = > >>>> 'initialize' > >>>>> RETURN > >>>>> END_SUBROUTINE > >>>>> > >>>>> > >>>>> With the newest version of MODELLER that I downloaded last > >>>>> week, > >>>> doesn't work > >>>>> anymore. I receive an error message in the end of.log file like > >> this: > >>>>> > >>>>> act10___551E> No such routine: > >>>>> recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > >>>>> > >>>>> Dynamically allocated memory at finish [B,kB,MB]: > >>>> 28478873 > >>>>> 27811.400 27.160 > >>>>> Starting time : > >> 2002/04/08 > >>>>> 14:20:40.274 > >>>>> Closing time : > >> 2002/04/08 > >>>>> 14:20:51.421 > >>>>> Total CPU time [seconds] : > >> 11.00 > >>>>> > >>>>> > >>>>> Could you help me please regarding this matter? Could you also > tell > >> me > >>>> if > >>>>> there is any dependency needed(some libraries, fortran, etc)? I > >>>>> am > >>>> using > >>>>> RedHat > >>>>> 7.2 with kernal 2.4.7-10 > >>>>> > >>>>> > >>>>> > >>>>> Thanks, > >>>>> > >>>>> Adrian Canutescu > >>>> > >>>> > >>> > >> > >> > > > >

1 0