- modeller_usage - salilab.org

source code for RMSD programme
by Shiyong Liu 18 Mar '03

18 Mar '03

Andrej Sali,��ã� I want to caculate RMSD between one protein and many other protein structures. I hardly found a good RMSD programme by google. Could you help me give me a RMSD programme? Shiyong ======= 2003-03-18 07:02:00 ��д��======= >Possibly so. > >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: owner-modeller_usage(a)salilab.org >> [mailto:owner-modeller_usage@salilab.org] On Behalf Of quentin kaas >> Sent: Tuesday, March 18, 2003 7:00 AM >> To: modeller_usage(a)salilab.org >> Subject: Re: Array too small. Increase MPAIRS >> >> >> I resolved my MPAIRS problem in using the top_heav.lib >> topology library >> instead of the top_allh.lib. As my model is quite big, the >> hydrogens may be >> too numerous to be handled by Modeller. >> Thank you for your help. >> >> Quentin Kaas >> >> Le Lundi 17 Mars 2003 16:08, Andrej Sali a �crit : >> > Without seeing the input/output files, it probably indicates a >> > difficult optimization problem that runs into many overlapping atom >> > pairs. Can you improve the alignment? >> > >> > Andrej >> >> > >. = = = = = = = = = = = = = = = = = = = = �� Shiyong Liu ��syliu(a)mdl.ipc.pku.edu.cn ��2003-03-19

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FW: Array too small. Increase MPAIRS
by Modeller Care 18 Mar '03

18 Mar '03

------ Forwarded Message From: quentin kaas <kaas(a)ligm.igh.cnrs.fr> Organization: CNRS - IGH Date: Fri, 14 Mar 2003 15:19:15 +0100 To: modeller-care(a)salilab.org Subject: Array too small. Increase MPAIRS I get a problem when I used Modeller when I do simple optimizations : "Array too small. Increase MPAIRS" I have seen in the archives that it was a problem with older version and I get and install the last version but it still give the same answer... Am I doing something wrong or is it a source code problem ? My top file is : SET OUTPUT_CONTROL = 1 1 1 1 1 READ_TOPOLOGY FILE = '$(LIB)/top_allh.lib' READ_PARAMETERS FILE = '$(LIB)/par.lib' READ_MODEL FILE = '../../1hsa' READ_ALIGNMENT FILE = 'model_MHCp.ali', ALIGN_CODES = '1hsa' 'MHCp' GENERATE_TOPOLOGY SEQUENCE = 'MHCp' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ = off WRITE_MODEL FILE = 'MHCp.ini' MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo' WRITE_RESTRAINTS FILE = 'MHCp.rsr' SWITCH_TRACE TRACE_OUTPUT = 1, FILE = 'MHCp.trc' OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 20 WRITE_MODEL FILE = 'MHCp.B' Thanks in advance Quentin Kaas, IMGT ------ End of Forwarded Message

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NMR and Crystallographic models
by Simon Holton 17 Mar '03

17 Mar '03

Dear All, I am trying to construct a model of a protein based on an NMR model of a homologous protein. Having read the modeller manual I see that the structureN command can be used for NMR models, but I cannot work out how best to use it. To make the most of the NMR data regarding conformational flexibility should I split the NMR structure into separate files, each containing a single conformation, or is there a more convenient way to incorporate this information? I guess what this comes down to is how structureX and structureN are interpreted by modeller? Many thanks for your help Simon Holton ************************************************************** Dr. Simon Holton Laboratory of Molecular Biophysics, Rex Richards Building, Department of Biochemistry, University of Oxford South Parks Road Oxford Tel: 01865 275379 Fax: 01865 275182 **************************************************************

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Specification of chain of output atom files.
by Richard Friedman 14 Mar '03

