- modeller_usage - salilab.org

problem_again
by vivek sharma 10 Sep '04

10 Sep '04

Sirs, I have mailed you sometime back but couldn't received reply, although I solved some problems, but still there are three of them which are hindering the work. It would be very kind if you suggest a solution to them. Problems are: 1. What each column in *.D* file, which contains details about the optimization, represents? Also, does this file contains details of optimization of molecular pdf as well as Molecular Dynamics? and how to differentiate between them? 2. Running Modeler gives the following warnings: Number of templates for coordinate transfer: 3 After transfering coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 3290 1048 TOP_________> 146 87 BUILD_MODEL INITIALIZE_XYZ = OFF build___466W> Some coordinates in MODEL not assigned. build___468W> Some coordinates in MODEL are still undefined. build___464W> Inventing the MODEL coordinates. I understand that these atoms are undefined because it doesn't found equivalent atoms (same atom name and equivalent residue) in templates but then those atoms are given coordinates by BUILD_MODEL command, but can you tell me how one can find out which are those 'still' undefined atoms , even which are not covered by 'BUILD_MODEL' command and why this is so? Please explain this a bit. 3. Also, another problem is: New residue types defined in restyp as well as top_heav.lib. I am using this type of restyp.lib (residue defined for use in template) 141 | AAA | ? | A123 | residue XXX 142 | BBB | " | A234 | patch for residue XXX 143 | BBB | | A345 | patch for residue XXX and alignment like template : ----/"/----- target : ----/?/?----- (for this patches are defined explicitly by PATCH command in top file) this reads the first (") residue but doesn't read the next () residue and gives error: ------------- rdabrk__291E> Sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES ------*---- 1 514 143 A345 141 A123 YVNLK" rdabrk__288W> Protein not accepted: 1 check_a_337E> Structure not read in: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 ------------- but when I change the PDB-3 name of residue from BBB to CCC in restyp.lib, then it works, but this needs me to change the residue name in PDB, but instructions of your restyp.lib suggests that same name of residue in PDB-3 are acceptable. Is this some type of probable bug? or I am doing some mistake? Also, patches are needed to be given some different PDB-1 and different CHARMM name, which I did. Please reply, if you need more details, please say so. Thanking you, sincerely, vivek sharma -- VIVEK SHARMA HBG BI

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Error message: Array too small. Increase MAXSEG
by Nancy Yu 02 Sep '04

02 Sep '04

Hi, Can anyone tell me what the following error message means? Dynamically allocated memory at amaxbnd [B,kB,MB]: 13309089 12997.157 12.693 openf5__224_> Open 11 OLD SEQUENTIAL 09-02-align.ali openf5__224_> Open 13 OLD SEQUENTIAL ./PNPmono.pdb defseg__223E> Array too small. Increase MAXSEG current maximum, current need: 30 31 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Thanx, Nancy

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problem!
by vivek sharma 02 Sep '04

02 Sep '04

Dear Modellers, Please explain these problems: 1. What each column in *.D* file, which contains details about the optimization, represents? Also, does this file contains details of optimization of molecular pdf as well as Molecular Dynamics? and how to differentiate between them? 2. Running Modeler gives the following warnings: Number of templates for coordinate transfer: 3 After transfering coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 3290 1048 TOP_________> 146 87 BUILD_MODEL INITIALIZE_XYZ = OFF build___466W> Some coordinates in MODEL not assigned. build___468W> Some coordinates in MODEL are still undefined. build___464W> Inventing the MODEL coordinates. I understand that these atoms are undefined because it doesn't found equivalent atoms (same atom name and equivalent residue) in templates but then those atoms are given coordinates by BUILD_MODEL command, but can you tell me how one can find out which are those 'still' undefined atoms , even which are not covered by 'BUILD_MODEL' command and why this is so? Please explain this a bit. Please clarify these two doubts, really important they are. sincerely, vivek sharma -- VIVEK SHARMA HBG BI

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Extracting alignment from already superposed structures
by Higueruelo Alicia (CAM) 02 Sep '04

02 Sep '04

Dear Modellers, I have already a few 3D structures (pdb) superposed, I would like to extract their sequences with their current structural alignment. I am using MALIGN3D, but I think it still aligns the structures itself. Could someone help me with that? Many thanks for your time, cheers, alicia __________________ Alícia Pérez Higueruelo Computational Chemist Celltech R&D Ltd Granta Park - Great Abington Cambridge CB1 6GS UK The information contained in this email is intended for the personal and confidential use of the addressee only. It may also be privileged information. If you are not the intended recipient then you are hereby notified that you have received this document in error and that any review, distribution or copying of this document is strictly prohibited. If you have received this communication in error, please notify Celltech immediately on: +44 (0)1753 534655, or email 'is(a)celltech.co.uk' Celltech Group plc 208 Bath Road, Slough, SL1 3WE, Berkshire, UK Registered Office as above.

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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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