November 2001 - modeller_usage

modeling residues with incomplete entries in the parameter library
by Yan Yao 13 Nov '01

13 Nov '01

hello all, I am modeling a set of mutants of cytochrome c using structure of cytochrome c from horse heart as template. the alignment is as such: >P1;1akk structureX:1akk: 1 : : 105 : :oxidized cytochrome c:horse heart: : GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYI PGTKMIFAGIKKKTEREDLIAYLKKATNE/h* >P1;1aaa sequence:1aaa: 1 : : 105 : :cytochrome c:rat: : GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAAGFSYTDANKNKGITWGEDTLMEYLENPKKY IPGTKMIFAGIKKKGERADLIAYLKKATNE/h* the model script is: Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET ALNFILE = 'alignment2.ali' # alignment filename SET KNOWNS = '1akk' # codes of the templates SET SEQUENCE = '1aaa' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET OUTPUT_CONTROL = 1 0 0 1 SET HYDROGEN_IO = on SET HETATM_IO = on SET WATER_IO = on SET TOPLIB = '${LIB}/top.lib' SET PARLIB = '${LIB}/par.lib' SET GENERATE_METHOD = 'transfer_xyz' SET TOPOLOGY_MODEL = 1 SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model the hetatm, water, hydrogen options were set on, the generate_method is as 'transfer_xyz', which is hoped to define the model coordinates before calling MAKE_RESTRAINTS according to the manual on "modeling residues with non-existing or incomplete entries in the topology and parameter libraries. but it kept on giving the __E strings in the log file as below which suggest the heme group has missing parameters.. addcr___E> cannot find params in params file: CHARMM atoms: NPH FE NP1 CPA IUPAC atoms : NA FE NB C1B atom indices: 1637 1636 1638 1645 residues : HEME HEME HEME HEME addprm__W> Adding params (mean,force,period) -10.78135 10.00000 3 for atoms $ I already tried the modeller6a version but does not help.. any suggestions would be greatly appreciated. Yan

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TEST from List Owner, please ignore...
by Bozidar Jerkovic 13 Nov '01

13 Nov '01

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modeling residues with incomplete entries in the parameter library
by Yan Yao 13 Nov '01

13 Nov '01

hello all, I am modeling a set of mutants of cytochrome c using structure of cytochrome c from horse heart as template. the alignment is as such: >P1;1akk structureX:1akk: 1 : : 105 : :oxidized cytochrome c:horse heart: : GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYI PGTKMIFAGIKKKTEREDLIAYLKKATNE/h* >P1;1aaa sequence:1aaa: 1 : : 105 : :cytochrome c:rat: : GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAAGFSYTDANKNKGITWGEDTLMEYLENPKKY IPGTKMIFAGIKKKGERADLIAYLKKATNE/h* the model script is: Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET ALNFILE = 'alignment2.ali' # alignment filename SET KNOWNS = '1akk' # codes of the templates SET SEQUENCE = '1aaa' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET OUTPUT_CONTROL = 1 0 0 1 SET HYDROGEN_IO = on SET HETATM_IO = on SET WATER_IO = on SET TOPLIB = '${LIB}/top.lib' SET PARLIB = '${LIB}/par.lib' SET GENERATE_METHOD = 'transfer_xyz' SET TOPOLOGY_MODEL = 1 SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model the hetatm, water, hydrogen options were set on, the generate_method is as 'transfer_xyz', which is hoped to define the model coordinates before calling MAKE_RESTRAINTS according to the manual on "modeling residues with non-existing or incomplete entries in the topology and parameter libraries. but it kept on giving the __E strings in the log file as below which suggest the heme group has missing parameters.. addcr___E> cannot find params in params file: CHARMM atoms: NPH FE NP1 CPA IUPAC atoms : NA FE NB C1B atom indices: 1637 1636 1638 1645 residues : HEME HEME HEME HEME addprm__W> Adding params (mean,force,period) -10.78135 10.00000 3 for atoms $ I already tried the modeller6a version but does not help.. any suggestions would be greatly appreciated. Yan

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Regarding energy minimization using modeller
by R Senthil Kumar 12 Nov '01

12 Nov '01

Dear friends, I got a initial model for my protein using modeller.Then i went for loop modelling for some of the regions that showed below the threshold value in verfiy3D program. After the loop modelling i want to do energy minimization using optimize.top file.The following is the top file i used for energy minimization. Example for: OPTIMIZE, SWITCH_TRACE # This will optimize stereochemistry of a given model, including # non-bonded contacts. READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib' READ_PARAMETERS FILE ='$(LIB)/par.lib' READ_MODEL FILE = 'topmodel6' SEQUENCE_TO_ALI ATOM_FILES= 'topmodel6', ALIGN_CODES = 'topmodel6' SEQUENCE_TO_ALI ADD_SEQUENCE =on, ATOM_FILES = ATOM_FILES 'topmodel6.ini', ; ALIGN_CODES = ALIGN_CODES 'topmodel6-ini' GENERATE_TOPOLOGY SEQUENCE = 'topmodel6-ini' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ = off WRITE_MODEL FILE = 'topmodel6.ini' # Generate the restraints: MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo' WRITE_RESTRAINTS FILE = 'topmodel6.rsr' ENERGY DYNAMIC_SPHERE = on SWITCH_TRACE TRACE_OUTPUT = 1, FILE = 'topmodel6.trc' OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 20 OPTIMIZE OPTIMIZATION_METHOD = 3, TEMPERATURE = 300, MAX_ITERATIONS = 50 OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 20 ENERGY WRITE_MODEL FILE = 'topmodel6.B' But it is not including heteroatoms in the energyminimized model.But the initial model has heteroatoms. And also the module i am using is correct or i have to do any changes.Because more energy minimization also causes misthreading of the molecule.Kindly give me some suggestions.Expecting for your reply very eagerly. Yours friendly, Senthil kumar.R

