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Problem with align2d
by Andrew Kiggundu 20 Jan '03

20 Jan '03

Hi Everybody here, I am new to the modelling world and have successfully installed Modeller v6.2 onto windows2000 PC. Got the tutorial to run fine. started modelling my protein. A series of errors I managed to sort out, using the manual, practical article, the FAQ and this list's archive. However, I have had to send in this somewhat simple problem that may have been addressed several times on the list but I have failed to figure out how to get out of it. I am trying first to align two sequences using align2d like so: READ_MODEL FILE = '1eqk.pdb' SEQUENCE_TO_ALI ALIGN_CODES = '1eqkA' READ_ALIGNMENT FILE = 'PapCys.ali', ALIGN_CODES = 'PapCys', ADD_SEQUENCE = ON ALIGN2D WRITE_ALIGNMENT FILE='PapCys-1eqk.ali', ALIGNMENT_FORMAT = 'PIR' WRITE_ALIGNMENT FILE='PapCys-1eqk.pap', ALIGNMENT_FORMAT = 'PAP' Then I get the following error message: iatmcls_286W MODEL atom not classified: ALA:OT1 ALA iatmcls_286W MODEL atom not classified: ALA:OT2 ALA I have checked all lib files and ALA seems well defined, However, I belive there may be a problem in the ieqk.pdb file which have not touched sine downloading from the PDB database. Can anybody help Andrew

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none restraints made
by alarcon＠lncc.br 16 Jan '03

16 Jan '03

Hi all I ran a very simpleton modelling procedure with mod6v2 and got this log file with none restraints made. The procedure spontaneously is aborted. The same procedure runs well when no HETATM are considered. Any hint will be helpful. rgds Frank Alarcon www.brgene.lncc.br ----------------------------------------------------------------------------- TOP FILE : ----------------------------------------------------------------------------- INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'serino_ed1.ali' SET KNOWNS = '1BH6' '1GCI' '1LW6' '1MEE' '1SCJ' '1SUP' '1THM' SET SEQUENCE = 'oooo' SET ATOM_FILES_DIRECTORY = './:../atom_files' SET STARTING_MODEL= 1 SET ENDING_MODEL = 5 SET HETATM_IO = on CALL ROUTINE = 'model' ------------------------------------------------------------------------- THE LOG FILE (ending...) ------------------------------------------------------------------------- Number of atoms to choose from, total : 3220 3220 Atom types to be searched for (ATOM_TYPES) : ALL Residue types to be searched for (RES_TYPES) : HET Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 439 1: 439: selatm__462_> Number of selected atoms : 13 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 438 : BLK --- 439 : BLK 2 TOP_________> 191 169 MAKE_RESTRAINTS Dynamically allocated memory at amprmcns [B,kB,MB]: 28880029 28203.152 27.542 make_re_417_> Restraint type to be calculated: distance r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 and the same goes on... ------------------------------------------------- WEBMAIL-LNCC Esta mensagem foi enviada utilizanto IMP.

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bond_length_violation/bond_error
by Ralf Schmid 13 Jan '03

13 Jan '03

Dear all, I'm modelling a protein with some additional NMR-restraints for hydrogens. It does work fine for about half of the models, for the other half I get very high scores in the MODELLER OBJECTIVE FUNCTION. This is due to violations of the bond length potential caused by wrong connections between Ns and Hs of an ARG residue (see logfile below), for the models with the 'good' scores the connections are OK. Any ideas what might mess up the N-H bonds? thanks in advance, ralf logfile: <snip> ------------------------------------------------------------------------ Feature 1 : Bond length potential List of the RVIOL violations larger than : 4.5000 #ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 774 53R 53R NH1 HH11 772 773 3.27 1.00 2.27 89.01 1.00 2.27 89.01 2 775 53R 53R NH1 HH12 772 774 2.57 1.00 1.57 61.57 1.00 1.57 61.57 3 776 53R 53R NH2 HH21 775 776 2.57 1.00 1.57 61.51 1.00 1.57 61.57 4 777 53R 53R NH2 HH22 775 777 3.27 1.00 2.27 89.02 1.00 2.27 89.02 ------------------------------------------------------------------------ <snip> ======================================= Dr. Ralf Schmid Institute of Cell and Molecular Biology The University of Edinburgh King's Buildings Michael Swann Building 3.14 Edinburgh EH9 3JR

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Many templates/targets
by Cvetan Stojkoski 09 Jan '03

09 Jan '03

Hey Modeller users, I'm trying to model 400+ proteins based on ~100 templates. I have an alignmentfile of 1500+ sequences comprising of the templates, targets and others. ClustalW was used to align the sequences. I have a few problems. - The sequences in the alignment file do not match the aminoacids present in the pdb files. _Generally_ the pdb files contain more residues than specified in the aligned sequence. Therefore I have to either concatonate the pdb files or specify the residues in the appropriate residues in the alignment file. - The ID codes in the alignment file do not match the atom file names. - There is no "second" line in each entry in the alignment file. Although all this can be done manually, I can't help but wonder if there is a way to automate/expidate the process. A paper published by Sanhez and Sali (1998) mentioned perl script that allowed for rapid progress through the various steps involved with modelling. Suggestions will be most appreciated. Some of the pdb files are complexes. If it can be avoided I'd prefer not to use these structures . However if I do decide to use some of them, I plan to minimise the E via MD (cns) of the protein (minus the ligand) before using it as a template. What are people's thoughts about this? Many thanks

