- modeller_usage - salilab.org

help about evaluate_model.log
by Purzelfrau＠gmx.de 19 Jan '07

19 Jan '07

Hello everybody, i have a question about the output-file evaluate_model.log. I looked in the basic_example from the Modellers Homepage and also in my own output files. In the most of the cases there is the following message: report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 1 2 1.480 serious non-bonded atom clash: 2 3 1.539 serious non-bonded atom clash: 2 7 1.493 serious non-bonded atom clash: 3 4 1.528 serious non-bonded atom clash: 4 5 1.817 serious non-bonded atom clash: 5 6 1.816 .... Can everybody explain what does it exactly mean? Is for example the number 1 the first atom in the template and 2 the second in the model or what does it mean? And what can i do that this message never comes? Thanks for all answers! Verena -- Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! Ideal für Modem und ISDN: http://www.gmx.net/de/go/smartsurfer

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(no subject)
by Purzelfrau＠gmx.de 19 Jan '07

19 Jan '07

-- Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! Ideal für Modem und ISDN: http://www.gmx.net/de/go/smartsurfer

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forrtl Error using the "/." construct
by Schmid, Dr R. 12 Jan '07

12 Jan '07

Dear all, I am trying to model a protein with a ligand using the "/." construct in the alignment and I am getting the following error: [ralf@localhost models]$ mod8v2 tens1.top forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Read Image PC Routine Line Source mod8v2_i386-intel 0837011A Unknown Unknown Unknown mod8v2_i386-intel 0836E555 Unknown Unknown Unknown mod8v2_i386-intel 0834064D Unknown Unknown Unknown ... mod8v2_i386-intel 080811C6 Unknown Unknown Unknown mod8v2_i386-intel 08080D81 Unknown Unknown Unknown libc.so.6 006F179A Unknown Unknown Unknown mod8v2_i386-intel 08080CC1 Unknown Unknown Unknown [ralf@localhost models]$ [ralf@localhost models]$ tail -20 tens1.log read_al_374_> Non-standard residue type,position,sequence: . 324 1 read_al_374_> Non-standard residue type,position,sequence: . 324 2 Read the alignment from file : tens1.ali Total number of alignment positions: 324 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1d5r 308 2 1d5r . 2 tensin1 309 2 tensin1 . TOP_________> 129 113 STRING_IF STRING_ARGUMENTS = TOP_VERSION 'accelrys', OPER; ATION = 'EQ' TOP_________> 130 117 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL 1d5r.pdb Dynamically allocated memory at amaxstructure [B,kB,MB]: 2652691 2590.519 2.530 openf5__224_> Open 11 OLD SEQUENTIAL 1d5r.pdb [ralf@localhost models]$ I should mention that the modelling process without ligand runs smoothly. I am using Modeller 8v2 on Linux RHE, 2.4.21-47.0.1.ELsmp kernel. Thanks in advance for any hints, Ralf

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Cómo instalar MODELLER
by Carlos Lozano 11 Jan '07

11 Jan '07

Hola a todos de la comunidad, la primer pregunta que me surge, es que no tengo ni idea de cómo instalar MODELLER en mi ibook. Sí alguién puede recomendarme algún tip, se lo agradecería. Carlos

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origin of blosum62.sim.mat and as1.sim.mat
by Joshua A. Speidel 11 Jan '07

11 Jan '07

Hello, I am curious about the origin of the blosum62.sim.mat and as1.sim.mat. When I look at the blosum62.sim.mat, I can't figure out the relationship between the numbers there, and the original blosum62 matrix. Initially, I thought that the Henikoff & Henikoff values were just scaled to between 0 and 1000, but that didn't seem to work. I can't find a reference for ALBASE3 mentioned in as1.sim.mat. Finally, if I wanted to use my own matrix, is it necessary for me to scale it to between 0 and 1000? Your help in understanding this is greatly appreciated, Josh

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Re: [modeller_usage] Ligands
by Esben Jannik Bjerrum 09 Jan '07