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ALIGN2D problem
by Dan Thomas Major 12 Nov '01

12 Nov '01

I'm trying to perform ALIGN2D of a target sequence with the sequence of a protein with with X-ray structure, but I keep on getting errors. The protein has several subunits, and I want to align with subunit A only. The top file is: READ_MODEL FILE = '1HZX.pdb', MODEL_SEGMENT '@:A' 'X:A', OUTPUT_CONTROL = 1 1 1 1 SEQUENCE_TO_ALI ALIGN_CODES = '1HZX' READ_ALIGNMENT FILE = 'hp2y1.seq', ALIGN_CODES = ALIGN_CODES 'hp2y1', ; ADD_SEQUENCE = on READ_TOPOLOGY FILE = '/u/ch/majord/modeller/modeller6a/modlib/top_heav.lib' ALIGN2D WRITE_ALIGNMENT FILE = 'hp2y1-1HZX.ali', ALIGNMENT_FORMAT = 'PIR' WRITE_ALIGNMENT FILE = 'hp2y1-1HZX.pap', ALIGNMENT_FORMAT = 'PAP', ; ALIGNMENT_FEATURES = 'indices helix beta' The error reported is: ... # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1HZX 641 3 1HZX undefined 2 hp2y1 373 1 hp2y1 TOP_________> 4 4 READ_TOPOLOGY FILE = '/u/ch/majord/modeller/modeller6a/mo; dlib/top_heav.lib' openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib//as1.sim.mat rdrrwgh_268_> Number of residue types: 20 dispers_247E> Internal error: 640 641 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 23066567 22525.945 21.998 Starting time : 2001/11/12 13:53:59.313 Closing time : 2001/11/12 14:41:13.406 Total CPU time [seconds] : 0.00 Thanks, Dan -- Dan Thomas Major (at Dr. B. Fischer's lab) Bar-Ilan University Ramat-Gan, Israel

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None
by Bogdan Morgun 07 Nov '01

07 Nov '01

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predict protein side-chain conformations
by Evers Andreas 06 Nov '01

06 Nov '01

Hallo Modellers! I would like to use Modeller to predict Side-Chain conformations of proteins (and subsequently compare the orientations with the original crystal structure). For this purpose I want to take a protein and align the sequence with itself, i.e. the alignment would look like this: ------------------------ >P1;1dlw structureX:1dlw: : : : : : : : SLFEQLGGQAAVQAVTAQFYANIQADATVATFFNGIDMPNQTNKTAAFLCAALGGPNAWTGRNLKEVHANMGVSN AQFTTVIGHLRSALTGAGVAAALVEQTVAVAETVRGDVVTV* >P1;seq unknown:seq: : : : : : : : SLFEQLGGQAAVQAVTAQFYANIQADATVATFFNGIDMPNQTNKTAAFLCAALGGPNAWTGRNLKEVHANMGVSN AQFTTVIGHLRSALTGAGVAAALVEQTVAVAETVRGDVVTV* ----------------------- To predict side chain conformation I somehow have to keep the backbone fixed and tell Modeller to model (only) the side-chains (without taking any information from the template protein). How can I do that? Thank you for your answer, Andreas

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modeling disulfide without template
by Tom Duncan 06 Nov '01

06 Nov '01

There are several good template structures for our target protein but, although it is known that a disulfide can form between a specific pair of cysteines in theses proteins (cysteines conserved in templates & target), the known structures show these cyteines as 15-20 angstroms apart. Nearby flexible loops or "hinge" regions can be identified. Would it be reasonable to model the target directly with a disulfide patch, or better to obtain an initial model based on the templates and then do more thorough MD/SA cycles with a restricted region of the model and S-S distance restraints before final refinement with the disulfide patch? 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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Regarding installation of modeller on linux-machine
by R Senthil Kumar 05 Nov '01

05 Nov '01

Dear friends, We tried to install modeller-4 on linux machine.while installing the modeller-4 the system was setting up mod_i386.Then we changed to mod_i486 and installation was successful.While trying to run the modeller it was showing ---> error while loading shared libraries; libf2c.so.0 cannot load shared object file.No such file or directory.help us to overcome this problem.Looking forward for your suggestions. R.Senthil kumar.

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Installation problem
by Diego Bustos 01 Nov '01

01 Nov '01

Dear All, I am trying to install modeller4 on a new PC with Suse linux7.0. After correction of the default HOSTTYPE setting (for some reason it is set to "i386-linux" on my machine instead of "i486-linux"), the "Install" script finishes surprisingly fast (may be due to the 1.2GHz CPU with RAM memory of 256 Mb) and without any error messages. Afterwards, I can`t started Modeller, because I can`t recognize any executable file. Does anybody know, what this means and how to avoid it? Thank you very much! Diego

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