- modeller_usage - salilab.org

modelling conformation
by Holger Kremmin 26 Apr '99

26 Apr '99

Hi, I want to model several short peptides with a special conformation. The templates have the polyproline II conformation, but the model-sequences are far divergent from the template-sequence. How can I model peptides (8-18 aa) with a given conformation ?

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atom type
by F. Zuccotto 22 Apr '99

22 Apr '99

Hello, I am trying to introduce a new molecule in to the top.lib library. I would like to know where I can find a description of the atom types used by modeller. Thanks fabio **************************** Fabio Zuccotto Biological NMR Centre Medical Sciences Building University Road Leicester LE1 9HN ENGLAND (UK) Tel. +44 (0)116 252 3071

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modeller for linux
by Gunnar Schotta 20 Apr '99

20 Apr '99

I want to use the modeller program on linux but ldd says that I need libf2c.so.0 Where can I get a binary of this library? I'm running Debian/GNU linux 2.1 (glibc2). Thank you!

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script file to obtain improved protein model?
by Antonello Romani 19 Apr '99

19 Apr '99

Dear users, I have set my input files to obtain an improved model of my protein. I wolud like to know if these files are right or wrong and if there are other stuff that I have to do to improve quality of my protein (I test it with Procheck or What_Check) ----------------------------------Build model--------------------------------------------------- # INCLUDE # Include the predefined TOP routines SET ALNFILE = 'xxxx.ali' # alignment filename SET SEQUENCE = 'myprot' SET LIBRARY_SCHEDULE = 1 SET MD_LEVEL = 'refine3' SET FINAL_MALIGN3D = 1 SET REPEAT_OPTIMIZATION = 15 SET RSTRS_REFINED = 2 SET MD_RETURN = 'MINIMAL' SET KNOWNS = 'template' # codes of the templates SET ATOM_FILES_DIRECTORY = 'xxxxxxxxxx' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 15 # Do a mixed minimization # Do homology modeling CALL ROUTINE = 'model' ------------------------------------------------------------------------------------------------ ----------------------------------Optimize stereochemistry-------------------------------------- # INCLUDE # Include the predefined TOP routines READ_TOPOLOGY FILE ='$(LIB)/top_heav.lib' READ_PARAMETERS FILE = '$(LIB)/par.lib' READ_MODEL FILE = 'myprot.pdb' SEQUENCE_TO_ALI ATOM_FILES = 'myprot.pdb', ALIGN_CODES= 'myprot' SEQUENCE_TO_ALI ADD_SEQUENCE = on,ATOM_FILES = ATOM_FILES 'myprot',ALIGN_CODES= ALIGN_CODES 'myprot' GENERATE_TOPOLOGY SEQUENCE = 'myprot' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ = off WRITE_MODEL FILE = 'myprot.ini' # GENERATE THE RESTRAINTS MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo' WRITE_RESTRAINTS FILE = 'myprot.rsr' ENERGY DYNAMIC_SPHERE = on SWITCH_TRACE TRACE_OUTPUT = 1, FILE = 'myprot.trc' ENERGY DYNAMIC_SPHERE = on OPTIMIZE DYNAMIC_LENNARD =on OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 10000 OPTIMIZE OPTIMIZATION_METHOD = 3, TEMPERATURE = 300, MAX_ITERATIONS = 10000,MD_RETURN = 'MINIMAL',EQUILIBRATE =20,; MD_TIME_STEP =2.0, CAP_ATOM_SHIFT = 0.1, RAND_SEED = -3065 OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 10000 ENERGY WRITE_MODEL FILE= 'myprot_optimize.pdb' ------------------------------------------------------------------------------------------------

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Re: modeller for linux
by Holger Kremmin 15 Apr '99

