June 2005 - modeller_usage

Some theoretical questions
by Dmitry Osolodkin 30 Jun '05

30 Jun '05

Dear colleagues, I recently started working with Modeller8v0, so I have some questions about the authenticity of the models which I get. First of all, if I use optimisation of my structure (exactly as described in Manual section 1.8.7.), do I need to minimise this system, for example, in Sybyl to get better model? Or the model which I get is good enough for using it without any further optimisation such as energy minimisation or molecular dynamics? Second, Modeller can build number of models by one script. For what can it be useful? And is there any difference between obtained models? What's the reason for such a difference? Third, is modelling of homomeric protein using the heteromeric template authentical? All subunits of heteromer have the same folding as my homomer and are homologous to my protein. Or can I build a model of one subunit of my protein using the best template subunit and then build a pentamer using the symmetry operations (rotation about C5 axis)? Is there such feature in Modeller? Hope for help, Dmitry Osolodkin.

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Re: [modeller_usage] Terminal patching (acetylation/amidation) in Modeller 7.7
by Modeller Caretaker 27 Jun '05

27 Jun '05

"Niels Johan Christensen" <s991418(a)student.dtu.dk> wrote: > A good deal of my previous work (calculation of various electronic > properties) is based on structures from non terminal patched MODELLER > 7.7 models. To be consistent, I would like to introduce the terminal > acetylation/amidation with MODELLER 7.7 and subsequently calculate > properties for (fragments of) these models. > > (Regarding "consistency", I am mainly considering the fact that I get > slightly different models from versions 7.7 and 8.1 despite using the > same template/sequence. The only difference in the input conditions, > is that in the former case I use TOP scipting while in the latter I > use Python.) Your reasoning is incorrect; the difference between Modeller 7v7 and 8v1 is that they were built with different Fortran compiler versions. Over time, the way the compiler vendors optimize code (e.g. the ordering of floating point operations) leads to very small changes in the results. You'll also notice that if you build models on a Windows machine, for example, that they'll differ from those built on a Linux box, for the same reason. The Python and TOP interfaces to Modeller give the same results (for equivalent scripts, on the same machine and Modeller version) and in fact are tested precisely to ensure this. Your script doesn't work in Modeller 7v7 because the patch residue CT2 in ${LIB}/top_heav.lib incorrectly adds hydrogens. This was one of the bugs fixed in Modeller 8v1. You can fix it yourself by comparing the top_heav.lib file from the two versions, and correcting the 7v7 copy. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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NOC 2.0 released
by Chenmengen 27 Jun '05

27 Jun '05

http://noc.ibp.ac.cn New features: Structure factors calculation and R factor validation Electron density synthesis MTZ(CCP4 format),CIF(PDB format),CV(CNS format)reflection data parsing Interface to RCSB PDB bug fixed: CCP4 format Map parsing Picture output Side-chain map-fitting

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no alignment
by Arnout Voet 26 Jun '05

26 Jun '05

dear modellers i am just starting with modeller and i want to make a model using different templates i have my template files, i have the sequence aligned and checked manually but the program gives me an error File "C:\Program Files\Modeller8v1\modlib\modeller\util\top.py", line 37, in check_alignment return _modeller.check_alignment(aln, io, libs, *args) modeller.error: check_a_335E> No alignment. i guess automodel does not like my aligment (although i only want this alignment) could someone please tell me how to cut out the alligment and only use the aligment i have (i have my templates as a pdb (6 different) and i have my aligment in the regular file format (file.ali) kind regards arnout voet

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Re: [modeller_usage] problem!
by vivek sharma 26 Jun '05

