February 2003 - modeller_usage

New to Modeller...
by Luis Rosales 25 Feb '03

25 Feb '03

Hi: Hi to all the modeller users in the list! Im new to modeller, and trying to build my first modeller derived model. I already knew the template I want to use and the sequence to model. When run my script I get the following error: check_a_337E> Structure not read in: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I assume the error is my definition of my set atoms file, the script Im using goes like this: SET ALNFILE = '01mod.ali' # alignment filename SET KNOWNS = '1cx1' # codes of the templates SET SEQUENCE = '1dnj' # code of the target SET ATOM_FILES_DIRECTORY = './:../PDB:./atom_files' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 2 # index of the last model SET DEVIATION = 4.0 # have to be >0 if more than 1 model SET RAND_SEED = -12312 # to have different models from another TOP file CALL ROUTINE = 'model' # do homology modelling I have my pdb file in ./atoms_files (named 1cx1.pdb) and my alnfile and sequence (01.mod.ali 1dnj.seq) in ./ >From the user manual I think my Atoms files directory is well defined, however Im stuck... There is some stupid/basic mistake Im overlooking? Thanks in advance, Luis Rosales

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no seq_search.dat file at the end
by vimalkumar v 21 Feb '03

21 Feb '03

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no seq_search.dat file at the end
by vimalkumar v 21 Feb '03

21 Feb '03

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Simulated annealing
by Modeller Care 21 Feb '03

21 Feb '03

This message originates from an email address that is not in the subscribers list. It has been approved by the list-owner. ----------------------------------------------------------------------- MODELLER users - I have succeeded through several rounds of template-based and loop modeling with MODELLER (v6.1). I would now like use my last model structure to build an all-atom model (include Hs), eliminate all template-based restraints, and try a round of simulated annealing with the other CHARMM parameters turned on. Can anyone show me an example of how to set this up? Any precautions for CHARMM settings? Many thanks, Tom Duncan -- Thomas M Duncan Research Associate Professor Dept Biochemistry & Molecular Biology Institute for Human Performance, Rm 4311 SUNY Upstate Medical University 750 E Adams St Syracuse, NY 13210

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error when using "model " command
by Guittet, Muriel 21 Feb '03

21 Feb '03

Dear Modeller’s users, I'm a real beginner with modeller (on Windows) and cannot manage to fix what seems to be a very simple case (according to what I've seen in the users' list). I created my alignment file (1fgk.ali.txt) >P1;pto-ad sequence:pto-ad:::::::: MGSKYSKATNSINDALSSSYLVPFESYRVPLVDLEEATNNFDHKFLIGHGVFGKVYKGVL RDGAKVALKRRTPESSQGIEEFETEIETLSFC-RHPHLVSLIGFCDERNEMILIYKYMEN GNLKRHLYG------------SDLPTMSMSWEQRLEICIGAARGLHYLHTRAIIHRDVKS INILLDENFVPKITDFGISKKGTELDQTHLSTVVKGTLGYIDPEYFIKGRLTEKSDVYSF GVVLFEVLCARSAIVQSLPREMVNLAEWAVESHNNGQLEQIVDPNLADKIRPESLRKFGD TAVKCLALSSEDRPSMGDVLWKLEYALRLQESVI* >P1;1FGK_A structureX:1fgk.ent:FIRST:A:LAST:A:::: ------------ELPEDPRWELPRD---RLVLGKPLG-----QVVLAEAIGL----PNRV TKVAVKMLKSDATEKD--LSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASK GNLREYLQARRPP------------EEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAA RNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSF GVLLWEIFTLGGSPYPGVP--VEELFKLLKEGHRMDKPSNCTN-ELYMMMR--------- ---DCWHAVPSQRPTFKQLVEDLDRIVALTS---* I also tried the following lines structureX:1fgk.ent:464:A:762:A:::: structureX:1fgk:FIRST:A:LAST:A:::: Downloaded the corresponding pdb file (1fgk.ent) And wrote the following script: INCLUDE SET ATOM_FILES_DIRECTORY = './:../../atom_files' SET STOP_ON_ERROR = 2 SET OUTPUT_CONTROL = 1 1 1 1 2 #READ_MODEL FILE = '1fgk.ent', MODEL_SEGMENT '464:A' '762:A' READ_MODEL FILE = '1fgk.ent', MODEL_SEGMENT 'FIRST:A' 'LAST:A' SET ALNFILE='1fgk.ali.txt' SET KNOWNS='1FGK_A' SET SEQUENCE='pto-ad' SET STARTING_MODEL=1 SET ENDING_MODEL=1 CALL ROUTINE = 'model' I don’t have any “log” file as described in the manual but could redirect the comments into an error file which always give me the same message: 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: 464: A To find out more, switch on maximal output by 'SET OUTPUT_CONTROL = 1 1 1 1 2' ………… pick_re_449W> No atoms selected; no restraints will be selected. pick_re_450E> Probably because no MODEL is in memory; use READ_MODEL. csrrng__299E> Atom index is out of bounds: 3 0 nselat__596E> Atom index is out of range (iatm,natm): 3 0 nselat__596E> Atom index is out of range (iatm,natm): 2 0 …………. At first, I got a message because the number of residues was different in the alignment file and the pdb file. I fixed it but it showed me that Modeller could access the pdb file. I checked the residues’ numbers in the both files. I tried to rename my file into 1fgk.pdb, to copy the pdb file in the modeller’s folder, to model only contiguous residues… and I have no more ideas. All the files (alignment, PDB, top) are in the same folder and I could run another top script creating the alignment, using the data of the pdb file (what proves that it could find and read it…) (that is another problem but I was surprised to see that, if some residues were missing in the pdb file (in my case res 486 to 490) , Modeller considered the residues 485 and 491 to be contiguous. The alignment could then not be very accurate.) Has someone any idea of what could get wrong in all of this? * Modeller returns many files (V99990001, B99990001, D00000001 which are empty) and RSR file (full of data) and “Configuration settings “ file which gives me some very strange 3D results. What are all these files ? * last question: is there any place where I could find the meaning of all the results, comments, warning and errors Modeller returns? Many thanks for your help! Muriel

