- modeller_usage - salilab.org

(no subject)
by Michael Grabe 13 Apr '05

13 Apr '05

dear modellers, what should i do if i want the homology derived restraints to have a larger weight in the creation of a model. that is i want my model to look more like the template structure at the expense of stereochemical considerations. thanks, michael ------------------------------------------------------------------------ -------------------------- Michael Grabe, Ph.D. HHMI/UCSF Genetics Development & Behavioral Science Building 1550 4th Street, GD 481 San Francisco, CA 94143-0725 tel: ++ 415.476.0421 http://itsa.ucsf.edu/~mgrabe

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tutorial on mod7v7
by Paula R.=?ISO-8859-1?Q?_Kuser_Falc=E3o?= 11 Apr '05

11 Apr '05

Hi, I am trying to do the modeller tutorial on a linux machine, with version mod7v7. After running seq_search for the TvDLH model the seqsearch.dat is empty, and I get the .log file as shown below. Would you know why I can't get any answer from my search? Thanks, Paula. Kind, OS, HostName, Kernel, Processor: 4, Linux japiim.cbi.cnptia.embrapa.br 2.4.20-42.9.legacysmp i 686 Date and time of compilation : 09/14/2004 11:06:39 Job starting time (YY/MM/DD HH:MM:SS): 2005/04/11 16:50:46.106 Dynamically allocated memory at amaxseq [B,kB,MB]: 69639 68.007 0.066 TOP_________> 2 2 SET SEARCH_RANDOMIZATIONS = 100 TOP_________> 3 3 SET MAXRES = 300 TOP_________> 4 4 SET FILE = 'TvLDH.seq' TOP_________> 5 5 SEQUENCE_SEARCH ALIGN_CODES = 'TvLDH', DATA_FILE = ON Dynamically allocated memory at amaxseq [B,kB,MB]: 614337 599.938 0.586 Dynamically allocated memory at amaxbnd [B,kB,MB]: 32806393 32037.492 31.287 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib//as1.sim.mat rdrrwgh_268_> Number of residue types: 20 openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.seq Searching a list of chains for similarity with a given sequence: Target sequence : TvLDH.seq List of test chains : ${MODINSTALL7v7}/modlib//CHAINS_3.0_40_XN.cod Number of test chains : 0 Residue-residue metric: ${MODINSTALL7v7}/modlib//as1.sim.mat Gap penalties U, V : -900.00 -50.00 Randomizations : 100 +/- range for sig2&3 : 10 SIGNIF_CUTOFF : 4.00 5.00 Top chains are listed : 20 (see the corresponding $MODINSTALL/modlib/seqfilt_*.grp file for more related PDB codes) RELATED_SEQUENCES # CODE_1 CODE_2 LEN1 LEN2 NID %ID %ID SCORE SIGNI SIGNI2 SIGNI3 ----------------------------------------------------------------------------- --- openf5__224_> Open 14 UNKNOWN SEQUENTIAL seqsearch.dat Dynamically allocated memory at finish [B,kB,MB]: 32806393 32037.492 31.287 Starting time : 2005/04/11 16:50:46.106 Closing time : 2005/04/11 16:50:46.882 Total CPU time [seconds] : 0.58 Paula Kuser Falcão Laboratório de Bioinformática Estrutural Embrapa Informática Agropecuária -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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problem!
by vivek sharma 09 Apr '05