14 Mar '03

Dear Modellers, How can I write a pdb file containing a chain specification? My top file is # Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to produce a large log file SET ALNFILE = 'monomer3.ali' # alignment filename SET KNOWNS = '1g2i' # codes of the templates SET SEQUENCE = 'prk7' # 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 My ali file is: C; alignment >P1;1g2i structureX:1g2i:1 :A:166 :A:Protease:Pyrococcus Horikosh: 2.00:-1.00 M---KVLFLTANEFEDVELIYPYHRLKEEGHEVYIASFE-RGTITGKHGYSVKVDLTFDKVNPEE-FDALVLPGG RAPERVRLNEKAVS-IARKMFSEGKPVASICHGPQILISAGVLRGRKGTSYPGIKDDMINAG-VEWVDAEVVVDG NWVSSRVPADLYAWMREFVKLLK----------------* >P1;prk7 sequence:prk7:1 :A:189 :A:park7:human: 2.00:-1.00 MASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVICPDASLEDAKKEGPYDVVVLPGG NLGAQNLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGCGSKVTTHPLAKDKMMNGGHYTYSENRVEKDG LILTSRGPGTSFEFALAIVEALNGKEVAAQVKAPLVLKD* I was hoping that inclusion of the chain designators in the prk7 sequence file, would produce a pdb file with the chain designators included, but that is not what had happened. How can I be sure that the output file includes the chain designation 'A' on every atom line? Thanks and best wishes, Rich -------------------------------------------------------------- Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Medical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman(a)cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "You don't have ot do any more work to write a book. You already wrote a book. Your course notes are a book. I've seen them lying on the floor of your office. I've seen course notes used for books on everything from Math to Origami. Just hand your course notes in. Make sure you hand in the ones with the apple juice spilled on it." -Isaac Friedman, age 13 Upon Isaac's attainment of his majority I am discontinuing the quotes from him.

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Modeller error message
by Richard Friedman 13 Mar '03

13 Mar '03

Dear Modellers, I am having difficulty getting modeller to run to completion. Here is my directory contents, my top and ali files, and an excerpt from my log file. I have also attached my complete pdb file and log file. I would greatly appreciate any suggestions as to how to get this modeller job to run to completion. My directory contents: 1g2a.atm.old 1g2i_b.pep comppdb monomer.msf park7-ig2i_b.pair park7.ssearch 1g2i.pdb 1g2i_b.tfa model-monomer.log monomer.ps park7-ig2i_c.pair xa.nrl3d.list 1g2i_a.pep 1g2i_c.pep model-monomer.top nm_007262.rsf park7.gap 1g2i_a.tfa 1g2i_c.tfa monomer.ali np_009193.rsf park7.pdb.netblastp 1g2i_b.pdb 1ga2.atm monomer.list park7-ig2i_a.pair park7.pep My top file # Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to produce a large log file SET ALNFILE = 'monomer.ali' # alignment filename SET KNOWNS = '1ga2' # codes of the templates SET SEQUENCE = 'prk7' # 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 My alignment file C; alignment >P1;1ga2 structureX:1ga2:1 : :166 : :Protease:Pyrococcus Horikosh: 2.00:-1.00 ---MKVLFLTANEFEDVELIYPYHRLKEEGHEVYIASFE-RGTITGKHGYSVKVDLTFDK VNPE-EFDALVLPGGRAPERVRLNEKAV--SIARKMFSEGKPVASICHGPQILISAGVLR GRKGTSYPGIKDDMINAG-VEWVDAEVVVDGNWVSSRVPADLYAWMREFVKLLK------ ----------* >P1;prk7 sequence:prk7:1 : :189 : :park7:human: 2.00:-1.00 MASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVICPDASLED AKKEGPYDVVVLPGGNLGAQ-NLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGC GSKVTTHPLAKDKMMNGGHYTYSENRVEKDGLILTSRGPGTSFEFALAIVEALNGKEVAA QVKAPLVLKD* The error message Read the alignment from file : monomer.ali Total number of alignment positions: 190 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1ga2 166 1 1ga2 Protease 2 prk7 189 1 prk7 park7 TOP_________> 121 107 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./1ga2.atm 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: 166 0 For alignment entry: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 The complete log file and pdb file are attached. Thanks and best wishes, Rich -------------------------------------------------------------- Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Medical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman(a)cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "You don't have ot do any more work to write a book. You already wrote a book. Your course notes are a book. I've seen them lying on the floor of your office. I've seen course notes used for books on everything from Math to Origami. Just hand your course notes in. Make sure you hand in the ones with the apple juice spilled on it." -Isaac Friedman, age 13 Upon Isaac's attainment of his majority I am discontinuing the quotes from him.

