September 2004 - modeller_usage

problem
by vivek sharma 29 Sep '04

29 Sep '04

Dear Sir, Thank you very much for all previous replies. I am having some problems, please provide a solution to them. 1. Is the value of objective function obtained after complete process of MODELER , system size specific? I mean when I model a system of > 500 residues (target), it generates >50000 restraints (3 templates used) and final value of objective function is >20000, but when I model a part of the target , taking respectively aligned template portions, approx 150 residues (target), the restraints generated are around 9000 and final value of objective function comes to 2000 units. So, this shows that smaller the system , lower the final value of objective function, same restraints selected in both cases and assume no violations. Please comment 2. Also, how can one decide that such high values of objective function are acceptable or not, assume there are no violations? (Please specify if you have such experience/idea of Modelling bigger proteins.) 3. Thirdly, from documentation I came to understand that, that when one wants to generate non bonded pair restraints as static ones, he has to include them in MAKE_RESTRAINTS command and keep all DYNAMIC_SPHERE, LENNARD, COULOMB, etc off. Can you tell me which is better , non bonded restraints used as static or non bonded restraints as dynamic (generated automatically by MODELER on fly)? Please explain. Thank you very much in advance. sincerely, Vivek Sharma Graduate Student (Biochemistry/Biophysics) University of Helsinki.

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use NMR as template
by remo 27 Sep '04

27 Sep '04

hi i'm Remo and i'm new with modeller... i'd like to know if : - is possible to use an NMR file with 24 structures as template - how to make in any way an averaged structure and then use this one as template - there are some useful tricks to handle NMR structures i hope in your help -- ----------------------------------------------------------- Dr Remo Calabrese, PhD Student Dipartimento di Biologia Evoluzionistica Sperimentale University of Bologna Via Irnerio,42 40126 Bologna Italy email: remo(a)biocomp.unibo.it tel. + 39 051 2094005 fax. + 39 051 242576 -----------------------------------------------------------

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problem
by vivek sharma 23 Sep '04

23 Sep '04

Dear Sir, I went through the model.top script and and tried to understand that how it works. But there are few problems in understanding that script, please guide me for these mentioned problems. 1. In OPTIMIZE process (VTFM optimization), the addition of restraints is governed by PICK_RESTRAINTS which in turn depend on SCHEDULE file (3rd column, NRNG), meaning thereby that only those restraints will be taken into consideration which applies on atoms, which comes in category as specified by Schedule file (3rd column). Although in .log file I found restraints are added step by step (N_SCHEDULE step) during optimization , are the atoms also added continously, or just explain a bit how this profile goes? 2. Out of curiosity I ask this question, if all restraints and all atoms are taken into consideration at a time, and then optimization is done, will that be better/efficient than the method it takes in model.top? 3. Also, I observed that this addition of restraints (for every N_SCHEDULE step) during optimization increases the value of objective function , and it finally stops at a higher value, will that value be considered final one or various such consequent optimization cycles should be carried out to finally lower down the value? Please reply , I will be very thankful to you. Hope to receive explainatory reply. Thanking you in advance, sincerely, -- VIVEK SHARMA Graduate Student, (Biochemistry/Biophysics) University of Helsinki

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Defining the centre of a helix and restraints
by John Simms 22 Sep '04

22 Sep '04

Hi All, I have a small problem. I work on GPCRs and would like to use some electron crystallography data. However, the data given are distances between the centres of transmembrane alpha helices rather than a specific atom eg CA. Does anyone know how I would specify the centre of a helix when using distance restraints?. Many Thanks in advance John

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Crash under 7v7
by John Penniston 21 Sep '04

21 Sep '04

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Problem with alignment file
by 柳田　亮 17 Sep '04

