- modeller_usage - salilab.org

error on hetatm modelling
by V Nadeem Ahmad 26 Aug '04

26 Aug '04

Dear Modeller, I was trying to do modelling with hetatm .it stopped after running a while can anyone help me where was the mistake. ## the top file is INCLUDE # Include the predefined TOP routines SET ALNFILE = 'align.pir' , KNOWNS= '1a57', SEQUENCE = 'seq' SET MODEL_TOPOLOGY = 1, HYDROGEN_IO = on, HETATM_IO = on, WATER_IO = on SET TOPOLOGY_LIBRARY = $(LIBS_LIB6V2)/top.lib SET PARAMETERS_LIBRARY = $(LIBS_LIB6v2)/par.lib CALL ROUTINE = 'model' # do homology modelli ----------------- the log file --------------------- assgn___544E> Variable name not recognized: MODEL_TOPOLOGY Command line: SET MODEL_TOPOLOGY = 1, HYDROGEN_IO = ON, HETATM_IO = ON, WATER_IO = ON assgn___525E> Error in TOP variable assignment. assgn___544E> Variable name not recognized: TOPOLOGY_LIBRARY Command line: SET TOPOLOGY_LIBRARY = $(LIBS_LIB6V2)/TOP.LIB assgn___525E> Error in TOP variable assignment. assgn___544E> Variable name not recognized: PARAMETERS_LIBRARY Command line: SET PARAMETERS_LIBRARY = $(LIBS_LIB6V2)/PAR.LIB assgn___525E> Error in TOP variable assignment. compile_563E> Please correct the errors reported above and rerun MODELLER. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 with regards Nadeem Ahmad

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A word on beta (strand) restraints
by Modeller Caretaker 25 Aug '04

25 Aug '04

A few queries have come up over time on how to get Modeller to restrain the model to an idealized beta strand, so here's a quick summary. See http://salilab.org/modeller/FAQ6v2.html#19 for information on how to specify secondary structure, including the 'STRAND' restraint type. This adds additional restraints to those derived from the homology. See http://salilab.org/modeller/manual6v2/node100.html for a description of the types of restraints added for secondary structure. In summary, both alpha and strand restraints add phi-psi restraints to force residue mainchain conformation into class A (for helices) or B/P (for strands). See modlib/mnch.lib for the representative dihedral angles of these classes. Note that Modeller attempts to fulfil all restraints, but violations will often occur, particularly when conflicts between user-defined and homology-derived restraints are present. This is less of a problem with helix restraints than with strands, as helix restraints enforce a number of distance restraints in addition to the phi-psi restraints, and so are in a sense 'stronger'. There is a bug in Modeller 6v2's generation of beta restraints; it generates phi-phi restraints rather than the correct phi-psi restraints. To correct this, take the .rsr file generated by Modeller. At the end of this file should be some lines similar to the following for your beta restraints (the following should be all on one line): R 9 1 4 25 8 6 0 327 329 330 332 327 329 330 332 1.0000 -2.3387 2.5656 0.5271 0.3072 -0.6670 Notice that the atom indices for the phi dihedral angle (columns 9 through 12, 327 329 330 332) are the same as those for what should be psi, columns 13 through 16. Correct the atom indices for psi, write out the new .rsr file, and then use the recipe in http://salilab.org/modeller/FAQ6v2.html#11 to override Modeller's restraints with your corrected ones. If in doubt about the atom indices, defining a helix restraint on the same residue range should yield the correct values (the bug is only for strand restraints). This bug is fixed in Modeller 7, which should be released in a few weeks. Until then, apologies for the workaround! Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mailing list: http://salilab.org/mailman/listinfo/modeller_usage

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problem_2
by vivek sharma 25 Aug '04

25 Aug '04

Sir, The MAPRES problem is solved , I needed to remove some atoms from the topology file to bring number less than 100 (which is hard coded value = 100). The heme molecules like heme a and heme o , contains more than 100 atomtypes (if hydrogens are included) and MAPRES limit is crossed in this case, but without Hydrogens being counted it goes pretty well. As in your topology file you have given MASS values of some Hydrogens while in in RESI types you didn't mentioned Hydrogens, why this is so? PLease clarify. Now, I have another problem: Running modeler gives such warnings: -------------- iatmcls_286W> MODEL atom not classified: HEB:FE HEB iatmcls_286W> MODEL atom not classified: HEB:NA HEB -------------- why this is so? and finally it stops due to the following error: -------------- nselat__596E> Atom index is out of range (iatm,natm): 4338 4337 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 -------------- what can be the reason for this reason ? please provide a solution to this problem. Thanks in advance. sincerely, vivek -- VIVEK SHARMA HBG BI

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problem
by vivek sharma 23 Aug '04