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Modelling to multimer
by Richard Friedman 10 Mar '03

10 Mar '03

Dear Modellers, I have a monomer sequence A1 that is homologous to the monomer of a multimer structurer B1....BN. I want to build a model of the multimer B1....BN with modeller. I can think of two ways ot do this: 1. Divide the pdb files of the multimers B1....BN into single pdb files. Then I build models on A1...AN matched to them. Then I merge the A1...AN PDB files to get A1...AN. 2. Model A1 against B1. strcuturally align the structure of A1 against B1...BN. My question: is there any way that I can build the multimer A1...AN in one step against B1...BN? Thanks and best wishes, Rich -------------------------------------------------------------- Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Medical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman(a)cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "I wish that all homework was a drawing contest". -Rose Friedman, age 6

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FW: Protein+Metal Ion?
by Modeller Care 10 Mar '03

10 Mar '03

------ Forwarded Message From: Oliver Hucke <Oliver.Hucke(a)physchem.uni-freiburg.de> Date: Fri, 07 Mar 2003 10:00:39 +0100 To: Modeller Care <modeller-care(a)salilab.org> Subject: Re: Protein+Metal Ion? Dear Marc, you might define the subroutine 'special_restraints' at the end of your top script introducing the bonds between the metal ligand atoms and the metal atom in form of e.g. harmonic potentials. In my case the following introduced 6 ligand-Fe bonds: SUBROUTINE ROUTINE = 'special_restraints' SET ATOM_IDS 'NE2:501' 'FE2:1185' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0.1 SET ATOM_IDS 'NE2:541' 'FE2:1185' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0.1 SET ATOM_IDS 'NE2:815' 'FE2:1185' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0.1 SET ATOM_IDS 'NE2:862' 'FE2:1185' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0.1 SET ATOM_IDS 'OE1:830' 'FE2:1185' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0.1 SET ATOM_IDS 'OE2:830' 'FE2:1185' RETURN END_SUBROUTINE Note: the numbers of the residues correspond to the modeller numbering scheme. You may get the correct numbers from an *.ini file. Info on the meaning of the ADD_RESTRAINT lines can be found in the chapter "specification of restraints" in the modeller manual Hope this helps! Best, Oliver > I would like to model a protein that contains Zn in the active site. In = > the template structure, two His residues are coordinated to the Zn. The = > target sequence also has these residues and the sequences display > 50% = > identity. How do I force the His residues to similarly coordinate the = > Zn in the modelled structure? If the Zn atom is in .pdb file, modeller = > doesn't seem to notice. Without the Zn atom present, the His = > sidechains simply flop around in the active site (not surprisingly). > > Marc Campitelli -- ____________________________________________________________________________ Oliver Hucke Inst. fuer Physikalische Chemie II Universitaet Freiburg Albertstr. 23a D-79104 Freiburg Tel. : +49-761-203-5130 (/-6179) Fax. : +49-761-203-6189 email: Oliver.Hucke(a)physchem.uni-freiburg.de ____________________________________________________________________________ ------ End of Forwarded Message

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Fluorescent residue
by John T. Penniston 07 Mar '03