26 Jun '05

Hello Benn, > > -------------------------- > > > > 1536 637 READ_TOPOLOGY FILE = TOPLIB > > > > openf5__224_> Open 11 OLD SEQUENTIAL > > ${MODINSTALL7v7}/modlib//top_heav.lib > > read_to_241E> Residue type defined multiple times: ALA > > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > Two possibilities: either your top_heav.lib file really does have ALA > defined multiple times, or you set ADD_TOPOLOGY to 'on' at some point > (it should be set to 'off'). If it isn't either of these, then I'd have > to see your input files to figure out what the problem is. Thanks, problem was: I was using the ADD_TOPOLOGY = 'on', although I needed to, but made few changes and it works fine. > > P.S. Please consider using a more descriptive subject for your mails > rather than "problem!" every time. ;) No problem!, there will be no 'problem' after this, this is the last time. ;-) Regards, Vivek -- VIVEK SHARMA HBG BI "Basic research is what I'm doing when I don't know what I'm doing." - Werner von Braun

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problem!
by vivek sharma 25 Jun '05

25 Jun '05

Dear Ben, I am regular user of MODELLER, I am still using 7v7 as I dont know Python much. I suddenly got an strange error while I was doing the loop modelling, I couldnt found any such previous email too which is in concern to this, so I need you help/comments in this concern. The whole structures are generated normally but when loop modelling procedure starts, it stops with following error. -------------------------- 1536 637 READ_TOPOLOGY FILE = TOPLIB openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib//top_heav.lib read_to_241E> Residue type defined multiple times: ALA recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 52416487 51187.977 49.988 Starting time : 2005/06/25 09:49:26.337 Closing time : 2005/06/25 10:44:12.188 -------------------------- I dont see any such multiple definition of ALA residue in my top_heav.lib file. Although the same top_heav file was read finely by program when it began generating topology. PLease place your comments. Regards, Vivek Sharma -- VIVEK SHARMA HBG BI "Basic research is what I'm doing when I don't know what I'm doing." - Werner von Braun

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violation of restraints
by Marsita M 25 Jun '05

25 Jun '05

hello everybody i'm a new user and i just would like to know, is there any units for the violation restraints? ( i calculated the total of the violations, and i just wondering if there is any units for that? ) thank you _________________________________________________________________ Undgå pop-ups med MSN Toolbar - http://toolbar.msn.dk hent den gratis!

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Incorrect Topology library?
by Jeff Bush 24 Jun '05

24 Jun '05

Hello Experienced Modeller users, I am wondering if anyone has seen the following error message and has any idea what I need to do to fix the problem. I have seen this question asked before while searching the archives. It was asked previously in 2003 by Seth Goldenberg, but I do not see a response in the archives. Perhaps someone replied directly to this gentleman. I would certainly be very appreciative of any help you might provide. Error Message Follows. Thanks, Jeff Bush TOP_________> 132 89 READ_TOPOLOGY FILE = TOPLIB openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib//top_heav.lib openf5__224_> Open 11 UNKNOWN SEQUENTIAL ${MODINSTALL7v7}/modlib/models.lib TOP_________> 133 90 READ_PARAMETERS FILE = PARLIB openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib//par.lib Dynamically allocated memory at amattacns [B,kB,MB]: 6138979 5995.097 5.855 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib//par.lib rdparf__232_> parameters BONDS ANGLS DIHEDS IMPROPS MRFP MODE 227 561 661 112 0 0 TOP_________> 134 91 CALL ROUTINE = 'create_topology' TOP_________> 135 106 GENERATE_TOPOLOGY ADD_SEQUENCE = OFF act54___590E> No topology generated for sequence: Lk Possibly because incorrect topology library is used. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1

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Terminal patching (acetylation/amidation) in Modeller 7.7
by Niels Johan Christensen 24 Jun '05