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How to change a pdb file's chain id without renumbering the residues using Modeller?
by Kong Lesheng 07 Jan '03

07 Jan '03

Hi, I have successed done this under Modeller 4. But under Modeller 6v2, the old script doesn't work. My top file is as follow: READ_MODEL FILE = 'xenl.pdb' RENAME_SEGMENTS SEGMENT_IDS = 'X', RENUMBER_RESIDUES = off WRITE_MODEL FILE = 'xenl.mol', HETATM_IO = on The log file reported that assgn___547E> Incorrect element type for variable: RENUMBER_RESIDUES Element, element type: OFF 4 Command line: RENAME_SEGMENTS SEGMENT_IDS = 'X', RENUMBER_RESIDUES = OFF assgn___525E> Error in TOP variable assignment. compile_563E> Please correct the errors reported above and rerun MODELLER. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I have checked the libary file top.ini in modeller4 and modeller6v2 about RENUMBER_RESIDUES. Under modeller4 , 64 LOGICAL RENUMBER_RESIDUES 1 on # whether to renumber residues from 1 to N Under modeller6v2, 41 INTEGER RENUMBER_RESIDUES 0 # starting residue index for renumbering residues Is it possible to change a pdb file's chain id without renumbering the residues ? Thank you very much! With best regards, Lesheng

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assign force field
by Yang Xiaolin 25 Dec '02

25 Dec '02

Deal all, When I assigned force field to a protein 3D coordinate, I was told that "total formal charges does not equal total partial charge". I have added hydrogen to this structure. And If i change to another force field, the same thing happened. Who can tell me how I can resolve this problem. Thanks. Happy New Year to all! Xiaolin Yang

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error 648 with modeller
by Cédric Bauvois 17 Dec '02

17 Dec '02

Hi, I have a problem with Modeller program to make mutagenesis project by using triton. I always obtain the error message in the run_output file: Kind, OS, HostName, Kernel, Processor: 4, Linux pcb311 2.4.19-16mdk i686 Date and time of compilation : 07/16/2002 11:42:16 Job starting time (YY/MM/DD HH:MM:SS): 2002/12/17 11:07:34.945 getprog_531; ROUTINE redefined: loop getprog_531; ROUTINE redefined: loop_restraints getprog_531; ROUTINE redefined: optimize getprog_531; ROUTINE redefined: getnames-loop getprog_531; ROUTINE redefined: build_ini_loop getprog_531; ROUTINE redefined: select_loop_atoms rdpir___648E; Alignment sequence not found in PDB file: 1 . 2dhc.pdb recover____E; ERROR_STATUS = STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 12188765 11903.090 11.624 Starting time : 2002/12/17 11:07:34.945 Closing time : 2002/12/17 11:07:39.685 Total CPU time [seconds] : 3.96 STOP can you explain how to resolve these error? thanks a lot! Bauvois cedric

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floating invalid
by Marcos Bonfadini 16 Dec '02

16 Dec '02

Hi, modellers I've got this message: TOP_________> 197 133 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 15156027 14800.808 14.454 make_re_417_> Restraint type to be calculated: distance forrtl: error (65): floating invalid Abort (core dumped) Can anyone tell me what went wrong? Thanks in advance Bonfá -- ////////////////////////////////////////////////// Marcos Bonfadini CBME-Centro de Bioteclogia Molecular e Estrutural Instituto de Física - USP / São Carlos Av.:Trabalhador Sãocarlense,400 - Centro C.P.369 - 13560-790 São Carlos - SP - Brazil Phone: ++55 16 273.9874, ++55 16 273.9868 FAX: ++55 16 273.9881 \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ Doações/Donations http://www.clickfome.com.br http://www.thehungersite.com http://www.doegratis.com.br

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leaving gaps in non aligned regions
by Gowthaman R 12 Dec '02

12 Dec '02

hello modellers, i am trying to model some proteins. but my protein has some region (internal) (15-20 amino acids) which does not have any corresponding region in the template sequence. i DO NOT want to model that region and in my final (3D) strucuture i want to have a gap in the corresponding internal region. other wise that region forms a loop or extended region ( makes the structre ugly ??). i wish to know how my alignement file should look like.... i tried following and did not solve the problem 1) putting " X " for the amino acids for which i dont want the 3D structure to be made 2) puting " - " for the same... waiting for ur reply gowthaman Phd Student ICGEB, India.

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# SET SELECTION_SEARCH = 'SPHERE_SEGMENT', SPHERE_RADIUS = 6
by Bozidar Yerkovich 11 Dec '02

11 Dec '02

On behalf of kinsellg(a)tcd.ie... Hi all, I've recently started using modeller and I've been able to generate models and loops, so far. I tried optimising my alignment and I've now hit this snag. I get this error when trying to generate loops. Also I havn't been able to get the command to optimise the loop envirionment to work yet. The top and log files are attached. # SET SELECTION_SEARCH = 'SPHERE_SEGMENT', SPHERE_RADIUS = 6 Any ideas?? I am very grateful for all your help, Gemma The error: TOP_________> 189 674 SET OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 200, MIN_ OM_SHIFT = 0.001 TOP_________> 190 675 OPTIMIZE SCHEDULE_STEP = 1 preppdf_457W> Both soft sphere and statistical potential terms selected. pair4___223E> Array too small. Increase MPAIRS current maximum, current need: 33600 33600 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 14325865 13990. Starting time : 2002/09/05 09:56:49. Closing time : 2002/09/05 09:57:00. Total CPU time [seconds] : 11.04

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