- modeller_usage - salilab.org

core dumps
by T. .R. Dafforn 01 Feb '00

01 Feb '00

Dear All, I have just installed modeller V5.0 and have found that when I run my old scripts the program gets as far as TOP______> 40 40 SET TOPLIB = '${LIB}/top_heav.lib' TOP______> 41 41 SET TOPOLO and then Core dumps... Does any one have any ideas or previous experience of this? Cheers tim -- Tim Dafforn Structural Medicine Department of Haematology CIMR University of Cambridge Wellcome-MRC Building (Level6) Hills Road Cambridge CB2 2XY Tel. (01223) 336829 Fax. (01223) 336827 http://smokeroom.cimr.cam.ac.uk/

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FW: [Fwd: Modeller mysteries]AF: handling HETATM entries in the middle of PDB file
by Kevin Truong 27 Jan '00

27 Jan '00

-----Original Message----- From: andras(a)rockvax.rockefeller.edu [mailto:andras@rockvax.rockefeller.edu]On Behalf Of Andras Fiser Sent: January 27, 2000 10:39 AM To: Andrej Sali; kevin.truong(a)utoronto.ca Subject: Re: [Fwd: Modeller mysteries]AF: handling HETATM entries in the middle of PDB file Hi Kevin, In this strange pdb file the hetatm entries inserted at several intermediate positions in the coordinate file. You tried to include them by including X-es in your alignment but it does not work like this. At first, if you do not read in HETATM entries, which is the default situation, (look at command HETATM_IO) than Modeller skips these entries so you do not need to include them in your alignment file either. Second, even if you include them you should not stick on the PDB file residue numbering (it is often chaotic): for some reason in your case the numbering skips by three at the HETATM enty although there is only one HETATM entry. You included 3 X-es accordingly, you need only one. Modeller renumbers the file by simply reading in order all the coordinate entries from the file irrespectively what numbering is associated with the entries in the PDB file. Third, if you do include HETATM entries you should indicate it by "." and not by "X". If you just replace your X-es to "." and instead of XXX you use a single "." your setup already works for me. I suggest you send your questions to the Modeller mailing list in the future, you might have answers from others and others also can learn. Please look at: http://salilab.org/cgi-bin/lwgate/lwgate/MODELLER_USAGE/ if you do not consider this mail as confidential please forward it to the list: modeller_usage(a)salilab.org best wishes, Andras > > Subject: Modeller mysteries > Date: Wed, 26 Jan 2000 19:51:03 -0500 > From: "Kevin Truong" <kevin.truong(a)utoronto.ca> > To: <sali(a)rockvax.rockefeller.edu> > > Hi Prof. Sali: > > My name is Kevin. I'm from Ikura's lab at the Ontario Cancer Institute. > I'm having some problems using modeller that I hope you can help me with. > I'm trying to model the RFP sequence with the GFP structure. > > I download the pdb file of 1ema from the PDB protein bank. > I ran the Modeller and it was not able to produce the predicted pdb file. > I have attached the following files: > > pdb1ema.ent pdb file used for Modeller > cFP484.ali ali generated by Threader > cFP484.top top script for Modeller > cFP484.log result of the Modeller run. > > I have no clue why this does not work. Can you help me? > > Thanks! > Kevin -- , Andras Fiser, PhD # phone: (212) 327 7206 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras

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a question
by Helene Valadie 25 Jan '00

25 Jan '00

Hello, I am student in France and I would like to know if it is possible to build a model with adding water molecules on a part of my molecule (for example, add water molecules only on the Nterm atoms of my molecule). Thank you, Helene VALADIE valadie(a)urbb.jussieu.fr

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ACCESSIBILITY_TYPE
by M. Germana Paterlini 18 Jan '00

18 Jan '00

How do I (or is it possible to ) to specify the solvent accessibility of residues with ACCESSIBILITY_TYPE in MAKE_CONSTRAINTS ? Is there a specific RESTRAINT_TYPE associated with it ? Here is my input # Test for restraints on accessibility (?) READ_TOPOLOGY FILE '$(LIB)/top_heav.lib' READ_PARAMETERS FILE ='$(LIB)/par.lib' SET ATOM_FILES_DIRECTORY = './' READ_MODEL FILE = 'test.ent', MODEL_SEGMENT = '1:' '7:' SEQUENCE_TO_ALI ATOM_FILES = 'test.ent', ALIGN_CODES = 'test.ali' SEQUENCE_TO_ALI ADD_SEQUENCE = on , ATOM_FILES = ATOM_FILES 'test.ini', ; ALIGN_CODES = ALIGN_CODES 'test-ini' GENERATE_TOPOLOGY SEQUENCE = 'test-ini' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ = off WRITE_MODEL FILE 'test.ini' SET ACCESSIBILITY_TYPE = 8 MAKE_RESTRAINTS RESTRAINT_TYPE = 'sphere' WRITE_RESTRAINTS FILE = 'test-1.rsr' ENERGY DYNAMIC_SPHERE = off ENERGY WRITE_DATA FILE = 'test' , OUTPUT='psa' Thanks Germana Paterlini Department of Medicinal Chemistry University of Minnesota Minneapolis, MN 55455