07 Mar '03

I'm attempting to make a model of a protein containing a fluorescent residue attached to a specific Lysine. The structure of the Lysyl-fluorophore is: (view it in a fixed font). Cl / NH2 N-C | / \ CH-CH2-CH2-CH2-CH2-NH-C N H H | \ / | | C=02H N-C C-C CH2-CH3 \ / \ / C C-N \ / \ C-C CH2-CH3 | | H H Both rings are aromatic, but I couldn't represent that above. I've modified all of the necessary files to account for the radius and mass of the Chlorine, and the name (TAK or t)of the new residue. I'm attaching a text file of one of my attempts to define this residue in the top_heav.lib file. Now I'm starting to modify the parameter file (par.lib), and have figured out at least part of how to do that, but modifying that file does not seem to give me a better looking residue. This residue should be flat from the 1st side chain N to the last N(CH2)2, including both rings. Mine generally come out slightly bent! The attached file assumes no changes to the parameter file. Can anyone give me help beyond what is in the manual? Thanks for your attention. John -- John T. Penniston, Ph.D. Dept. of Biochemistry and Molecular Biology Guggenheim 16, Mayo Clinic 200 First St. SW Rochester, MN 55905 USA RESI TAK 0.00000 ATOM N NH1 -0.17091 ATOM CA CT1 0.11455 ATOM CB CT2 -0.06545 ATOM CG CT2 -0.06545 ATOM CD CT2 -0.06545 ATOM CE CT2 0.066 ATOM NZ1 NH1 -0.293 ATOM CH1 CPH2 0.488 ATOM NQ1 NN3A -0.387 ATOM NQ2 NN3A -0.406 ATOM CI1 CN5 0.390 ATOM CI2 CN2 0.544 ATOM NK1 NN3A -0.29091 ATOM CLK CL -0.318 ATOM CK1 CA -0.055 ATOM CL1 CA -0.002 ATOM CL2 CA -0.001 ATOM CM1 CA -0.115 ATOM CM2 CA -0.114 ATOM CN1 CA 0.198 ATOM NX1 NH1 -0.228 ATOM CO1 CT2 0.074 ATOM CP1 CT3 -0.166 ATOM CO2 CT2 0.074 ATOM CP2 CT3 -0.166 ATOM C C 0.83455 ATOM O O -0.18545 BOND CB CA CG CB CD CG CE CD NZ1 CE CH1 NZ1 BOND NQ1 CH1 NQ2 CH1 CI1 NQ1 CI2 NQ2 NK1 CI1 BOND NK1 CI2 CLK CI2 BOND CK1 CI1 CL1 CK1 CL2 CK1 CM1 CL1 CM2 CL2 BOND CN1 CM1 CN1 CM2 CN1 NX1 NX1 CO1 NX1 CO2 BOND CO1 CP1 CO2 CP2 BOND N CA O C C CA C +N IMPR C CA +N O CA N C CB CE NZ1 CH1 NQ1 IMPR NZ1 CH1 NQ1 CI1 CH1 NQ1 CI1 NK1 NQ1 CI1 NK1 CI2 IMPR CI1 NK1 CI2 NQ2 NK1 