17 Sep '04

Please help me. I cannot figure out this error. -- MODELLER 7v7, Sep 12, 2004 09:15pm Kind, OS, HostName, Kernel, Processor: 4, Darwin 7.5.0 Power Macintosh Date and time of compilation : 09/14/2004 09:31:49 Job starting time (YY/MM/DD HH:MM:SS): 2004/09/17 20:55:55.058 TOP_________> 109 749 SET ALNFILE = 'align.txt' TOP_________> 110 750 SET KNOWNS = '1stc' TOP_________> 111 751 SET SEQUENCE = 'pkcAcat' TOP_________> 112 752 SET ATOM_FILES_DIRECTORY = './' TOP_________> 113 753 SET STARTING_MODEL = 1 TOP_________> 114 754 SET ENDING_MODEL = 1 TOP_________> 115 755 SET HETATM_IO = ON TOP_________> 116 756 CALL ROUTINE = 'model' TOP_________> 117 419 CALL ROUTINE = 'getnames' TOP_________> 118 534 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 119 535 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 120 536 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 121 537 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 122 538 SET ROOT_NAME = SEQUENCE TOP_________> 123 539 RETURN TOP_________> 124 420 CALL ROUTINE = 'homcsr' TOP_________> 125 112 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 84067 82.097 0.080 openf5__224_> Open 20 OLD SEQUENTIAL align.txt rdpir___270E> Error reading/processing file: align.txt recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 84067 82.097 0.080 Starting time : 2004/09/17 20:55:55.058 Closing time : 2004/09/17 20:55:57.131 Total CPU time [seconds] : 1.88 -- >P1;1stc structureX:1stc:15::350::::: GNAAAAKKGSEQESVKEFLAKAKEDFLKKWESPAQNTAHLD-----QFERIKTLGTGSFG RVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVN-FPFLVKLEFSFKDNS NLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLI DQQGYIQVTDFGFAKRVKGR---TWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEM AAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDI KNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEE-------EIRVSINEKCG KEFSEF* >P1;pkcAcat sequence:pkcAcat:1::336::::: EGDEEGNMELRQKFEKAKLGPAGNKVISPSEDRKQPSNNLDRVKLTDFNFLMVLGKGSFG KVMLADRKGTEELYAIKILKKDVVIQDDDVECTMVEKRVLALLDKPPFLTQLHSCFQTVD RLYFVMEYVNGGDLMYHIQQVGKFKEPQAVFYAAEISIGLFFLHKRGIIYRDLKLDNVML DSEGHIKIADFGMCKEHMMDGVTTRTFCGTPDYIAPEIIAYQPYGKSVDWWAYGVLLYEM LAGQPPFDGEDEDELFQSIMEHNVSYPKSLSKEAVSICKGLMTKHPAKRLGCGPEGERDV REHAFFRRIDWEKLENREIQPPFKPKVCGKG-AENFDKFFTRGQPVLTPPDQLVIANIDQ SDFEGF*

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RE: [modeller_usage] Problem with alignment file
by Schweikardt, Thorsten 17 Sep '04

17 Sep '04

Hi Charles (?), check your input pdb file, find out if all aminoacids in your alignment are present in your pdb file. You should also specify the chain ID in your alignment, your chain of interest is called "E": structureX:1stc:15:E:350:E:::: do you really have a space in front of "P1;1stc"? Maybe that's also a problem, but I do not know how your system handles this (you are using a Mac, right?) Best wishes, Thorsten Schweikardt Molecular Biophysics University of Mainz, Germany > -----Original Message----- > From: modeller_usage-bounces(a)salilab.org > [mailto:modeller_usage-bounces@salilab.org] On Behalf Of ?? ? > Sent: Friday, September 17, 2004 2:06 PM > To: modeller_usage(a)salilab.org > Subject: [modeller_usage] Problem with alignment file > > > Please help me. I cannot figure out this error. > > -- > > MODELLER 7v7, Sep 12, 2004 09:15pm > > Kind, OS, HostName, Kernel, Processor: 4, Darwin 7.5.0 Power > Macintosh > Date and time of compilation : 09/14/2004 09:31:49 > Job starting time (YY/MM/DD HH:MM:SS): 2004/09/17 20:55:55.058 > > TOP_________> 109 749 SET ALNFILE = 'align.txt' > > TOP_________> 110 750 SET KNOWNS = '1stc' > > TOP_________> 111 751 SET SEQUENCE = 'pkcAcat' > > TOP_________> 112 752 SET ATOM_FILES_DIRECTORY = './' > > TOP_________> 113 753 SET STARTING_MODEL = 1 > > TOP_________> 114 754 SET ENDING_MODEL = 1 > > TOP_________> 115 755 SET HETATM_IO = ON > > TOP_________> 116 756 CALL ROUTINE = 'model' > > TOP_________> 117 419 CALL ROUTINE = 'getnames' > > TOP_________> 118 534 STRING_IF STRING_ARGUMENTS = MODEL > 'undefined', OPERATION; > = 'EQ', THEN = 'STRING_OPERATE > OPERATION = > CONCATENA; > TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = > MODEL' > > TOP_________> 119 535 STRING_IF STRING_ARGUMENTS = CSRFILE > 'undefined', OPERATI; > ON = 'EQ', THEN = 'STRING_OPERATE > OPERATION = > CONCATE; > NATE, STRING_ARGUMENTS = SEQUENCE > .rsr, RESULT = > CSRFILE; > ' > > TOP_________> 120 536 STRING_OPERATE OPERATION = > 'CONCATENATE', > ; > STRING_ARGUMENTS = SEQUENCE '.sch', > RESULT = > SCHFILE > > TOP_________> 121 537 STRING_OPERATE OPERATION = > 'CONCATENATE', > ; > STRING_ARGUMENTS = SEQUENCE '.mat', > RESULT = > MATRIX_FI; > LE > > TOP_________> 122 538 SET ROOT_NAME = SEQUENCE > > TOP_________> 123 539 RETURN > > TOP_________> 124 420 CALL ROUTINE = 'homcsr' > > TOP_________> 125 112 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = > KNOWNS SEQUE; > NCE > > > Dynamically allocated memory at amaxseq [B,kB,MB]: > 84067 > 82.097 0.080 > openf5__224_> Open 20 OLD SEQUENTIAL align.txt > rdpir___270E> Error reading/processing file: align.txt > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > Dynamically allocated memory at finish [B,kB,MB]: > 84067 > 82.097 0.080 > Starting time : > 2004/09/17 > 20:55:55.058 > Closing time : > 2004/09/17 > 20:55:57.131 > Total CPU time [seconds] : 1.88 > > -- > >P1;1stc > structureX:1stc:15::350::::: > GNAAAAKKGSEQESVKEFLAKAKEDFLKKWESPAQNTAHLD-----QFERIKTLGTGSFG > RVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVN-FPFLVKLEFSFKDNS > NLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLI > DQQGYIQVTDFGFAKRVKGR---TWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEM > AAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDI > KNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEE-------EIRVSINEKCG > KEFSEF* > > > >P1;pkcAcat > sequence:pkcAcat:1::336::::: > EGDEEGNMELRQKFEKAKLGPAGNKVISPSEDRKQPSNNLDRVKLTDFNFLMVLGKGSFG > KVMLADRKGTEELYAIKILKKDVVIQDDDVECTMVEKRVLALLDKPPFLTQLHSCFQTVD > RLYFVMEYVNGGDLMYHIQQVGKFKEPQAVFYAAEISIGLFFLHKRGIIYRDLKLDNVML > DSEGHIKIADFGMCKEHMMDGVTTRTFCGTPDYIAPEIIAYQPYGKSVDWWAYGVLLYEM > LAGQPPFDGEDEDELFQSIMEHNVSYPKSLSKEAVSICKGLMTKHPAKRLGCGPEGERDV > REHAFFRRIDWEKLENREIQPPFKPKVCGKG-AENFDKFFTRGQPVLTPPDQLVIANIDQ > SDFEGF* > > >

