modeller_usage July 2002

modeller_usage@salilab.org

24 participants
27 discussions

glutamates patch
by Valeria Costa 26 Jul '02

26 Jul '02

Dear Modellers, I have to patch two glutamates to form a carboxyl-carboxylate pair. I thought it was sufficient to add at the end of my input the ad hoc version of the subroutine 'special_patches', ------------------------- SUBROUTINE ROUTINE = 'special_patches' PATCH RESIDUE_TYPE = 'GLUP', RESIDUE_IDS = '72' '282' RETURN END_SUBROUTINE ------------------------- but it doesn't work. My approach was probably too naive. Do you have suggestions? Thanks in advance

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selecting the alignment matrix
by Alessandro Contini 25 Jul '02

25 Jul '02

Hi, I'm pretty new with modeller, so I'm asking if anybody knows how to change the default alignment matrix. Thanks -- Dott. Alessandro Contini Istituto di Chimica Organica, Facoltà di Farmacia Università degli Studi di Milano Via Venezian, 21 20133 Milano Tel. +390250314480 Fax +390250314476 http://users.unimi.it/istchimorg/pagconthtm.htm

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Modelling Dimers
by Michael Buck 25 Jul '02

25 Jul '02

I have a question about modelling dimers. What I am trying to do is model a homodimer. I have tried to few things that might work, but I am not really sure. What I did: 1. Edited the pdb file for the template, making it all one subunit 2. My alignment file has the 60 amino acids from the first dimer then chain of glycines then next 60 amino acids from the second dimer. 3. After I model, remove the chain of glycines and add back the B domain letter to the pdb file. The models look good. What does the group think? Will these models be accurate? Will the restraints between the two dimers be included in the models? Can I edit the restraints to remove the bad restraints located at the end of the first dimer and beginning of the second? Below is the alignment: I edited the 1a0a template change B domain to A and adjusting the amino acid numbers. >P1;1a0aSP structureX:1a0aSP:1:A:112:A:Pho4:yeast: 2.00:-1.00 MKRESHKHAEQARRNRLAVALHELASLIPAEWKQQN---VSAAPSKATTVEAACRYIRHLQQNGST--------------MKRESHKHAEQARRNRLAVALHELASLIPAEWKQQN---VSAAPSKATTV* >P1;1hlo sequence:1hloModel: : : ::Max:Human: 2.00:-1.00 DKRAHHNALERKRRDHIKDSFHSLRDSVP--SLQGE------KASRAQILDKATEYIQYMGGGGGGGGGGGGGGGGGGGGDKRAHHNALERKRRDHIKDSFHSLRDSVP--SLQGE------KASRAQIL* ************************************************ Michael Buck NCSU Genetics mjbuck(a)unity.ncsu.edu Phone (919)515-5759 Fax (919)515-3355 http://www4.ncsu.edu/~mjbuck *************************************************

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main chain atoms
by Carlos Sosa 22 Jul '02

22 Jul '02

Hi, I would like to know how to select main chain atoms for superposition Thanks Carlos Sosa

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MAXSPL problem
by Tommy Wang 19 Jul '02

19 Jul '02

Hi Bozidar, I got the following error message. I suspect some preset limit in the fortran code has been exceeded once again like the MPAIRS case. crsplin_459E> Increase MAXSPL to at least 440 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I can pass all the necessary files if u need it to reproduce the problem. best regards

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PDB problem
by Frederico Moreno 18 Jul '02

18 Jul '02

Hi, I'm using a correct pdb files. I got this message below. What's wrong? openf5__224_> Open 11 OLD SEQUENTIAL /home/pepeu/Modeller/modeller6v2/examples/Lectin/1h9p.pdb rdpdb___303E> No atoms were read from the specified input PDB file: 1) Possibly because an incorrect/non-existent PDB file is specified. 2) Possibly because the segment is specified incorrectly in the alignment file or by the TOP variable MODEL_SEGMENT. That is, the beginning residue number and/or chain id in MODEL_SEGMENT may not be found in the input PDB file; MODEL_SEGMENT: 1: To find out more, switch on maximal output by 'SET OUTPUT_CONTROL = 1 1 1 1 2' rdabrk__288W> Protein not accepted: 1 rdabrk__290E> Number of residues in the alignment and pdb files are different: 237 0 For alignment entry: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Moreno _______________________________________________________________________ Yahoo! Encontros O lugar certo para encontrar a sua alma gêmea. http://br.encontros.yahoo.com/

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Alignment problem
by Frederico Moreno 18 Jul '02

18 Jul '02

Dear Bozidar, I had problem when trying to get some a protein model. What do I have to do? I used the PIR alignment format also. My Top file is: INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'alignment.seg.pap' # alignment filename SET KNOWNS = '1h9p' # codes of the templates SET SEQUENCE = '1drg' # 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 The alignment file seems to be ok: Kind, OS, HostName, Kernel, Processor: 4, Linux localhost.localdomain 2.4.18-6mdkenterprise i686 Date and time of compilation : 07/05/2002 17:30:36 Job starting time (YY/MM/DD HH:MM:SS): 2002/07/18 13:08:16.425 TOP_________> 105 705 SET ALNFILE = 'alignment.seg.pap' TOP_________> 106 706 SET KNOWNS = '1h9p' TOP_________> 107 707 SET SEQUENCE = '1drg' TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = './:../atom_files' TOP_________> 109 709 SET STARTING_MODEL = 1 TOP_________> 110 710 SET ENDING_MODEL = 1 TOP_________> 111 711 CALL ROUTINE = 'model' TOP_________> 112 399 CALL ROUTINE = 'getnames' TOP_________> 113 509 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 114 510 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 115 511 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 116 512 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 117 513 SET ROOT_NAME = SEQUENCE TOP_________> 118 514 RETURN TOP_________> 119 400 CALL ROUTINE = 'homcsr' TOP_________> 120 106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153.583 2.103 openf5__224_> Open 11 OLD SEQUENTIAL alignment.seg.pap Dynamically allocated memory at amaxbnd [B,kB,MB]: 2560929 2500.907 2.442 openf5__224_> Open 11 OLD SEQUENTIAL alignment.seg.pap Read the alignment from file : alignment.seg.pap Total number of alignment positions: 0 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1h9p 0 1 2 1drg 0 1 TOP_________> 121 107 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND check_a_337E> Structure not read in: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2560929 2500.907 2.442 Starting time : 2002/07/18 13:08:16.425 Closing time : 2002/07/18 13:08:17.598 Frederico Moreno _______________________________________________________________________ Yahoo! Encontros O lugar certo para encontrar a sua alma gêmea. http://br.encontros.yahoo.com/