09 Jan '07

Hi Joel Have you tried to include an @ in your alignment file?according to restyp.lib (in mollib directory) it should correspond to ATP. I dont know how about the quality of the parameters are, but its a starter. And theres a starter for tweaking in top_heav.lib. If theres no ATP (or similat molecule) in you template You'll need to add some constraints to some atoms between your protein and ATP to restrict it to a position near the binding site. Happy Modelling Esben Bjerrum __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Ligands
by Joel Tyndall 08 Jan '07

08 Jan '07

Hi all, I'm wanting to add in an ATP molecule based on my template to my modelled structure. I have looked at the FAQ and it does seem a laborious task to write the CHARM topology files etc. I was wondering if there was a database of ligands (wiki? type thing) or a web based converter ( i have already looked at Prodrg in dundee) or if someone wants to share their top files for ATP. ...Or any alternative methods out there? I'm currently using 8v2 but with old scripts and will upgrade soon. Cheers joel -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin 9054 New Zealand Pukenga Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 913 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034

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modeller model and modbase model
by hori koshii 07 Jan '07

07 Jan '07

Hi all, Has anyone come across with the models on MODBASE? How does that compare to our own models built by using "MODELLER"? (I know they are both using MODELLER, but the protein I am working on, have very different "insertion" loops from my results and modbase's) I have been trying to build a protein model using MODELLER8, but recently come across with one already available on the MODBASE. I think there is actually only one good template (over 30%) for my target. I used MODELLER 8 to build 1000 models and pick out the ones with lower DOPE scores. The loop conformations in my model and the one on MODBASE are quite different. I am curious espeically about the loop insertions. So, I am wondering how come they are very different? Could anyone from this forum give me any comment about this please? Thank you :) Sincerely yours, __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Problems about disulfide bonds
by 饶�� 03 Jan '07

03 Jan '07

Dear Mr.: I have some questions about two commonds model.patch_ss_templates() and model.patch_ss().First,I don't know what exactly does these two commonds want to do.In my opinion,the earler can indicate wether the disulfide bonds exist and where are they and the later has the same function of which the target is the protein which is modeled.But after I have run the commond and used the mdl.energy() commond,I don't how to understant the output file.I don't know what information I can get from the .log file. In fact,what I am doing now is to model a protein which has a hign homology with another protein of which the structure has been known.The template is thermophilic and has a disulfide bond.The target has two cys amino acids in the same places where the template form the disulfide bond.However,after the target model has been established,the Chimera software indicate that no disulfide bond exists.The target protein has no ability of thermostability.So I want to use the MODELLER software to explore the differences between them and find out what factors influence the target protein and make it can't be thermophilic.The disulfide bond is the first element I take into account. How do I solve the problems above? I am very appreciate your advises. Yours sincerely, Rao Ben __________________________________________________ 赶快注册雅虎超大容量免费邮箱? http://cn.mail.yahoo.com

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homodimer modelling
by drugdesign 31 Dec '06

31 Dec '06

modeller_usage(a)salilab.org Dear Modeller users, I need to model a homodimer from a homodimer templare. How my alignment file must look like? I mean I have problems with aminoacids numbers and chain names. How to solve this problems? I've attached all input files. Do I need to rename and renumber sequence or I can complete the task without it? Respectively yours, Andrew MODELLER 8v1, Jun 20, 2005 11:37am PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2005 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux Home 2.6.8-24-default i686 Date and time of compilation : 06/20/2005 12:25:12 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2006/11/18 01:06:28.018 openf5__224_> Open 11 OLD SEQUENTIAL $(LIB)/restyp.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/resdih.lib rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/radii.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/radii14.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch1.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch2.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch3.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 runcmd______> alignment.append(align_codes=['mfzd', 'fzd1'], atom_files=[], file='fzd1.pir', (def)remove_gaps=True, (def)alignment_format='PIR', add_sequence=True, (def)rewind_file=False, (def)close_file=True) openf___224_> Open fzd1.pir Dynamically allocated memory at amaxalignment [B,kB,MB]: 2124923 2075.120 2.026 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2126623 2076.780 2.028 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2130023 2080.101 2.031 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2136823 2086.741 2.038 openf5__224_> Open 13 OLD SEQUENTIAL mfzd.pdb rdpir___648E> Alignment sequence not found in PDB file: 1 mfzd.pdb

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