October 2008 - modeller_usage

dopehr_loopmodel crashed
by Mauricio Carrillo Tripp 17 Nov '08

17 Nov '08

I'm trying to do a loop refinement calculation with the dopehr_loopmodelclass, modeller 9v4. Here's the python script I'm using: from modeller import * from modeller.automodel import * log.verbose() # request verbose output env = environ() # directories for input atom files env.io.atom_files_directory = ['./', 'PDB/'] a = dopehr_loopmodel(env, alnfile='TTN.ali', knowns='2g8gOligo', sequence='1s58', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 1 a.md_level = None # No refinement of model a.loop.starting_model = 1 a.loop.ending_model = 1 a.loop.md_level = refine.fast a.make() After a few hours of running, it stop. Here's the last part of the log: ... randomi_498_> Atoms,selected atoms,random_seed,amplitude: 36972 36056 1 5.0000 randomi_496_> Amplitude is > 0; randomization is done. preppdf_458W> Both Lennard-Jones and statistical potential terms selected. Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 327553569 319876.531 312.379 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 554709537 541708.562 529.012 preppdf_458W> Both Lennard-Jones and statistical potential terms selected. check_inf__E> Atom 31754 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated. >> Summary of successfully produced models: Filename molpdf DOPE score GA341 score ---------------------------------------------------------------------- 1s58.B99990001.pdb 75059.09375 -361379.46875 0.78559 >> Summary of failed loop models: 1s58.BL00010001.pdb check_inf__E> Atom 31754 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated. Dynamically allocated memory at finish [B,KiB,MiB]: 549216697 536344.438 523.774 Starting time : 2008/10/24 10:37:24 Closing time : 2008/10/24 12:51:48 Total CPU time [seconds] : 8018.72 The model part went OK, but when it tried to do the loop refinement it went crazy (the coordinates in1s58.BL00010001.pdb are all messed up). I'm also testing the other two classes (loopmodel and dope_loopmodel) and they've been running for a long while now, so I don't know if they'll work or not. I'd just like to know if I'm doing something wrong or I just ran into some kind of glitch or bug in the dopehr algorithm. Thanks! -- 0 | Mauricio Carrillo Tripp, PhD / | Department of Molecular Biology, TPC6 0 | The Scripps Research Institute \ | 10550 North Torrey Pines Road 0 | La Jolla, California 92037 / | trippm(a)scripps.edu 0 | http://www.scripps.edu/~trippm ** Aut tace aut loquere meliora silentio **

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Re: [modeller_usage] modeling of phosphorylated polypeptide
by Xiao-Ping Zhang 11 Nov '08

11 Nov '08

Dear Alden, Thank you for your reply and your information. My idea is very similar to the idea presented in this nice paper. But the the approaches they used are beyond the limit of my knowledge. I hope some one can implement their results into a public available program (for example, Modeller, PyMol or Deep Viewer). Direct homology modeling of phosphorylated polypeptide may not make any sense if the template used is not phosphorylated because the conformational change. But if a molecular modeling program allows to add the phosphate group on a model (similar to adding S-S bridge in Modeller) followed by MD simulation, the final model could make sense (Groban et al's paper is very encouraging). I noticed that in the topological library of Modeller9v4, there are information for "converting (patching?) tyrosine to monoanionic phosphotyrosine (PRES TP1)", but no information on converting Thr, Ser and Asp. I wonder if any body tried to patch a model from Tyrosine to phosphotyrosine with Modeller. Is there any possibility to implement information for other residues for patching purpose? Is there any other free program which has this functionality? Thank you for your comments and suggestions. Best regards, Xiao-Ping At 02:16 AM 10/29/2008, you wrote: >Perhaps homology modelling is not the best method. This might help: > >http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1440919 > >Best of luck. > >~alden > > >Xiao-Ping Zhang wrote: > > Hi, > > > > Many proteins are phosphorylated in vivo and and the status of their > > phosphorylation correlate to their function. The residues which are > > phosphorylated (Thr, Tyr or Ser) can be determined by mass spectrometry. > > I wonder how to build a phosphorylated model directly or how to apply a > > patch on a model to get a phosphorylated model in Modeller? > > > > Thank you advance for your suggestions. > > > > Xiao-Ping Zhang > > > > > > > > _______________________________________________ > > modeller_usage mailing list > > modeller_usage(a)salilab.org > > https://salilab.org/mailman/listinfo/modeller_usage > > > >

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modeling of phosphorylated polypeptide
by Xiao-Ping Zhang 11 Nov '08

11 Nov '08

Hi, Many proteins are phosphorylated in vivo and and the status of their phosphorylation correlate to their function. The residues which are phosphorylated (Thr, Tyr or Ser) can be determined by mass spectrometry. I wonder how to build a phosphorylated model directly or how to apply a patch on a model to get a phosphorylated model in Modeller? Thank you advance for your suggestions. Xiao-Ping Zhang

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interpolating missing residues
by BIN ZHANG 11 Nov '08

11 Nov '08

Hi, All: I was trying to add missing residues in pdb file according to the page: http://salilab.org/modeller/wiki/Missing%20residues But, one thing I don't understand is how can I get the "alignment.ali" file? Aslo, it seems to me the command complete_pdb() can also do the job? http://salilab.org/modeller/manual/node403.html Is this true? If so, what's the difference between these 2? Thanks a lot. Bin ------------------------------------------------------------- The tree of liberty must be refreshed from time to time with the blood of patriots and tyrants.