CI2 NQ2 CH1 CI2 NQ2 CH1 NZ1 IMPR CE NZ1 CH1 NQ1 IMPR CI1 NK1 CI2 CLK CH1 NQ2 CI2 CLK !CH1 NQ1 CI1 CK1 IMPR CI2 NK1 CI1 CK1 CK1 CI1 NK1 CI2 IMPR CL2 CL1 CK1 CI1 CL1 CK1 CI1 NK1 CL2 CK1 CI1 NQ1 IMPR CI1 CK1 CL1 CM1 !CI1 CK1 CL2 CM2 IMPR CK1 CL1 CM1 CN1 CL1 CM1 CN1 CM2 IMPR CM1 CN1 CM2 CL2 CN1 CM2 CL2 CK1 IMPR CL1 CM1 CN1 NX1 CL2 CM2 CN1 NX1 IMPR CM1 CM2 CI1 CLK CM1 CI1 NZ1 NQ2 IMPR NK1 NQ1 NQ2 NZ1 NK1 CI1 CI2 CH1 CHI NQ1 NQ2 NK1 IMPR CI1 CLK CH1 NQ1 IC -C N CA C 1.3496 122.4500 180.0000 109.8600 1.5227 IC N CA C +N 1.4544 109.8600 180.0000 117.1200 1.3511 IC +N CA *C O 1.3511 117.1200 180.0000 121.4000 1.2271 IC CA C +N +CA 1.5227 117.1200 180.0000 124.6700 1.4565 IC N C *CA CB 1.4544 109.8600 123.6400 112.2600 1.5552 IC N CA CB CG 1.4544 110.7000 180.0000 115.9500 1.5475 IC CA CB CG CD 1.5552 115.9500 180.0000 114.0100 1.5384 IC CB CG CD CE 1.5552 115.9500 180.0000 114.0100 1.5384 IC CG CD CE NZ1 1.5475 114.0100 180.0000 107.09 1.45 IC CD CE NZ1 CH1 1.5384 107.0900 180.0000 120.00 1.35 IC CE NZ1 CH1 NQ1 1.45 120.00 180.0000 120.00 1.26 IC NZ1 NQ2 *CH1 NQ1 1.35 120.0000 180.0000 120.00 1.26! IC NQ1 NZ1 *CH1 NQ2 1.26 120.0000 180.0000 120.00 1.26! IC NZ1 CH1 NQ1 CI1 1.35 120.0000 -180.0000 120.00 1.26 IC NZ1 CH1 NQ2 CI2 1.35 120.0000 -180.0000 120.00 1.26 IC CH1 NQ1 CI1 NK1 1.26 120.0000 -0.1900 120.00 1.26 IC NK1 NQ2 *CI2 CLK 1.26 120.0000 -180.0000 120.00 1.72 IC NK1 NQ1 *CI1 CK1 1.26 120.0000 -180.0000 120.00 1.4 IC NQ1 CI1 CK1 CL1 1.2600 120.0000 180.0000 120.00 1.4 IC NQ1 CI1 CK1 CL1 1.2600 120.0000 180.0000 120.00 1.4 IC NK1 CI1 *CK1 CL2 1.27 120.0000 -180.0000 120.00 1.4 IC CI1 CK1 CL1 CM1 1.4 120.0000 -180.0000 120.00 1.4 IC CI1 CK1 CL2 CM2 1.4 120.0000 -180.0000 120.00 1.4 IC CK1 CL2 CM2 CN1 1.4 120.0000 0.000 120.00 1.4 IC CK1 CL1 CM1 CN1 1.4 120.0000 180.000 120.00 1.4 IC CL1 CK1 CI1 NK1 1.4 120.0000 180.000 120.00 1.26 IC CN1 NX1 CO1 CP1 1.35 120.0 120. 109. 1.53 IC CM1 CN1 NX1 CO1 1.4 120.0 -180. 120. 1.46 IC CN1 NX1 CO2 CP2 1.35 120.0 120. 109. 1.53 IC CM2 CN1 NX1 CO2 1.4 120.0 180. 120. 1.46 IC CM2 CM1 *CN1 NX1 1.4 120.5500 -178.9800 120.4100 1.35 PATC FIRS NTER LAST CTER

