- modeller_usage - salilab.org

Regarding modeller usage
by R Senthil Kumar 27 Nov '01

27 Nov '01

Dear modeller users, After i am getting the initial model using modeller if any bad regions are there(loop regions) i am using the following module for refinement. INCLUDE SET SEQUENCE = 'topmodel' SET MODEL = 'topmodel.pdb' SET STARTING_MODEL = 1 SET ENDING_MODEL = 2 CALL ROUTINE = 'loop' SUBROUTINE ROUTINE = 'select_atoms' PICK_ATOMS SELECTION_SEGMENT = '0:' '3:', SELECTION_STATUS ='initialize' RETURN END_SUBROUTINE Actually i want to know whether the following module does the refinement of the loop or the loop building with some other loop.Please tell what is the exact use of this module.Expecting for your reply. Yours friendly, Senthil kumar.R

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Re: Crash in running the SEQUENCE_SRCH
by Tsu-Sheng Wang 22 Nov '01

22 Nov '01

Dears: I already tried the modeller6a in the RedHat 6.2. However, it still stoped in some step. I mailed the sequence and the log files to you. friendly, Jack ----- Original Message ----- From: "Andrej Sali" <sali(a)mail.rockefeller.edu> To: "Azat Badretdinov" <azat(a)accelrys.com>; "Tsu-Sheng Wang" <g894284(a)life.nthu.edu.tw> Cc: <modeller_usage(a)salilab.org> Sent: Thursday, November 15, 2001 12:33 AM Subject: RE: Crash in running the SEQUENCE_SRCH if still a problem, would you please try it with the pre-release of modeller 6 (ask bozidar(a)rockefeller.edu) if still a problem, would you please email us the input files. thanks, andrej -----Original Message----- From: owner-modeller_usage(a)salilab.org [mailto:owner-modeller_usage@salilab.org]On Behalf Of Azat Badretdinov Sent: Wednesday, November 14, 2001 9:56 AM To: Tsu-Sheng Wang Cc: modeller_usage(a)salilab.org Subject: Re: Crash in running the SEQUENCE_SRCH At 03:38 PM 11/14/01 +0800, Tsu-Sheng Wang wrote: >Dears: > > When I run below program, it will be crash. > >INCLUDE >SET OUTPUT_CONTROL = 1 1 1 1 1 >SET ATOM_FILES_DIRECTORY = '/usr/local/lib/pdb' >SET OUTPUT = 'SHORT' # 'LONG' >SET SIGNIF_CUTOFF = 8 3 >SET SEARCH_RANDOMIZATIONS = 10 >SET STOP_ON_ERROR = 2 >CALL ROUTINE = 'sequence_srch', SEGFILE = 'ny10.chn', SEQUENCE = 'ny10' > > I want to use this program to get the alignment and using the alignment >to get the template sequence and get the model by homology modelling. > The ny10.chn is one chain protein with 68 a.a. , and I set the >ATOM_FILES_DIRECTORY is the all PDB files in my server. This program will >be crash after abour the 45 min. I don't know what's wrong. My server is >RedHat Linux 7.1 with PIII 1G cpu and 512Mb ram. 7.1 is notorious for its bugs. It crashes randomly blastpgp jobs too at certain conditions. I would advise you to reproduce it on 6.2. >Your friendly, >Jack Wang > > -- Azat Badretdinov, Accelrys

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Regarding modelling
by R Senthil Kumar 16 Nov '01

16 Nov '01

Dear modellers, I have started my Ph.D in the field of Molecular modelling and drug design.So,i need some comments about my modelling procedure.Please verify the modelling protocol that i am following to build the model and post-modelling procedures and give some good comments. 1. Obtaining the models with the help of modeller 2.Choose the model that is having lowest objective function. 3.Verify the model using Verify3D- program. 4.The regions that shows below the threshold value.Do the loop modelling and try to improve that region. 5.After improving the regions check it with also PORCHECK results for stereochemical evaluation. 6.Do the energy minimization with 50 cycles with fixing backbone and without charges.Then release the backbone and without charges for 50 cycles.Then with charges for 50 cycles. 7. Then verify it with PROSAII energy verification program. Expecting for your reply.Thanks in advance. Yours friendly, Senthil kumar.R

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Crash in running the SEQUENCE_SRCH
by Tsu-Sheng Wang 14 Nov '01

14 Nov '01

Dears: When I run below program, it will be crash. INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ATOM_FILES_DIRECTORY = '/usr/local/lib/pdb' SET OUTPUT = 'SHORT' # 'LONG' SET SIGNIF_CUTOFF = 8 3 SET SEARCH_RANDOMIZATIONS = 10 SET STOP_ON_ERROR = 2 CALL ROUTINE = 'sequence_srch', SEGFILE = 'ny10.chn', SEQUENCE = 'ny10' I want to use this program to get the alignment and using the alignment to get the template sequence and get the model by homology modelling. The ny10.chn is one chain protein with 68 a.a. , and I set the ATOM_FILES_DIRECTORY is the all PDB files in my server. This program will be crash after abour the 45 min. I don't know what's wrong. My server is RedHat Linux 7.1 with PIII 1G cpu and 512Mb ram. Your friendly, Jack Wang

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Regarding energy minimization using modeller
by R Senthil Kumar 14 Nov '01

14 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(is this top file can be used for energy minimization). 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.How to include heteroatoms in the file. 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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[Fwd: ALIGN2D problem]
by Dan Thomas Major 14 Nov '01

14 Nov '01

-- Dan Thomas Major (at Dr. B. Fischer's lab) Bar-Ilan University Ramat-Gan, Israel

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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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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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