15 Apr '99

Look at http://rpmfind.net/linux/RPM/openlinux/1.3/col/contrib/RPMS/f2c-19960205-5. i386.html Be sure that the lib-directory is in the path. Holger Kremmin > ---------- >>Von: Gunnar Schotta <schotta(a)genetik.uni-halle.de> >>An: modeller_usage(a)salilab.org >>Betreff: modeller for linux >>Datum: Don, 15. Apr 1999 11:30 Uhr >> > >> I want to use the modeller program on linux but >> ldd says that I need libf2c.so.0 >> Where can I get a binary of this library? >> I'm running Debian/GNU linux 2.1 (glibc2). >> Thank you! >> >>

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ANNOUNCEMENT: ModBase database of comparative protein structure models
by sali＠rockvax.rockefeller.edu 16 Mar '99

16 Mar '99

ModBase database of comparative protein structure models Roberto Sanchez and Andrej Sali http://salilab.org/modbase/ ModBase is a queryable database of many annotated comparative protein structure models. The models consist of coordinates for all non-hydrogen atoms in the modeled part of a protein. They are derived by an automated modeling pipeline relying mainly on the program MODELLER. The database currently contains 3D models for substantial segments of 15-23% of proteins in the genomes of M. genitalium, M. jannaschii, E. coli, S. cerevisiae, and C. elegans. In total, there are models for 3,732 proteins. The database also includes fold assignments and alignments on which the models were based. In addition, special care is taken to assess the overall quality of the models and their accuracy at the residue level. In the future, ModBase will grow to reflect (i) the growth of the sequence databases, (ii) the growth of the database of known protein structures, (iii) and improvements in the software for calculating the models. It is expected that the Swiss-Prot+TrEMBL protein sequence database will be processed by the end of 1999. ModBase is introduced in R. Sanchez & A. Sali. Proc. Natl. Acad. Sci. USA 95, 13597-13602, 1998.

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Re: HETATM
by Tony Pemberton 17 Feb '99

17 Feb '99

Dear Users, Thanks to all who contributed to solving this problem for me. I now have my HETATM (Zn) included in my output model. Andras Fiser's solution worked best, which was posted to this BBS. Regards, Tony Pemberton ********************************************************************* Mr. A.J.Pemberton Tel: +121-414-3388 c/o Dept. Rheumatology, Fax: +121-414-3982 Medical School, E-mail: A.J.Pemberton(a)bham.ac.uk The University of Birmingham, Birmingham B15 2TT. U.K. *********************************************************************

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Re: [Fwd: HETATM (fwd)]
by Andras Fiser 16 Feb '99