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automodel vs loopmodel
by Mauricio Carrillo Tripp 11 Nov '08

11 Nov '08

When I run the automodel or the loopmodel classes, either way I get a target.B99990001.pdb for the structure of the final model. From the documentation, I understand that in the case of the loopmodel, an extra pdb file will be produced with refined loops. My question is: Should the models in files target.B99990001.pdb be the same whether I use automodel or loopmodel? (provided I'm using the same optimizations and all, I'm just changing the class name in the python script) Thanks! -- 0 | Mauricio Carrillo Tripp, PhD / | Department of Molecular Biology, TPC6 0 | The Scripps Research Institute \ | 10550 North Torrey Pines Road 0 | La Jolla, California 92037 / | trippm(a)scripps.edu 0 | http://www.scripps.edu/~trippm ** Aut tace aut loquere meliora silentio **

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adding two residues of different peptides
by prasun kumar 11 Nov '08

11 Nov '08

Dear users, There is a PATCH for adding sulfide bridge among two sulfur atom in a peptide.Can we use this concept for adding two residues of two different peptides at a certain angle........... please give me some suggestions thanx in advance -- PRASUN (ASHOKA)

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adding two proteins
by prasun kumar 11 Nov '08

11 Nov '08

Dear users, I am trying to add two proteins by means of making bond between the residues of both the proteins.Can we do this using modeller. this question came into my mind because of the DISULFIDE bond that we can make using modeller. if there is any method then please help me thanx in advance -- PRASUN (ASHOKA)

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keeping original residue numbers in final model
by Mauricio Carrillo Tripp 11 Nov '08

11 Nov '08

Hi, I'm new in Modeller (9v4) and I haven't been able to find an answer to the following question anywhere I've looked: Is there a way to keep the original target's residue numbering in the final model instead of having them sequentially numbered starting at 1? As an example, this is my target's sequence (NOTE: "-" are not gaps, are missing/unknown residues): >P1;1s58 SEQUENCE:1s58.ali : 19 :A: 554 :A:::0.00:0.00 ------------------NPVKSMWSEGATFSANSVTCTFSRQFLIPYDP EHHYKVFSPAASSCHNASGKEAKVCTITPIMGYSTPWRYLDFNALNLFFS PLEFQHLIENYGSIAPDALTVTISEIAVKDVTDKTGGGVQVTDSATGRLC MLVDHEYKYPYVLGQGQDTLAPELPIWVYFPPQYAYLTVGDVNTQGISGD SKKLASEESAFYVLEHSSFQLLGTGGTATMSYKFPPVPPENLEGCSQHFY EMYNPLYGSRLGVPDTLGGDPKFRSLTHEDHAIQPQNFMPGPLVNSVSTK -------------TGLSTGTSQNTRISLRPGPVSQPYHHWDTDKYVTGIN AISHGQTTYGNAEDKEYQQGVGRFPNEKEQLKQLQGLNMHTYFPNKGTQQ YTDQIERPLMVGSVWNRRALHYESQLWSKIPNLDDSFKTQFAALGGWGLH QPPPQIFLKILPQSGPIGGIKSMGITTLVQYAVGIMTVTMTFKLGPRKAT GRWNPQPGVYPPHAAGHLPYVLYDPTATDAKQHHRHGYEKPEELWTAKSR VHPL * The final model's PDB starts with residue number 1 and ends with residue number 523 (number of residues in the sequence). What I would like to get is a model's PDB starting at residue 19, jumping from residue 300 to residue 314 and so, ending at residue 554. Thanks in advance for any pointers! -- 0 | Mauricio Carrillo Tripp, PhD / | Department of Molecular Biology, TPC6 0 | The Scripps Research Institute \ | 10550 North Torrey Pines Road 0 | La Jolla, California 92037 / | trippm(a)scripps.edu 0 | http://www.scripps.edu/~trippm ** Aut tace aut loquere meliora silentio **

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to build ions
by vidhya ganesh 11 Nov '08

11 Nov '08

Hi, I am new to modeller. I am using mod9v4. I have quite few doubts. I performed homology modeling of particular protein , done all steps and got a model. But i have to know, how to build ions in my model?? Thanks Best Regards vidhya

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How to change directory path for atom files
by khuram sb 11 Nov '08

11 Nov '08

Hi, I want to ask that when modeller directory (Work Station) is changed from C directory (default) than how path of atom files is changed? I want to know the whole procedure of changing directories and giving the right path for atom files. Thanks, Khramsb

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