23 Aug '04

Dear Modeler man, I have one problem in Modeler, it would be great if you can tell me the solution. Actually, I have included few big residues in TOP_HEAV(many atoms) library of Modeler and made changes everywhere required. It shows the following error; --------------------- penf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//top_heav.lib read_to_223E> Array too small. Increase MAPRES current maximum, current need: 100 101 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 --------------------- what is the reason? Where I can get this variable MAPRES to change? I also tried to remove some residues from TOP_HEAV library but it didn't worked out, removing residues in such a way appears a bit strange, so please suggest a different solution if available. Also, as I have changed TOP_HEAV, restyp.lib is also needed to be changed or not, but as error suggest some problem in TOP_HEAV only? please suggest some solution. thanks in advance, best, vivek -- VIVEK SHARMA HBG BI

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Hetatm error
by Shamshad Zarina 23 Aug '04

23 Aug '04

Dear Modeller users, I am facing a strange problem recently. I use linux version of modeller 6v2. I am trying to add NADP molecule to my protein. NADP is a part of template file and models are prepared without any problem. However, in one protein, one bond in NADP was missing in the final model file which was present in template. Another protein showed an oxygen atom in the vicinity of NADP without any bonds. There were no errors reported. I wonder where the actual bonds have gone. Any ideas? Best, Shamshad __________________________________ Do you Yahoo!? Yahoo! Mail is new and improved - Check it out! http://promotions.yahoo.com/new_mail

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very low sequence identity...
by limnoha 21 Aug '04

21 Aug '04

I did a sequence-search but the signi scores of sequences were very low(below 4). How can I select the template among these sequences? Do you have any other method to do modelling a target like this? Do you have any example about this situation? Please help me... Thank you!!

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few minute problems
by vivek sharma 11 Aug '04

11 Aug '04

Dear modeller people, these questions be a immature to ask as I don't know the complete algorithm, but as they came to my mind, so they are as follows; 1. If only optimization of molecular pdf is performed , not the molecular dynamics simulation, will there still be violations and if so then why, as molecular pdf optimization must keep all features in limits? 2. Is there any feature , which comes under category of both stereochemical as well as homology derived restraints? If then will that be optimized separately for both? best regards -- VIVEK SHARMA

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Does Modeller work on x86_64?
by benne278 02 Aug '04

02 Aug '04

Has anyone used modeller successfully on an Intel x86_64 system? I am trying to use 6v2 on a 3.4 GHz machine running RedHat Enterprise 3 and Modeller seg-faults even on the supplied example jobs. My actual jobs crash too, of course, and they run fine on a PIII Linux system I have access to. So either my system is not configured correctly or there is a problem running on x86_64. Are there any libraries I should check, or any other issues I should be aware of for running on x86_64? The examples do this: [bennette@localhost examples]$ ./Run_tests DIR: ./align-model-steps /HOME/software/modeller/bin/mod6v2: line 38: 13124 Segmentation fault (core dumped) $NICE ${EXECUTABLE} $STEERF >$LOGF DIR: ./all-steps /HOME/software/modeller/bin/mod6v2: line 38: 13132 Segmentation fault (core dumped) $NICE ${EXECUTABLE} $STEERF >$LOGF STOP ... etc. ... The log file for my job shows that the program doesn't report any errors, it just dies after saying it is calculating distance restraints: http://abacavir.pharmacy.umn.edu/~bennette/modeller/model-default.log.txt Thanks for any suggestions, Dr. Eric Bennett Center for Drug Design University of Minnesota

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RE: [modeller_usage] More Doubts
by Cesar Avila 30 Jul '04

30 Jul '04

>I'm trying to model another protein (HSP) and I'm having trouble again. >Please look the second line of my alignment file >structureX:1uy7:2:A:236:A:::-1.00:-1.00 Dear Elton, I have seen your log messages and downloaded the pdb file to test it on my PC. It seems that you have the same problem I had some time ago. The problem appears when there are missing atoms in the structure. If you see the REMARKS section at the pdb file you will get a complete list of missing atoms in the model. You have to delete these from the alignment files, so modeller can match the residues in the alignment with the ones in the pdb file. Replace the missing residues with gaps in the alignment and you will be able to continue with your work. You have to note also that you will have to modify the second line of the alignment since the first residue in the structure is 16:A, not 2A. I hope you solve your problem. Best regards, Cesar Avila Universidad Nacional de Tucuman Argentina ___________________________________________________________ 100mb gratis, Antivirus y Antispam Correo Yahoo!, el mejor correo web del mundo http://correo.yahoo.com.ar

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Loop refinement and symmetry
by David Piper 29 Jul '04

29 Jul '04

Modellers, When refining loops, can symmetry restraints be included also? For instance, if I have a tetrameric model protein and want to model a ~15 residue loop, constrain a portion of that loop to an alpha helix, and maintain tetrameric symmetry, can I simply add the special_restraints one would use for secondary structure and symmetry after the loop definition? I tried that approach and the resulting PDB file has absurdly bizarre dihdrals etc. Attached is an example of the .top file I tried. Any insight would be appreciated, thanks, David Piper

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