16 Feb '99

Dear Tony, We got your files with the problem described below. Your Modeller run did not give you not only the hetatm but any output since it reported an error in the *.log file. It was complaining about the alignment. This is the most usual problem, users must pay attention to it. The log file clearly says, that there is a discrepancy in the number of residues among the seq.s and the pdb files: the number of residues are different in all cases. there are several problems: 1., you forgot to indicate in the header of each pir format alignmnet seq. that the number of residues is one resides longer, since you wanted to include a heteroatom as well. (e.g. see below ,instead of 500 you need 501) 2., Modeller learns from the pdb templates what kind of atom or residue to be read in: you indicated in the sequence that there is a "zn" hetatm, which is misleading. In the pir format you have single letter codes: Modeller thought you have 2 additional residues, a "z" and an "n". You need only to put "." to show that something else to be read in from the pdb files at that position. If you wants to have specificly Zn than you a., have to put "z" in the sequence, and b., ZN2 in the PDB files. The CHARMM atom types are listed in $MODINSTALL/modlib/restyp.lib. Modeller clearly complained that you have too many residues in the sequences (in all of them) i.e. z, n, and "." as well for a single hetatm. i.e. e.g.: original: >P1;1glu_B structureX:1glu_znf_b: 458: B : 500: B: Glucocorticoid Receptor: : : GSCKVFFKRAVEGQ-HNYLCAGRNDCIIDKIRRKN-------CPACRY-RKC/.zn* correct: >P1;1glu_B structureX:1glu_znf_b: 458: B : 501: B: Glucocorticoid Receptor: : : GSCKVFFKRAVEGQ-HNYLCAGRNDCIIDKIRRKN-------CPACRY-RKC/z* the corrected alignment file with your top script now produces structures to me, though you need figure out additional marginal problems. e.g. your templates at certain positions are too different etc. good luck for the future, andras > > > > > > A.J.Pemberton wrote, > > > > > > > Dear users, > > > > > > > >I have set my steering file to activate the HETATM usage (modeller 4): > > > > > > > >SET TOPOLOGY_MODEL = 1, HETATM_IO = on, HYDROGEN_IO = on, WATER_IO = on > > > > > > > >as per FAQ question 15 > > > > > > > >but modeller is not giving me HETATMs is the pdb output, why? > > > > > > > >Regards, > > > > > > > >Tony > > > > > > > >********************************************************************* > > > >Mr. A.J.Pemberton Tel: +121-414-3388 > > > >c/o Dept. Rheumatology, Fax: +121-414-3982 > > > >Medical School, E-mail: A.J.Pemberton(a)bham.ac.uk > > > >The University of Birmingham, > > > >Birmingham B15 2TT. > > > >U.K. > > > >********************************************************************* > > > > > > > > > I have the same problem !!! > > > > > > > > > Antonello Romani > > > > > > > > > > > > > > > ___________________________________________________________________________ > > > Antonello Romani > > > Istituto di Patologia Generale > > > Plesso Biotecnologico Integrato > > > Facolta' di Medicina e Chirurgia > > > Universita' degli Studi di Parma > > > via Volturno 39 > > > 43100 Parma > > > > > > Tel: +39 0521 903 764 > > > Fax :+39 0521 903 742 > > > > > > E-Mail : A.Romani(a)leonardo.biomed.unipr.it > > > > > > > > > ___________________________________________________________________________ -- , Andras Fiser, PhD # phone: (212) 327 7206 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras

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Re: HETATM
by Derek Smith 15 Feb '99

15 Feb '99

Dear Tony and Antonello, I too had the problem of not getting heteroatoms in my models when I had specified HETATM_IO = on. I sorted it out as follows... 1. Is the HETATM already parameterised in MODELER? if so... 2. Have you specified the HETATM in the alignment file? I use MODELER through QUANTA, which puts heteroatoms into the PDB input files but doesn't automatically put heteroatoms into the sequence alignment, so I have to edit the file manually. 3. Have you aligned the HETATMs for template and model sequence? If the hetatm for template and model sequence are not equivalent then your hetatm occurs in the postion of what would be the next C-alpha atom in your chain. It's very basic I know - but sometimes mistakes can happen. I hope it works out for you both. Derek.

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HETATM
by A.Romani＠leonardo.biomed.unipr.it 15 Feb '99

15 Feb '99

-------- A.J.Pemberton wrote, > Dear users, > >I have set my steering file to activate the HETATM usage (modeller 4): > >SET TOPOLOGY_MODEL = 1, HETATM_IO = on, HYDROGEN_IO = on, WATER_IO = on > >as per FAQ question 15 > >but modeller is not giving me HETATMs is the pdb output, why? > >Regards, > >Tony > >********************************************************************* >Mr. A.J.Pemberton Tel: +121-414-3388 >c/o Dept. Rheumatology, Fax: +121-414-3982 >Medical School, E-mail: A.J.Pemberton(a)bham.ac.uk >The University of Birmingham, >Birmingham B15 2TT. >U.K. >********************************************************************* I have the same problem !!! Antonello Romani ___________________________________________________________________________ Antonello Romani Istituto di Patologia Generale Plesso Biotecnologico Integrato Facolta' di Medicina e Chirurgia Universita' degli Studi di Parma via Volturno 39 43100 Parma Tel: +39 0521 903 764 Fax :+39 0521 903 742 E-Mail : A.Romani(a)leonardo.biomed.unipr.it ___________________________________________________________________________

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