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What is de problem??
by Juan Palacios 16 Jul '02

16 Jul '02

MODELLER 6v2, 17 Feb 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 sys_____214E> File probably does not exist. Perhaps you have to increase swap space size. Filename: 1026244802 Command : uname -rnsm > 1026244802 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 0 0.000 0.000 Starting time : 2002/07/09 16:00:02.767 Closing time : 2002/07/09 16:00:02.892 Total CPU time [seconds] : 0.09 Thanks

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Fwd: modeller top files
by Bozidar Yerkovich 12 Jul '02

12 Jul '02

from one of our fellow MODELLERs... Can anyone help? B.. ---------- Forwarded Message ---------- Subject: modeller top files Date: Fri, 12 Jul 2002 12:17:13 +0100 From: "Rosh Karunaratne" <HIDDEN> To: bozidar(a)salilab.org thanks for your help last week Ive been reading through the online modeller manual (version6) and am having trouble creating the 'right' top file for my ali file that I have created. Below are two of the examples i have tried (both using the modeller manual) but when I run procheck on the last *.B9999 file I get heavy violations and bad contatcs between atoms. All I am interested in is creating the 'best model' within least violations etc Is there a pre-prepared top file that you know of that will do this task? Thanks for your help Rosh INCLUDE #rho1 SET ALNFILE = 'name.ali' SET HETATM_IO = on SET KNOWNS = '1abc' SET SEQUENCE = '123456' SET ATOM_FILES_DIRECTORY = '/d/d120/u/fkaru01/' SET STARTING_MODEL = 1 SET ENDING_MODEL = 1 SET DO_LOOPS = '1' SET LOOP_STARTING_MODEL =1 SET LOOP_ENDING_MODEL= 25 SET LOOP_MD_LEVEL = 'refine_5' CALL ROUTINE = 'model' or SET ALNFILE = 'name.ali' SET KNOWNS = '1abc' SET SEQUENCE = '123456' SET ATOM_FILES_DIRECTORY = '/d/d120/u/fkaru01/' SET STARTING_MODEL = 2 SET ENDING_MODEL = 2 CALL ROUTINE = 'very_fast' CALL ROUTINE = 'model' _________________________________________________________________ MSN Photos is the easiest way to share and print your photos: http://photos.msn.com/support/worldwide.aspx -------------------------------------------------------

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new user
by erase test 11 Jul '02

11 Jul '02

Dear All! I/m a new user of modeller , before a time ago, i made teh download of modeller 6v2 , and just now i installed in my computer , linux/redhat 6.2. in instalation i make all thing complete give the key and the all instalation it's ok!! when i go ro run a some example from tutorial, if i run initial.top all works but if i run compare.top i have a problems : TOP_________> 5 5 COMPARE OUTPUT = 'LONG' pdbnam__217W> Filename for PDB code not found: 1fdx.B99990001 Directories: ./:../atom_files Extensions : :.atm:.pdb:.ent:.crd openf5__224_> Open 11 OLD SEQUENTIAL ./1fdx.atm openf5__224_> Open 11 OLD SEQUENTIAL file-not-found openf5__225E> File does not exist: file-not-found get_nal_378E> Error reading sequence from PDB file: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 i know that mean they can't found the file , why? the file are there, more question when i run a example from bin direcoty, they have a errors too: assgn___544E> Variable name not recognized: MAX_ITERATIONS_STORE Command line: SET MAX_ITERATIONS_STORE = MAX_ITERATIONS assgn___525E> Error in TOP variable assignment. assgn___547E> Incorrect element type for variable: ARGUMENTS Element, element type: REFINE_HOT_ONLY 3 Command line: IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN 'GO_TO __BEGIN_MD' assgn___525E> Error in TOP variable assignment. assgn___544E> Variable name not recognized: VIOL_REP_STORE Command line: SET VIOL_REP_STORE = VIOL_REPORT_CUT assgn___525E> Error in TOP variable assignment. assgn___547E> Incorrect element type for variable: ARGUMENTS Element, element type: RSTRS_REFINED 3 Command line: IF ARGUMENTS = RSTRS_REFINED 0, OPERATION = 'EQ', T HEN 'SET VIOL_REPORT_CUT = 4 4 4 4 4 999 999 999 999 999 999 999 999 999 999 999 999 4 4 4 999 999 999 999 999 999 999 999 999 999 999' assgn___525E> Error in TOP variable assignment. and more, some one can exaplind me why i didn't get a normal anwser? i really dont want to run under by windows , i really dont have this type of machine ;-) and don't want best regads, -miki roit

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modeller_usage July 2002