24 Jun '05

Dear all, First of all, thanks to Ben Webb for answering my question regarding acetylation in MODELLER 8.1. Now, I would like to do the same thing in MODELLER 7.7, but mod7v7.exe error terminates when I run my script. I have included my script and excerpt from the .log file below. It is rather peculiar that the .log says: ''Atom index is out of bounds: 708 706'', since these indices are indeed present in the .ini file. What goes wrong? Thank you. Best Regards, Niels Johan Christensen >>> My script <<< ------------------------------------------------------ INCLUDE SET PATCH_DEFAULT = off SET ALNFILE = 'VaLd-TRIL16C-HAND.PIR' SET KNOWNS = 'merged.pdb' SET SEQUENCE = 'TRIL16C' SET STARTING_MODEL = 1 SET ENDING_MODEL = 5 CALL ROUTINE = 'model' STOP SUBROUTINE ROUTINE = 'special_patches' PATCH RESIDUE_TYPE='ACE', RESIDUE_IDS='1:' PATCH RESIDUE_TYPE='CT2', RESIDUE_IDS='30:' RETURN END_SUBROUTINE ------------------------------------------------------- >>> The .LOG file <<<< getprog_531W> ROUTINE redefined: special_patches check_ali___> Checking the sequence-structure alignment. Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- END OF TABLE delete__443_> Restraints marked for deletion were removed. Total number of restraints before, now: 6869 6678 csrrng__299E> Atom index is out of bounds: 708 706 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1

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Re: your message in Modeller user list.
by Ezequiel H Panepucci 24 Jun '05

24 Jun '05

drugdesign wrote: > Dear Ezequiel, > I've read your message in Modeller user list. I have similar problems on Suse 9.2 and also on Windows 2000. Have you solved these problems? > What was the cause of the problems? I had copied only the subdirectory automodel/ therefore all example data was missing and the program crashed instead of indicating "file not found". it is a bug which is fixed in the latest release. the problem could also happen due to stacksize limits, use "limit stacksize unlimited" if this is the case Zac > Respectively yours, > Adnrew Voronkov > > > I've recently installed Modeller 8v0 on Linux (Centos 4 which is derived from Redhat Enterprise Linux 4) and it is giving me a hard time. > > Below is what happens running examples/automodel/model-default.py. > > It happens using both the *tar.gz or *rpm installs. > > It gives similiar problems on Redhat 9 as well. > > > $ mod8v0 model-default.py > forrtl: severe (174): SIGSEGV, segmentation fault occurred > > Image PC Routine Line Source > libc.so.6 009F6B3D Unknown Unknown Unknown > mod8v0_i386-intel 0812A85D Unknown Unknown Unknown > mod8v0_i386-intel 08106CC8 Unknown Unknown Unknown > mod8v0_i386-intel 082A6647 Unknown Unknown Unknown > mod8v0_i386-intel 082A7E0A Unknown Unknown Unknown > mod8v0_i386-intel 082ED02E Unknown Unknown Unknown > mod8v0_i386-intel 08258A54 Unknown Unknown Unknown > mod8v0_i386-intel 082A5252 Unknown Unknown Unknown > mod8v0_i386-intel 082A7E0A Unknown Unknown Unknown > mod8v0_i386-intel 082A5ECD Unknown Unknown Unknown > mod8v0_i386-intel 082A7628 Unknown Unknown Unknown > mod8v0_i386-intel 082A7E0A Unknown Unknown Unknown > mod8v0_i386-intel 082A5ECD Unknown Unknown Unknown > mod8v0_i386-intel 082A7E0A Unknown Unknown Unknown > mod8v0_i386-intel 082A7FB6 Unknown Unknown Unknown > mod8v0_i386-intel 082C9800 Unknown Unknown Unknown > mod8v0_i386-intel 082CA0E6 Unknown Unknown Unknown > mod8v0_i386-intel 082CB1EB Unknown Unknown Unknown > mod8v0_i386-intel 080D40A7 Unknown Unknown Unknown > mod8v0_i386-intel 08076E94 Unknown Unknown Unknown > mod8v0_i386-intel 08076B2D Unknown Unknown Unknown > libc.so.6 009A1E33 Unknown Unknown Unknown > mod8v0_i386-intel 080769C1 Unknown Unknown Unknown > > -- Ezequiel PANEPUCCI, Ph.D. - Institut Pasteur Plate-Forme 6 - Cristallogénèse et Diffraction des Rayons X Telephone: +33 (0)1.4061.3930 Portable: +33 (0)6.1314.3906

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