- modeller_usage - salilab.org

randomize...why do it ??
by Himanshu Grover 21 Jul '04

21 Jul '04

hi, I was just wondering why it is required to randomize the coordinates of initial model or may be rotate their dihedrals before running the optimization routine (VTFM)... how would the results be affected if i don't randomize?? Actually, my resulting structure becomes worse if i randomize and then optimize rather than directly optimizing. any suggestions?? Secondly, I am not able to use rotate_dihedrals command somehow... it gives an error. if anyone knows how to use it, please tell me what all changes are required to be made before I use this command. The default *.top files give an error at the call, if I just change RAND_METHOD = randomize_dihedrals in __defs.top, and leave everything else as it is. this is an abstract of my log file which shows the segment generating error. ------------------**********------------------------- rotate__517_> Local optimization around Phi setodih_515_> Residues,dihedral type,all-selected,optimized: 605 2 604 574 rotate__517_> Local optimization around Psi chgidih_247E> Internal error: recover____E> ERROR_STATUS >= STOP_ON_ERROR: ------------------**********------------------------- is there anything that I am missing?? yours sincerely, Himanshu Grover

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core dumped when reading my restraint file
by daniele bemporad 21 Jul '04

21 Jul '04

Hi all When in my .top file I include: # Redefine the rd_restraints routine: SUBROUTINE ROUTINE = 'rd_restraints' # This is the default homology-derived restraints: READ_RESTRAINTS FILE = CSRFILE , ADD_RESTRAINTS = off # This is the additional user provided file: READ_RESTRAINTS FILE = 'my_restraint.rsr' , ADD_RESTRAINTS = on SET ADD_RESTRAINTS = off RETURN END_SUBROUTINE modeller dies with no message and dumps a core. It seems to read my_restraint.rsr , because if I introduce mistakes in the format they are recognised and also because the lines in my_restraint.rsr are present in the core file. I tried to locate: READ_RESTRAINTS FILE = 'my_restraint.rsr' , ADD_RESTRAINTS = on into the "special_restraints" subroutine, but the result is still that modeller dies and dumps a core. I have noticed that if I write "READ_RESTRAINTS FILE = 'my_restraint.rsr' " without "ADD_RESTRAINTS = on" then everything works fine. But as far as I understand the program, this would make modeller forget about the homology-derived restraints, wouldn't it ? Am I making some stupid mistake ? Is there a problem with my compilation or with this version of the program ? Any help is greatly appreciated. Many thanks Daniele __________________________________ Do you Yahoo!? Vote for the stars of Yahoo!'s next ad campaign! http://advision.webevents.yahoo.com/yahoo/votelifeengine/

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Re: [modeller_usage] Restraints Problem
by akshay17 20 Jul '04

20 Jul '04

Dear Sir, I tried removing Extra lines from my .rsr file and still got the following error. ____________________________________________________________ _ Executing Modeler Additional output in file angim_06.log and in angim_06.log.moltabfile, angim_06.log.restabfile, angim_06.log.viotabfile* lib-4190 : UNRECOVERABLE library error A numeric input field contains an invalid character. Encountered during a list-directed READ from an internal file (character variable) IOT Trap Abort (core dumped) ____________________________________________________________ _ Please advise. Shall, i write MODELLER 5 or MODELLER 6v2 in my .rsr file. I am attaching my .rsr file again. Thanks Akshay Patny. > On Fri, Jul 16, 2004 at 04:41:03PM -0500, akshay17 wrote: > > I recently joined Modeller mailing list and i am also > > new to the program. > > > > I am using Modeler as an interface from Insight II. I > > have been trying to give my own restraints during the > > model generation as a .rsr file. I tried using both the > > MODELER FORMAT as well as the USER FORMAT restraint > > files. The problem is whenever i submit my job, it does > > not complete and gives error in log file one of which is > > the following: "Incorrect record identifier in restraint > file; card:" > > You have blank lines in your restraints file; Modeller6v2 > doesn't understand these. Take them out and all should be > well. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org > http://www.salilab.org/modeller/ Modeller mailing list: > http://salilab.org/mailman/listinfo/modeller_usage > Akshay Patny (Graduate Student @ PhD) Department of Medicinal Chemistry School of Pharmacy, University of Mississippi 417, Faser Hall, University, MS - 38677 Tel : 662-915-1286(Off.), 662-236-3059(Res.) E-mail : akshaypatny(a)indiatimes.com, akshay17(a)olemiss.edu Web : www.olemiss.edu [Attachment: Constraints_USER.rsr] Akshay Patny (Graduate Student @ PhD) Department of Medicinal Chemistry School of Pharmacy, University of Mississippi 417, Faser Hall, University, MS - 38677 Tel : 662-915-1286(Off.), 662-236-3059(Res.) E-mail : akshaypatny(a)indiatimes.com, akshay17(a)olemiss.edu Web : www.olemiss.edu

