August 2004 - modeller_usage

Re: [modeller_usage] constraining backbone atoms using modeller?
by Thomas Duncan 31 Aug '04

31 Aug '04

Diana - Probably the simplest way does not involve MODELLER. Check out SCWRL (http://dunbrack.fccc.edu/SCWRL3.php) it's a simple program designed for the exact task you described. It is available for various operating systems. Good luck, Tom >>> "Diana C.Mustard" 08/30/04 03:19AM >>> Hi, I would like to use modeller to put sidechains on my 'backbone only' structures, but without moving the backbone atoms at all. Could you tell me if this is possible and maybe point me to the part of the manual which describes the process. Many Thanks Diana ________________________________________________________________________________ Diana C. Mustard Room 234 Dept Computing Science University of Aberdeen Kings College Aberdeen, Scotland, UK 00 44 (0)1224 273114 http://www.csd.abdn.ac.uk/~dmustard

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should there be entries of SSBOND after patch_ss_template in target model?
by dougyoung＠tmicha.net 30 Aug '04

30 Aug '04

: Dear Modellers, For those who have used this command before, do you see entries of SSBOND in your target model files? I haven't seen any. Thanks Doug _____________________________________ Join our fight against SPAM! www.Tmicha.net - your SPAM-free mailbox

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restraining dihedral angles
by Han Choe 30 Aug '04

30 Aug '04

Hello Modellers, I use the follwoing example to restrain a distance . SET ATOM_IDS 'OD2:97:' 'NZ:120:' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 4.0 0.2 But I don't know how to restrain mainchain and sidechain dihedral angles. Would someone explain or post an example script? Best regards, Han Han Choe, PhD Department of Physiology University of Ulsan, College of Medicine Songpagoo Poongnapdong 388-1 Seoul 138-736, Korea

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(no subject)
by Han Choe 30 Aug '04

30 Aug '04

Dear Modeller, My top file contains user-defined restraints involving hydrogen atoms. When I add 'SET DO_LOOPS =1' to the top file, the modeller has the following error. add_res_442E> One or more atoms absent from MODEL: O:381: HD1:381: I guess this is related to that LOOPS optimizes nonhydrogen atoms. Is there a way around this problem? Best regards, Han Han Choe, PhD Department of Physiology University of Ulsan, College of Medicine Songpagoo Poongnapdong 388-1 Seoul 138-736, Korea

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few problems
by vivek sharma 30 Aug '04