09 Apr '05

Dear sir, Please have a look to this error. I made a normal modeller run (7v7) to generate 50 structures for a target sequence of about 500 residues using 3 different templates. But after generating 6 intial structure, it died with this following details, this log file was pretty big in size and contained this detail. I regularly use MODELER , but this a new kind of error I faced, what can be the reason? ---------------------- 25 Phi/Psi pair of dihedral restraints : 1.0000 26 Distance restraints 4 (SDCH-SDCH) : 1.0000 27 Distance restraints 5 (X-Y) : 1.0000 28 NMR distance restraints 6 (X-Y) : 1.0000 29 NMR distance restraints 7 (X-Y) : 1.0000 30 Minimal distance restraints : 1.0000 31 Non-bonded restraints : 1.0000 32 Atomic accessibility restraints : 1.0000 33 Atomic density restraints : 1.0000 34 Absolute position restraints : 1.0000 35 Dihedral angle difference restraints : 1.0000 Initial value of energy before optimization : ---------------- Current energy : ???????????????? Symmetry term within energy : 0.0000 Number of iterations : 200 Number of calls to energy function : 0 Number of updates of dynamic contacts : 5 Number of non-updates of dynamic contacts : 196 Final maximal atomic shift : ???????? TEMPERATURE : 150.000 EQUILIBRATE : 20 EQUILIBRATE : T Seed for the random number generator (RAND_SEED) : 1 Molecular dynamics time step (MD_TIME_STEP) : 4.000 CAP_ATOM_SHIFT : 0.390 Maximal energy, step : ---------------- 0 Minimal energy, step : ???????????????? 200 Average energy, stand.dev. : ???????????????????????????????? Average atomic shift along one axis : ???????? MODEL returned : FINAL ------before this whole log file was filled up with this; -------------- ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? --------------- looks like some bond/bonds has gone too short and that might have affected the energy of system to go out of limits. But how can I found out which bond is that or some details like that? Hoping for a quick reply, Best regards, Vivek -- VIVEK SHARMA HBG BI "I never think of the future - it comes soon enough." A.Einstein

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(no subject)
by Michael Grabe 08 Apr '05

08 Apr '05

dear modellers, i use the BUILD_MODEL command to introduce a mutation into a template structure, but I want to generate different rotomer conformations and get some kind of score for the trial without going through the entire "model" routine. I just want to look at very local rearrangements and not worry about the rest of the protein that is exactly the same. does anyone have any suggestions or test scripts that can help me with this. thanks a lot, michael ------------------------------------------------------------------------ -------------------------- Michael Grabe, Ph.D. HHMI/UCSF Genetics Development & Behavioral Science Building 1550 4th Street, GD 481 San Francisco, CA 94143-0725 tel: ++ 415.476.0421 http://itsa.ucsf.edu/~mgrabe

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Same coordinates
by Joanne Hanna 08 Apr '05

08 Apr '05

Hi I am trying to use modeller to rebuild 5 missing resdiues from a protein that I wish to do some MD on. Whilst I have managed to do this, the x, y and z corrdinates of the modeller output models are all slightly different for each atom for the region of the protein of known structure (i am modelling the sequence against its structure minus the 5 residues). As I was hoping to add to this new complete structure the coordinates of the ligands in the original pdb file, I was wondering if there is any way to define that all the coordinates should be excactly the same as those from the original structure and the only alterations would be the addition of the positions of the 5 'new' residues. Thanks Jo

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question re. Modeller6v2 (re. fold)
by Vicente Reyes 04 Apr '05

04 Apr '05

Dear Dr. Sali & colleagues, I used Modeller6v2 to build 3-D models of some unsolved protein sequences, using as input sequence alignments obtained from the threading program, 123D. Since Modeller performs a partial rfefinement of the structure it builds, do you think it is possible that the fold of the final 3-D structure would be different from the fold of the alignment template found by 123D? Have you seen a case where the fold was altered by the refinement performed by Modeller? How often does this happen and in what particular cases? Thank you very much for your time and your help. Very sincerely yours, V. Reyes ====================================================== >>>>>>>>>>>> VICENTE M. REYES, Ph.D. <<<<<<<<<<<< Dept. of Pharmacol., Sch. of Pharm. & Pharm. Sci., & Integrative Biosci. Dept., S.D. Supercomputer Center Univ. of California-San Diego, La Jolla, CA 92093-0505

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request
by selvaraj manikandan mani 04 Apr '05