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RMS and DRMS functions of COMPARE again
by Binbin Liu 19 Jul '04

19 Jul '04

Hello, just have to make my question more detailed. I would like to calculate RMSD for ALL ATOMS between template and the models. Binbin -- Binbin Liu Bioinformatics Ph.D student School of Biomedical Sciences University of Leeds, Leeds,LS2 9JT England, UK Phone: (44)113 343 3072 Email: bmbbl(a)bmb.leeds.ac.uk

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RMS and DRMS functions of COMPARE
by Binbin Liu 19 Jul '04

19 Jul '04

Hello there, 'compare' can be used to calculate the RMSD between the template and models. In general, during homology modelling, there can be residues mutated in the sequence alignment so that the different numbers of atoms are superimposed in Catesian space. I wonder how MODELLER work out the RMSD under this situition? Thanks a lot. Binbin -- Binbin Liu Bioinformatics Ph.D student School of Biomedical Sciences University of Leeds, Leeds,LS2 9JT England, UK Phone: (44)113 343 3072 Email: bmbbl(a)bmb.leeds.ac.uk

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loop positioning
by John Simms 17 Jul '04

17 Jul '04

Hi All, A quick question. I have a pair of beta strands in a GPCR. Experimental evidence suggests that the distal portion (2nd beta strand of the loop lies underneath the proximal part of the loop (1st beta strand). I have used modeller to model this region , but all of the models have the distal part ontop of the proximal part :-(. Does anyone know how I can restrain the orinetation of the loop fragments so that the start of the loop is ontop of the end on the loop. Thanks again John

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Error: Array too small. Increase MAXBND
by K S Doctor 16 Jul '04