30 Aug '04

Dear Sir, I have mentioned here few warnings, not errors, but as they affect final model, I need to handle them, please explain the reasons behind them and method to remove them. Although, necessary changes I have tried to make in all possible files and I have mentioned about them here. Sorry, its a bit lengthy mail, but plz spare out some time frm your schedule to explain these. PS: I have added residues to top_heav.lib and using my own par.lib which also includes all required parameters for new residues added in top_heav.lib (may be some few are missing). 1. I have included few new residue types in top_heav.lib and made necessary changes in res_type.lib also, but still it gives the statement > Non-standard residue type,position,sequence: / 655 1 > Non-standard residue type,position,sequence: + 656 1 > Non-standard residue type,position,sequence: + 657 1 like this, although its not a warning, but why this is so? and where the change is needed to be made? 2. This is warning, is it serious enough or not and how to remove this? fndatmi_285W> Number of residues <> number of atoms; atom code: 516 513 CA fndatmi_285W> Number of residues <> number of atoms; atom code: 541 538 CA fndatmi_285W> Number of residues <> number of atoms; atom code: 547 544 CA 3. Are these atoms for which no coordinates are defined, the undefined ones? meaning there by that these types are either not present in top_heav.lib or par.lib . So how to handle this or MODELER itself is handling it. build___466W> Some coordinates in MODEL not assigned. build___468W> Some coordinates in MODEL are still undefined. build___464W> Inventing the MODEL coordinates. 4. Serious one: I have used my own par.lib not the one which is supplied with MODELER, and it shows the following warnings , I think this means that there are no parameters available for these dihedrals and MODELER is assigning the values by some means (random generation). So, if I am able to get the values of dihedrals, then by putting the values in my par.lib, these warnings can be removed, am I right? And if I dont found these values anywhere, then to what level these MODELER generated values are acceptable? r_stere_607W> Cannot find params in params file: CHARMM atoms : CT1 NH3 C CT2 IUPAC atoms : CA N C CB Atom indices : 2 1 7 3 Residues : MET MET MET MET addprm__440W> Adding params (mean,force,period): 33.6945 60.0000 0 For atoms: CT1 NH3 C CT2 r_stere_607W> Cannot find params in params file: CHARMM atoms : CT1 NH1 C CT2 IUPAC atoms : CA N C CB Atom indices : 10 9 15 11 Residues : LEU LEU LEU LEU addprm__440W> Adding params (mean,force,period): 33.6297 60.0000 0 For atoms: CT1 NH1 C CT2 r_stere_607W> Cannot find params in params file: CHARMM atoms : CT1 CT3 CT3 CT2 IUPAC atoms : CG CD1 CD2 CB Atom indices : 12 13 14 11 Residues : LEU LEU LEU LEU addprm__440W> Adding params (mean,force,period): 32.3756 60.0000 0 5. While restraints making , it shows the following warnings, i dont understand these, please explain. make_re_417_> Restraint type to be calculated: phi-psi_binormal openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mnch1.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mnch1.mdt irddata_401_> USER SYMMETRY, SYMMETRY: 1 T SYMMETRIC = .T. ==> NALN*NALN/2 SYMMETRIC = .F. ==> NALN*NALN All protein pairs always generated. rdabrk__292W> Too many neighbours; overflow ignored: 51 50 rdabrk__292W> Too many neighbours; overflow ignored: 51 50 rdabrk__292W> Too many neighbours; overflow ignored: 51 50 rdabrk__292W> Too many neighbours; overflow ignored: 51 50 rdabrk__292W> Too many neighbours; overflow ignored: 51 50 rdabrk__292W> Too many neighbours; overflow ignored: 51 50 rdabrk__292W> Too many neighbours; overflow ignored: 51 50 errdih__638_> Missing atoms in a dihedral, residue index, residue type: 1 512 LEU errdih__638_> Missing atoms in a dihedral, residue index, residue type: 1 513 LYS errdih__638_> Missing atoms in a dihedral, residue index, residue type: 4 513 LYS 6. this also , I hope to be a serious one. Although , topology file includes the residues with same details as in pdb, i.e. same PDB atom names, all specific CHARMM atom names, etc. but what does this warning signify,please explain. make_re_417_> Restraint type to be calculated: distance iup2crm_279W> IUPAC atom not found in topology library; residue type index: N A 143 Possible reasons are a non-standard PDB file, or a new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library. iup2crm_279W> IUPAC atom not found in topology library; residue type index: N B 143 Possible reasons are a non-standard PDB file, or a new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library. iup2crm_279W> IUPAC atom not found in topology library; residue type index: N C 143 Possible reasons are a non-standard PDB file, or a new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library. These are 6 questions, please explain the possible cures for these. Thanks in advance, sincerely, vivek sharma -- VIVEK SHARMA HBG BI

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constraining backbone atoms using modeller?
by Diana C.Mustard 30 Aug '04

30 Aug '04

Hi, I would like to use modeller to put sidechains on my 'backbone only' structures, but without moving the backbone atoms at all. Could you tell me if this is possible and maybe point me to the part of the manual which describes the process. Many Thanks Diana ________________________________________________________________________________ Diana C. Mustard Room 234 Dept Computing Science University of Aberdeen Kings College Aberdeen, Scotland, UK 00 44 (0)1224 273114 http://www.csd.abdn.ac.uk/~dmustard

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multi-chain modelling
by V.Nadeem Ahmad 29 Aug '04

29 Aug '04

Dear Modeller, I want to build a model A in the presence of Model B ie to get an effect of presence of Model B on A.i used the alignment as follows >model_A aaaaaaaaaaaaaaabbbbbbbbbbbbb >templateA aaaaaaaaaaaaaaa------------- >Model_B ---------------bbbbbbbbbbbbbb Is this alignment correct. and what script i sould use since i want to use Model B for creating an environment but not for modelling.is this approach correct for multi chain modelling? with regards Nadeem Ahmad

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MAXATM
by bcur001＠ec.auckland.ac.nz 26 Aug '04