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Modeller stops with error
by Daniel John Rigden 07 Jan '00

07 Jan '00

Hi Modellers I wonder if anyone can help me solve a problem I'm having with modeller. I'm using two templates to construct a model of a protein. Modeller stops with the following messages iup2crm_E> IUPAC atom not found in topology library: OG iup2crm_E> residue type undefined recover__> MODELLER_STATUS >= STOP_ON_ERROR: 1 1 This happens when it's calculating Ca-Ca restraints. I can't find any strange residues in my input file and asking for maximum output from modeller doesn't give me any new information. I think the problem lies with the second message since I have had the first making earlier models with just a single template and modeller did not stop. I'll attach a larger chunk of the log file at the end of this message. Thanks very much in advance for any help. Daniel Rigden +-------------------------------------------------------------------------+ | Dr Daniel John Rigden | | CENARGEN/EMBRAPA | e-mail: daniel(a)cenargen.embrapa.br | | S.A.I.N. Parque Rural, Final W5 | http://www.cenargen.embrapa.br | | Asa Norte | Phone: +55 (61)348-4741 | | 70770-900, Brasilia-D.F.-BRAZIL | Fax: +55 (61)340-3624 | +-------------------------------------------------------------------------+ TOP______> 159 125 SET RES_TYPES = 'STD' TOP______> 160 126 SET DISTANCE_RSR_MODEL = 5, MAXIMAL_DISTANCE = MAX_CA-CA_; DISTANCE TOP______> 161 127 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = ON TOP______> 162 128 SET RESTRAINT_GROUP = 9 TOP______> 163 129 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'CA' Number of atoms to choose from, total : 4025 4025 Atom types to be searched for (ATOM_TYPES) : CA Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 510 1: 510: Selection residue step (SELECTION_STEP) : 1 selatm___> Number of selected atoms : 510 List of segments of contiguous residues with at least one selected atom: SEGMENT RNUM AA --- RNUM AA LEN 1 1 SER --- 510 LEU 510 TOP______> 164 130 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'CA' Number of atoms to choose from, total : 4025 4025 Atom types to be searched for (ATOM_TYPES) : CA Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 510 1: 510: Selection residue step (SELECTION_STEP) : 1 selatm___> Number of selected atoms : 510 List of segments of contiguous residues with at least one selected atom: SEGMENT RNUM AA --- RNUM AA LEN 1 1 SER --- 510 LEU 510 TOP______> 165 131 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Restraint type to be calculated: distance iup2crm_E> IUPAC atom not found in topology library: OG iup2crm_E> residue type undefined recover__> MODELLER_STATUS >= STOP_ON_ERROR: 1 1

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looking for HUGE modeller version for SGI Octane
by Ton ter Laak 08 Dec '99

08 Dec '99

Dear All, We got Modeller running on our SGI Octane with one R12000 processor using the mod_r10000-IRIX6.5-MAXRES=1300_MAXSEQ40 executable of Modeller (the executable for R10000). However, for one of our projects with large proteins we would like to use a MAXRES-2400 or MAXRES-2500 version (MAXSEQ < 10) of Modeller. Unfortunately the mod_IRIX6.5_MIPS3_MAXRES=2500 executables (for MIPS3) do not work on the Octane. Maybe somenone knows whether there is a mod_r10000-IRIX6.5-MAXRES=2500 available ? How could we obtain such an executable ? Is someone in the Modeller community able to generate this executable ? with best regards, Ton ter Laak Computational Medicinal Chemistry Farmacochemistry, Vrije Universiteit Amsterdam, The Netherlands tel: +31-20-4447611 fax: +31-20-4447610 email: terlaak(a)chem.vu.nl

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Re: Modeller
by Azat Badretdinov 06 Dec '99