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Protein+Metal Ion?
by Modeller Care 07 Mar '03

07 Mar '03

Non-member submission forwarded by the list-owner -------------------------------------------------------------------------- I would like to model a protein that contains Zn in the active site. In = the template structure, two His residues are coordinated to the Zn. The = target sequence also has these residues and the sequences display > 50% = identity. How do I force the His residues to similarly coordinate the = Zn in the modelled structure? If the Zn atom is in .pdb file, modeller = doesn't seem to notice. Without the Zn atom present, the His = sidechains simply flop around in the active site (not surprisingly). Marc Campitelli

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FW: New to Modeller !!
by Andrej Sali 05 Mar '03

05 Mar '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: Andrej Sali [mailto:sali@salilab.org] Sent: Wednesday, March 05, 2003 7:05 PM To: 'Urmi Doshi' Subject: RE: New to Modeller !! I suggest you run the executable directly $MODINSTALL6v2/bin/mod6v2_iris4d modfile.top Check that the executable is identified as such (the x flag in the ls -ls output), and make sure it did not get corruputed during ftp. If you cannot set the stacksize limit to a large enough value, you need to ask your sysadmin to do it for you. Some sysadmins set system wide limitations that are frequently not very helpful ;-) I am not sure this is the problem here ... 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: owner-modeller_usage(a)salilab.org > [mailto:owner-modeller_usage@salilab.org] On Behalf Of Urmi Doshi > Sent: Wednesday, October 02, 2002 3:30 PM > To: modeller_usage(a)salilab.org > Subject: Re: New to Modeller !! > > > Thank you all. I tried mod and mod6v2 , but doesn't run. I > get this message everytime I start the UNIX shell limit > stacksize unlimited : can't remove limit which is set in > .cshrc. Is this the reason why modeller does not seem to work? -Urmi > ----- Original Message ----- > From: "Peter C. Lai" <sirmoo(a)cowbert.2y.net> > To: "Luis Rosales" <ludwig(a)biomedicas.unam.mx> > Cc: "Bozidar Yerkovich" <bozidar(a)salilab.org>; "Urmi Doshi" > <urdoshi(a)wam.umd.edu>; <modeller_usage(a)salilab.org> > Sent: Tuesday, March 04, 2003 7:51 PM > Subject: Re: New to Modeller !! > > > > I am using a default installation on my SGI Octane. 'mod6v2' is the > > shell script in $MODINSTALL6v2/bin, which calls mod6v2_iris4d (since > > iris4d is what > $EXECUTABLE_TYPE6v2 is > > set > to) > > LIBS_LIB6v2 is set to $MODINSTALL6v2/modlib/libs.lib. > > > > hope that helps in terms of configuration. > > > > On Tue, Mar 04, 2003 at 04:53:01PM -0600, Luis Rosales wrote: > > > Hi: > > > > > > Maybe your command for modeller is not "mod", mine is > mod6v2 and is > > > the default I got from the installation script... > > > > > > Hope this helps, > > > > > > Luis > > > > > > > > > ----- Original Message ----- > > > From: "Bozidar Yerkovich" <bozidar(a)salilab.org> > > > To: "Urmi Doshi" <urdoshi(a)wam.umd.edu> > > > Cc: <modeller_usage(a)salilab.org> > > > Sent: Tuesday, March 04, 2003 3:36 PM > > > Subject: Re: New to Modeller !! > > > > > > > > > > > > > > Urmi, > > > > Did you source your .cshrc file? > > > > Bozidar > > > > > > > > On Tue, 1 Oct 2002, Urmi Doshi wrote: > > > > > > > > > Hi, > > > > > > > > > > I have just installed Modeller exactly the way as given in the > User's > > > Manual on an SGI Fuel. However, when I try running the > command "mod > > > model-default" which is a script file available with > modeller, the > > > error message I get is " 'mod' command not found". > > > > > > > > > > I am sure there's something silly that I am missing, but can't > figure > > > out. Is there any stack requirement for running MODELLER on SGI > > > FUEl? > > > > > Can anyone help me start using MODELLER ? > > > > > > > > > > - Urmi Doshi > > > > > > > > > > > > > > > -- > > Peter C. Lai > > University of Connecticut > > Dept. of Molecular and Cell Biology > > Yale University School of Medicine > > SenseLab | Research Assistant > > http://cowbert.2y.net/ > > > > >

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