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Announcing MODELLER 7v7
by Modeller Caretaker 16 Sep '04

16 Sep '04

Dear MODELLER user, MODELLER 7v7 is now available for download, for Linux (both i686 PC, and Itanium 2), Windows, Mac OS X, Sun, SGI and Alpha (AIX binaries to follow shortly). This release fixes a number of minor bugs in 6v2, introduces some new commands for handling profiles, improves structure handling by using PDB rather than CHARMM naming for toplogy libraries, and offers many other new features. Please refer to the Modeller website at http://salilab.org/modeller/, in particular the 7v7 release notes at http://salilab.org/modeller/release.shtml, for futher information on downloading, registering, and installing Modeller. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mailing list: http://salilab.org/mailman/listinfo/modeller_usage

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problem_again
by vivek sharma 10 Sep '04

10 Sep '04

Sirs, I have mailed you sometime back but couldn't received reply, although I solved some problems, but still there are three of them which are hindering the work. It would be very kind if you suggest a solution to them. Problems are: 1. What each column in *.D* file, which contains details about the optimization, represents? Also, does this file contains details of optimization of molecular pdf as well as Molecular Dynamics? and how to differentiate between them? 2. Running Modeler gives the following warnings: Number of templates for coordinate transfer: 3 After transfering coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 3290 1048 TOP_________> 146 87 BUILD_MODEL INITIALIZE_XYZ = OFF build___466W> Some coordinates in MODEL not assigned. build___468W> Some coordinates in MODEL are still undefined. build___464W> Inventing the MODEL coordinates. I understand that these atoms are undefined because it doesn't found equivalent atoms (same atom name and equivalent residue) in templates but then those atoms are given coordinates by BUILD_MODEL command, but can you tell me how one can find out which are those 'still' undefined atoms , even which are not covered by 'BUILD_MODEL' command and why this is so? Please explain this a bit. 3. Also, another problem is: New residue types defined in restyp as well as top_heav.lib. I am using this type of restyp.lib (residue defined for use in template) 141 | AAA | ? | A123 | residue XXX 142 | BBB | " | A234 | patch for residue XXX 143 | BBB | | A345 | patch for residue XXX and alignment like template : ----/"/----- target : ----/?/?----- (for this patches are defined explicitly by PATCH command in top file) this reads the first (") residue but doesn't read the next () residue and gives error: ------------- rdabrk__291E> Sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES ------*---- 1 514 143 A345 141 A123 YVNLK" rdabrk__288W> Protein not accepted: 1 check_a_337E> Structure not read in: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 ------------- but when I change the PDB-3 name of residue from BBB to CCC in restyp.lib, then it works, but this needs me to change the residue name in PDB, but instructions of your restyp.lib suggests that same name of residue in PDB-3 are acceptable. Is this some type of probable bug? or I am doing some mistake? Also, patches are needed to be given some different PDB-1 and different CHARMM name, which I did. Please reply, if you need more details, please say so. Thanking you, sincerely, vivek sharma -- VIVEK SHARMA HBG BI

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Error message: Array too small. Increase MAXSEG
by Nancy Yu 02 Sep '04

02 Sep '04

Hi, Can anyone tell me what the following error message means? Dynamically allocated memory at amaxbnd [B,kB,MB]: 13309089 12997.157 12.693 openf5__224_> Open 11 OLD SEQUENTIAL 09-02-align.ali openf5__224_> Open 13 OLD SEQUENTIAL ./PNPmono.pdb defseg__223E> Array too small. Increase MAXSEG current maximum, current need: 30 31 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Thanx, Nancy

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