16 Jul '04

How do I deal with the following error: getf____223E> Array too small. Increase MAXBND current maximum, current need: 6180 6181 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I am running a 479 AA protein + a HETATM (NAG or "1") which is described in /modlib/restyp.lib I have had no problem running the dimer 479 AA * 2 , but without the HETATM. I am attaching the top file and representative ali, the PDB is the public one. Simply setting SET MAXBND = 6181 in the TOP file did not work (error) thanks, Kutbuddin @ The Burnham Institute - SD, CA ;1ew2monomer >P1;1EW2_A structureX:1ew2_A:1:A:::PLAP:Homo sapien:: IIPVEEENPDFWNREAAEALGAAKKLQPAQTAAKNLIIFLGDGMGVSTVTAARILKGQKK DKLGPEIPLAMDRFPYVALSKTYNVDKHVPDSGATATAYLCGVKGNFQTIGLSAAARFNQ CNTTRGNEVISVMNRAKKAGKSVGVVTTTRVQHASPAGTYAHTVNRNWYSDADVPASARQ EGCQDIATQLISNMDIDVILGGGRKYMFRMGTPDPEYPDDYSQGGTRLDGKNLVQEWLAK RQGARYVWNRTELMQASLDPSVTHLMGLFEPGDMKYEIHRDSTLDPSLMEMTEAALRLLS RNPRGFFLFVEGGRIDHGHHESRAYRALTETIMFDDAIERAGQLTSEEDTLSLVTADHSH VFSFGGYPLRGSSIFGLAPGKARDRKAYTVLLYGNGPGYVLKDGARPDVTESESGSPEYR QQSAVPLDEETHAGEDVAVFARGPQAHLVHGVQEQTFIAHVMAFAACLEPYTACDLAPP/ 1* >P1;1ew2_delta sequence:1ew2_delta:::::::: IIPVEEENPDFWNREAAEALGAAKKLQPAQTAAKNLIIFLGDGMGVSTVTAARILKGQKK DKLGPEIPLAMDRFPYVALSKTYNVDKHVPDSGATATAYLCGVKGNFQTIGLSAAARFNQ CNTTRGNEVISVMNRAKKAGKSVGVAAAARVQHASPAGTYAHTVNRNWYSDADVPASARQ EGCQDIATQLISNMDIDVILGGGRKYMFRMGTPDPEYPDDYSQGGTRLDGKNLVQEWLAK RQGARYVWNRTELMQASLDPSVTHLAAAAEPGDMKYEIHRDSTLDPSLMEMTEAALRLLS RNPRGFFLFVEGGRIDHGHHESRAYRALTETIMFDDAIERAGQLTSEEDTLSLVTADHSH VFSFGGYPLRGSSIFGLAPGKARDRKAYTVLLYGNGPGYVLKDGARPDVTESESGSPEYR QQSAVPLDEETHAGEDVAVFARGPQAHLVHGVQEQTFIAHVMAFAACLEPYTACDLAPP/ 1* # default model INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'monomer_v4.ali' # alignment filename SET KNOWNS = '1EW2_A' # codes of the templates SET SEQUENCE = '1ew2_delta' # 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) SET HETATM_IO = on # SET WATER_IO = off # ;SET MAXBND = 6181 # based on output log need CALL ROUTINE = 'model' # do homology modelling

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Restraints Problem
by akshay17 16 Jul '04

16 Jul '04

Dear Sir I recently joined Modeller mailing list and i am also new to the program. I am using Modeler as an interface from Insight II. I have been trying to give my own restraints during the model generation as a .rsr file. I tried using both the MODELER FORMAT as well as the USER FORMAT restraint files. The problem is whenever i submit my job, it does not complete and gives error in log file one of which is the following: "Incorrect record identifier in restraint file; card:" I am attaching my .top file, restraints file and also the log file here. Please suggest me to fix this problem. I will be glad. Thanks Akshay Patny Akshay Patny (Graduate Student @ PhD) Department of Medicinal Chemistry School of Pharmacy, University of Mississippi 417, Faser Hall, University, MS - 38677 Tel : 662-915-1286(Off.), 662-236-3059(Res.) E-mail : akshaypatny(a)indiatimes.com, akshay17(a)olemiss.edu Web : www.olemiss.edu

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(no subject)
by karl schweighofer 16 Jul '04