26 Aug '04

Hello, I'm looking for any assistance anyone can offer with the following problem. I am attempting to create a model of a nitroreductase, and I'm getting the following error. addatms_223E> Array too small. Increase MAXATM current maximum, current need: 2964 2965 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 The only reference to it in the archives that I have found, just notes it as a possible bug. I'm a fairly new user and am attempting to follow the manuals guidance on this. It appears to occur when I call GENERATE_TOPOLOGY SEQUENCE in the TOP file. My TOP file looks something like : SET OUTPUT_CONTROL = 1 1 1 1 1 SET ATOM_FILES_DIRECTORY = './:../atom_files' READ_TOPOLOGY FILE='$(LIB)/top.lib' READ_PARAMETERS FILE='$(LIB)/par.lib' READ_MODEL FILE='1ICV' SEQUENCE_TO_ALI ATOM_FILES = '1ICV', ALIGN_CODES='1ICV' SEQUENCE_TO_ALI ADD_SEQUENCE=off, ATOM_FILES=ATOM_FILES '1ICV.ini',; ALIGN_CODES = ALIGN_CODES '1ICV-ini' GENERATE_TOPOLOGY SEQUENCE = '1ICV-ini' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ=off MAKE_RESTRAINTS RESTRAINT_TYPE='stereo' WRITE_MODEL FILE='1icv.ini' The 1ICV file is a downloaded, unaltered pdb file. Any ideas as to what's happening? Thanks. Ben.

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error on hetatm modelling
by V Nadeem Ahmad 26 Aug '04

26 Aug '04

Dear Modeller, I was trying to do modelling with hetatm .it stopped after running a while can anyone help me where was the mistake. ## the top file is INCLUDE # Include the predefined TOP routines SET ALNFILE = 'align.pir' , KNOWNS= '1a57', SEQUENCE = 'seq' SET MODEL_TOPOLOGY = 1, HYDROGEN_IO = on, HETATM_IO = on, WATER_IO = on SET TOPOLOGY_LIBRARY = $(LIBS_LIB6V2)/top.lib SET PARAMETERS_LIBRARY = $(LIBS_LIB6v2)/par.lib CALL ROUTINE = 'model' # do homology modelli ----------------- the log file --------------------- assgn___544E> Variable name not recognized: MODEL_TOPOLOGY Command line: SET MODEL_TOPOLOGY = 1, HYDROGEN_IO = ON, HETATM_IO = ON, WATER_IO = ON assgn___525E> Error in TOP variable assignment. assgn___544E> Variable name not recognized: TOPOLOGY_LIBRARY Command line: SET TOPOLOGY_LIBRARY = $(LIBS_LIB6V2)/TOP.LIB assgn___525E> Error in TOP variable assignment. assgn___544E> Variable name not recognized: PARAMETERS_LIBRARY Command line: SET PARAMETERS_LIBRARY = $(LIBS_LIB6V2)/PAR.LIB assgn___525E> Error in TOP variable assignment. compile_563E> Please correct the errors reported above and rerun MODELLER. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 with regards Nadeem Ahmad

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A word on beta (strand) restraints
by Modeller Caretaker 25 Aug '04

25 Aug '04

A few queries have come up over time on how to get Modeller to restrain the model to an idealized beta strand, so here's a quick summary. See http://salilab.org/modeller/FAQ6v2.html#19 for information on how to specify secondary structure, including the 'STRAND' restraint type. This adds additional restraints to those derived from the homology. See http://salilab.org/modeller/manual6v2/node100.html for a description of the types of restraints added for secondary structure. In summary, both alpha and strand restraints add phi-psi restraints to force residue mainchain conformation into class A (for helices) or B/P (for strands). See modlib/mnch.lib for the representative dihedral angles of these classes. Note that Modeller attempts to fulfil all restraints, but violations will often occur, particularly when conflicts between user-defined and homology-derived restraints are present. This is less of a problem with helix restraints than with strands, as helix restraints enforce a number of distance restraints in addition to the phi-psi restraints, and so are in a sense 'stronger'. There is a bug in Modeller 6v2's generation of beta restraints; it generates phi-phi restraints rather than the correct phi-psi restraints. To correct this, take the .rsr file generated by Modeller. At the end of this file should be some lines similar to the following for your beta restraints (the following should be all on one line): R 9 1 4 25 8 6 0 327 329 330 332 327 329 330 332 1.0000 -2.3387 2.5656 0.5271 0.3072 -0.6670 Notice that the atom indices for the phi dihedral angle (columns 9 through 12, 327 329 330 332) are the same as those for what should be psi, columns 13 through 16. Correct the atom indices for psi, write out the new .rsr file, and then use the recipe in http://salilab.org/modeller/FAQ6v2.html#11 to override Modeller's restraints with your corrected ones. If in doubt about the atom indices, defining a helix restraint on the same residue range should yield the correct values (the bug is only for strand restraints). This bug is fixed in Modeller 7, which should be released in a few weeks. Until then, apologies for the workaround! Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mailing list: http://salilab.org/mailman/listinfo/modeller_usage

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