04 Apr '05

Respected sir, I have downloaded MODELLER and when I want to use it I could not get the concept like how to get the alignment file and the script file when I went through the manual.I would like to do a modelling of the following sequence: >dmpr MPIKYKPEIQHSDFKDLTNLIHFQSMEGKIWLGEQRMLLLQFSAMASFRREMVNTLG IERAKGLFLRHGYQSGLKDAELARKLRPNASEVGMFLAGPQMHSLKGLVKVRPTELD IDKEYGRFYAEMEWIDSFEVEICQTDLGQMQDPVCWTLLGYACAYSSAFMGREIIFKE VSCRGCGGDKCRVIGKPAEEWDDVASFKQYFKNDPIIEELYELQSQLLSLRTNLDKQE GQYYGIGQTPAYQTVRNMMDKAAQGKVSVLLLGETGVGKEVIARSVHLRSKRAAEPFV AVNCAAIPPDLIESELFGVEKGAFTGATQSRMGRFERADKGTIFLDEVIELSPRAQASL LRVLQEGELERVGDNRTRKIDVRVIAATHEDLAEAVKAGRFRADLYYRLNVFPVAIPAL RERREDIPLLVEHFLQRFHQEYGKRTLGLSDKALEACLHYSWPGNIRELENVIERGIIL TDPNESISVQALFLRAPEEPQTASERVSLDGVLIQPGNGQGSWISQLLSSG LSLDEIEESLMREAMQQANQNVSGAARLLGLSRPALAYRLKKIGIEG and the PDB ID for the templete is 1NY5. Sir,please do help me how can I proceed further.

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TYROSINE KINASE HOMOLOGY MODELLING
by Obdulia Rabal 29 Mar '05

29 Mar '05

Dear modellers, Could anybody advise to me a standard / traditional manner of dealing with domain tyrosine kinase insert (KID) when homology modelling tyrosine kinases? I have looked for some literature but only a pair of references remark this point. Thanks in advance Obdulia

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dear modeller
by arul prakasam 27 Mar '05

27 Mar '05

dear modeller iam modeling a model which has hetero atom FE in it active site the FE is present in my template and in my target.so in order to model my model with hetero atom what should i do. sir in library of atom residue(i.e .,in modlib/restyb.lib) as FE is not found what should i give pdb three and one letter code and CHARMM code. is this process is correct thanking in regards Yahoo! India Matrimony: Find your life partneronline.

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Problem with modeller7v7
by Magali Cottevieille 25 Mar '05

25 Mar '05

Dear Sir, I need your help about a problem I encounter with modeller 7v7 : I have the following error message : Array too small. Increase MANGPF I can't find where I can modify the value of MANGPF !!! Maybe it will be helpful for you to know that I have modified parameter and topology files to add the definitions of a Fe4S4 cluster. Thanks a lot for your help. Best regards, Magali Cottevieille. --------------------------------------------------------------------------------- MODELLER 7v7, Sep 12, 2004 09:15pm PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2004 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, 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 lagaffe.lmcp.jussieu.fr 2.6.10-1.770_FC2 i686 Date and time of compilation : 09/14/2004 11:06:39 Job starting time (YY/MM/DD HH:MM:SS): 2005/03/25 14:53:53.585 rdparf__223E> Array too small. Increase MANGPF current maximum, current need: 600 601 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 77847 76.022 0.074 Starting time : 2005/03/25 14:53:53.585 Closing time : 2005/03/25 14:53:55.735 Total CPU time [seconds] : 1.09 -- Magali COTTEVIEILLE Laboratoire de Minéralogie Cristallographie Paris, Campus BOUCICAUT case 115, 140 Rue de Lourmel 75015 Paris, France. Tel: +33 (0)1 44 27 52 41 Fax: +33 (0)1 44 27 37 85 E-mail : magali.cottevieille(a)lmcp.jussieu.fr URL : http://www.lmcp.jussieu.fr/~cottevie/

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