16 Jul '04

Hello, I am trying to protonate at ADP molecule with modeller6. THe ADP residue is specified in the library, but I keep getting this error: gener___479E> Must not use patching residues here. Residue type index, residue type: 33 # recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Here is the script for the protonation: # This will read a specified atom file, generate all hydrogen atoms, # add atomic radii and charges, and write the model to a PDB file in # the GRASP format. This can be used with GRASP to display electrostatic # properties without assigning charges and radii in GRASP. INCLUDE SET TOPLIB = '$(LIB)/TOP.LIB' SET PARLIB = '$(LIB)/PAR.LIB' READ_TOPOLOGY FILE = '$(LIB)/TOP.LIB' READ_PARAMETERS FILE = '$(LIB)/PAR.LIB' SET TOPOLOGY_MODEL = 1, HYDROGEN_IO = on, HETATM_IO = on, WATER_IO = on SET ATOM_FILES_DIRECTORY = './' # directories for input atom files READ_MODEL FILE = 'adp.pdb' RENAME_SEGMENTS SEGMENT_IDS = 'A' SEQUENCE_TO_ALI ATOM_FILES = 'adp', ALIGN_CODES = 'adp' SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES 'adp.pdb', ; ALIGN_CODES = ALIGN_CODES 'adp' GENERATE_TOPOLOGY SEQUENCE = 'adp' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ = off, BUILD_METHOD = 'INTERNAL_COORDINATES' WRITE_MODEL FILE = 'protoadp.pdb', MODEL_FORMAT = 'GRASP' And here is the ADP PDB File: HETATM 569 PB ADP X 68 14.423 48.400 0.539 HETATM 570 O1B ADP X 68 15.523 47.578 -0.057 HETATM 571 O2B ADP X 68 14.303 48.106 2.067 HETATM 572 O3B ADP X 68 14.698 49.918 0.358 HETATM 573 PA ADP X 68 11.796 47.376 0.153 HETATM 574 O1A ADP X 68 12.031 45.921 0.312 HETATM 575 O2A ADP X 68 11.228 48.083 1.373 HETATM 576 O3A ADP X 68 13.146 48.057 -0.376 HETATM 577 O5' ADP X 68 10.874 47.635 -1.110 HETATM 578 C5' ADP X 68 11.196 47.105 -2.379 HETATM 579 C4' ADP X 68 10.286 47.636 -3.486 HETATM 580 O4' ADP X 68 9.080 46.895 -3.526 HETATM 581 C3' ADP X 68 9.861 49.060 -3.289 HETATM 582 O3' ADP X 68 9.602 49.725 -4.510 HETATM 583 C2' ADP X 68 8.559 48.875 -2.526 HETATM 584 O2' ADP X 68 7.781 49.993 -2.657 HETATM 585 C1' ADP X 68 7.956 47.654 -3.193 HETATM 586 N9 ADP X 68 7.087 46.896 -2.257 HETATM 587 C8 ADP X 68 7.503 45.956 -1.333 HETATM 588 N7 ADP X 68 6.392 45.519 -0.679 HETATM 589 C5 ADP X 68 5.314 46.174 -1.216 HETATM 590 C6 ADP X 68 3.977 46.114 -0.937 HETATM 591 N6 ADP X 68 3.529 45.338 0.072 HETATM 592 N1 ADP X 68 3.138 46.928 -1.662 HETATM 593 C2 ADP X 68 3.573 47.780 -2.658 HETATM 594 N3 ADP X 68 4.896 47.853 -2.965 HETATM 595 C4 ADP X 68 5.741 47.039 -2.222 Any ideas why this won't work? Thanks kindly, Karl Schweighofer karl(a)mail.arc.nasa.gov

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pseudo-atom usage?
by Daniel Rigden 16 Jul '04

16 Jul '04

Hi all Can anyone help with an example of the use of additional restraints involving pseudoatoms? I've read the relevant sections of the manual http://salilab.org/modeller/manual/node99.html http://salilab.org/modeller/FAQ.html#8 and it's still not clear to me. The FAQ has this example of a user-added restraint SET ATOM_IDS 'CA:35:A' 'CA:40:A' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 10.0 0.1 How to define pseudo-atoms instead of single real atoms? Alternatively, if the restaint were added in a file, how to specify defined pseudo-atoms within the format? R Form Modality Feature Group Numb_atoms Numb_parameters 0 Atom_indices Parameters R 3 1 1 1 2 2 0 437 28 1.5000 0.1000 In my case, I'd like to make a helix (which I'll define as a pesudoatom) in a large insertion pack better, more compactly against the rest of the protein. Has anyone any experience with similar situations? Many thanks in advance Daniel Rigden -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4414 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K.

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