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completing incomplete PDBs
by Christoph Nimptsch 20 Feb '03

20 Feb '03

Hi, assume, I have a PDB file template with some residues missing, e.g. 5 Amino acids at the beginning, 10 in the middle and 2 at the end of the sequence. Now, I use Modeller to complete the template (I align the PDB to its sequence) and use it for homology modelling. Is this a common procedure? What do you think about it? Will the completed template be reliable or should I leave the gaps of the template unfixed in homology modelling? Thanks in advance, Christoph Nimptsch ------------------------------------------ Christoph Nimptsch Apotheker Pharmazeutisches Institut Arbeitskreis Prof. Kovar Universität Tübingen Auf der Morgenstelle 8 D-72076 Tuebingen Tel.: 07071 / 29 73047 Fax.: 07071 / 29 2470 mailto:christoph.nimptsch@uni-tuebingen.de ------------------------------------------

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homology modelling
by Vidya Harini 12 Feb '03

12 Feb '03

Hi, I have the following confusion kindly give me some suggestions... If there are a set of sequences which are 50% identical in sequence and a homology model has been built for one of them, is it possible to use this model in analysing the features of its other related members on the same model. Thanks in advance vvh

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FW: Problems on installation (fwd)
by Andrej Sali 11 Feb '03

11 Feb '03

-- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 Email sali(a)salilab.org; Web http://salilab.org -----Original Message----- From: Bozidar Yerkovich [mailto:bozidar@salilab.org] Sent: Tuesday, February 11, 2003 6:41 PM To: Andrej Sali Subject: Problems on installation (fwd) ---------- Forwarded message ---------- Date: Tue, 11 Feb 2003 12:00:21 -0000 From: "edward grew (BITS)" <edward.grew(a)bbsrc.ac.uk> To: "'bozidar(a)salilab.org'" <bozidar(a)salilab.org> Subject: Problems on installation I have just installed Modeller6v2 on a Unix system with the path set to i386-absoft. make install seems to work fine but when trying to run modeller using the mod command i get the following error. ? FORTRAN Runtime Error: ? Bad file specification ? OPEN(UNIT=11,... Any advice on how to rectify this problem would be gratefully recieved. thanks very much for your time Edward Grew

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FW: Problems on installation (fwd)
by Andrej Sali 11 Feb '03

11 Feb '03

-- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 Email sali(a)salilab.org; Web http://salilab.org -----Original Message----- From: Bozidar Yerkovich [mailto:bozidar@salilab.org] Sent: Tuesday, February 11, 2003 6:41 PM To: Andrej Sali Subject: Problems on installation (fwd) ---------- Forwarded message ---------- Date: Tue, 11 Feb 2003 12:00:21 -0000 From: "edward grew (BITS)" <edward.grew(a)bbsrc.ac.uk> To: "'bozidar(a)salilab.org'" <bozidar(a)salilab.org> Subject: Problems on installation I have just installed Modeller6v2 on a Unix system with the path set to i386-absoft. make install seems to work fine but when trying to run modeller using the mod command i get the following error. ? FORTRAN Runtime Error: ? Bad file specification ? OPEN(UNIT=11,... Any advice on how to rectify this problem would be gratefully recieved. thanks very much for your time Edward Grew

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RE: too many helices
by Andrej Sali 06 Feb '03

06 Feb '03

This is probably due to a very large dimension of the whole system (relative to the number of atoms). I suggest you email me your input file so I can narrow down the problem. Best, Andrej -- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 Email sali(a)salilab.org; Web http://salilab.org > -----Original Message----- > From: yinja(a)email.uc.edu [mailto:yinja@email.uc.edu] > Sent: Thursday, February 06, 2003 5:28 PM > To: sali(a)salilab.org > Subject: too many helices > > > Hi, Dr. Sali, > i am running a modeller job, in which there are 45 segment to > enforced to form helix. the job log file complained as > folllows: > =============================================================== > TOP_________> 173 132 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', > ADD_RESTRAIN; > TS = 'ON' > > make_re_417_> Restraint type to be calculated: distance > cnctarea_E> Too many cubes. Increase MAXCUBES. kjidim, > maxcubes: 239250 > 50000 =============================================================== > how do i do to by-pass it? two similar jobs have been done > with few number of helices restraints. thanks. > > > Jian Yin > post-doc > university of cincinnati >

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