06 Dec '99

Dear Ton, I am replying publicly, 'cause apparently there is no confidential information in your letter, and it might be helpful for others to know. First of all, it is just warning. Second, it directly indicates that there is something wrong either with objective function - unrealistic restraints produced by unrealistic template (with clashes for example) or the structure at some point has become very unrealistic (again - lotsa atom-atom clashes). In my experience, it happened sometimes when I was using pseudoatoms (for NMR-obtained restraints) or hydrogen models. Please also check if the settings for topology model (TOPOLOGY_MODEL) and library (TOPLIB) correlate with each other. Hope this helps. PS. It is just a warning. Azat Ton ter Laak wrote: > > Dear Azat, > > thank you very much helping us out with our > stack limit. It helped ! The programm Modeller is running ! > > But now we have loads of other error messages when running > modeller. Do you recognize them ? > > chkder___W> DVZ(i) out of bounds: 214 214nan > chkder___W> DVX(i) out of bounds: 216 216nan > chkder___W> DVY(i) out of bounds: 216 216nan > chkder___W> DVZ(i) out of bounds: 216 216nan > chkder___W> DVX(i) out of bounds: 217 217nan > chkder___W> DVY(i) out of bounds: 217 217nan > chkder___W> DVZ(i) out of bounds: 217 217nan > chkder___W> DVX(i) out of bounds: 218 218nan > chkder___W> DVY(i) out of bounds: 218 218nan > > Thanks in advance, > > Ton ter Laak -- - Azat Badretdinov, Ph.D. - Molecular Simulations Inc. - 9685 Scranton Road - San Diego CA 92121-3752 - Phone: (858) 799 5728

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Modeller on SGI Octane
by Ton ter Laak 03 Dec '99

03 Dec '99

Dear All, We are trying to get Modeller running on our SGI Octane. We tried to run the following machine versions of Modeller4 mod_IRIX6.5_MIPS3_MAXRES%3D2500_MAXSEQ%3D1 mod_IRIX6.5_MIPS3_MAXRES%3D2500_MAXSEQ%3D5 In both cases the error prompted by the (IRIX6.5.5) system when running Modeller4: "critical error. killed: process or stack limit exceeded" Has anyone had similar problems running Modeller on an Octane ? May be someone knows the amount of stack needed for Modeller ? Our SGI Octane has the following configuration: 1 270 MHZ IP30 Processor CPU: MIPS R12000 Processor Chip Revision: 2.3 FPU: MIPS R12010 Floating Point Chip Revision: 0.0 Main memory size: 256 Mbytes Instruction cache size: 32 Kbytes Data cache size: 32 Kbytes Secondary unified instruction/data cache size: 2 Mbytes We hope that someone can help us, thanks, Ton ter Laak Dr. A.M. ter Laak Computational Medicinal Chemistry Farmacochemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands tel: +31-20-4447611 fax: +31-20-4447610 email: terlaak(a)chem.vu.nl

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queries
by Dr Ahsan Salim 29 Nov '99

29 Nov '99

I have been doing structural studies on various eye lens crystallins by homology modelling using modeller 4. I have some queries in this regard. 1.The final models have no residues in the disallowed region of the Ramachandaran plot as well as there are no bad contacts. Is this evaluation enough for structure verification? 2. I want to mutate one residue in these models and I have gone thru the top files for mutation. For reasons unknown to me, I could not use it correctly. Besides the file needs the name of the residue to be mutated and the one to be inserted instead but not the position. If the specific name is given, all residues of the same name gets mutated. 3. The other important studies that I want to carry out is the effect of sugar binding to the structure as well as binding of the small molucules like phosphate, cyanate etc. I used Web lab Viewer Pro version to paste and connect the small mol. to my protein.When I cleaned the entire structure using "clean structure" command in Web lab, it leaves so many bad contacts and many residues in the disallowed region of the Ramachandaran plot. So I decided to use the molecular dynamics and energy minimization by MODELLER. The topology files do not have these small molecules in the list. So it leaves the structure to be more disturbed. Can you make the topology files if specified or can you help me sort out how to make one? Well these are so many questions! Can you please suggest something. Thanks asmat salim HEJ Res Inst of Chem Univ of Karachi Pakistan PS:How can I join your mailing list?

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loop refinement
by M. Germana Paterlini 10 Nov '99

10 Nov '99

I generated several loop conformations using the 'loop' routine. The top file is similar to example 3 of the manual, with the addition of gemetrical constraints on the end of loops. I am refining 20 a.a. out of a 27-loop segment. The refined loop conformations still have residues located in unfavorable regions of the phi/psi plot, i.e. phi> 0 (non Gly, or Asn). Typically, there are 1-4 residues in these regions. Only 2% of my conformations have all residues with phi<0. Are such occurrencies typical of the refinement procedure? If not, how can I prevent this for happening? Thanks Germana Germana Paterlini Dept. of Medicinal Chemistry Minneapolis, MN 55455 germana1(a)vwl.medc.umn.edu

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