- modeller_usage - salilab.org

windows problem?
by Jaimin Shah 16 Jan '04

16 Jan '04

Dear all, A colleague of mine ran the same .TOP file in a Linux PC and it worked. As I am more conversant with Windows, please let me know what problem could be there that disables me from getting models (the problem previously posted)in it, i.e, it hangs at: openf5__224_> Open 11 OLD SEQUENTIAL galk.rsr openf5__224_> Open 11 OLD SEQUENTIAL galk.rsr Sincerely, Jaimin Shah M.Sc. (Biotechnology) I.I.T. Powai

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Can MODELLER use temperature B-factors?
by Karsten Suhre 16 Jan '04

16 Jan '04

Dear all, I have a simple question : Can MODELLER use the B-factors of in the template structures, e.g. to modify the weight given to different constrains? Thank you very much, Karsten (IGS-CNRS, Marseille, France).

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by nick jones 15 Jan '04

15 Jan '04

I have a problem with modeller. Ehen I input the command: C:\mod6v2\bin\mod.bat model-default.top in the ms dos prompt, by the file not found it says alignment.top How do I fix this and what does it mean? Sincerely --------------------------------- Do you Yahoo!? New Yahoo! Photos - easier uploading and sharing

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kindly suggest
by Jaimin Shah 15 Jan '04

15 Jan '04

I encounter the following problem once I execute a TOP file using Modeller: Dynamically allocated memory at amprmcns [B,kB,MB]: 17981749 17560. 301 17.149 openf5__224_> Open 11 OLD SEQUENTIAL galk.rsr openf5__224_> Open 11 OLD SEQUENTIAL galk.rsr It gets stuck here. (galk is my target sequence.) ps: I am looking forward to constructing a no. of models as soon as possible. Thankfully, Jaimin Shah M.Sc. (Biotechnology) I.I.T. Powai

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confused
by Jaimin Shah 14 Jan '04

14 Jan '04

Upon executing the MAKE_RESTRAINTS command, the following is displayed: >> ENERGY; Differences between the model's features and restraints: preppdf_449W> No atoms selected; no restraints will be selected. preppdf_450E> Probably because no MODEL is in memory; use READ_MODEL. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Upon executing the READ_MODEL command, I receive the following: iatmcls_286W> MODEL atom not classified: LEU:OT1 LEU Please give your suggestions. Thanking you, Jaimin Shah M.Sc. (Biotechnology) I.I.T. Powai

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a new hurdle-plz correct
by Jaimin Shah 14 Jan '04

14 Jan '04

Thanking the team for all the help so far. I am encounter a new problem: openf5__224_> Open 11 OLD SEQUENTIAL galk.rsr openf5__224_> Open 11 OLD SEQUENTIAL galk.rsr It gets stuck here. No progress is made from here on. I have to forcibly turn the program off. With regards, Jaimin Shah M.Sc. (Biotechnology) I.I.T. Powai

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structure not read in
by Jaimin Shah 13 Jan '04

13 Jan '04

Dear Sir, I am a novice for this program. I would really appreciate it if you can expedite matters for me by solving my hurdles. I am getting the message: check_a_343_> >> BEGINNING OF COMMAND check_a_337E> Structure not read in: 1 1 Thanking you, Sincerely, Jaimin Shah M.Sc. (Biotechnology) I.I.T. Powai

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set restraints violations directory
by Antoine Leimgruber 09 Jan '04

09 Jan '04

Hello, I use this kind of commands in my top files. SET DIRECTORY = 'path_to_topfile' SET ATOM_FILES_DIRECTORY = 'path_to_topfile' SET OUTPUT_DIRECTORY = 'path_to_topfile' However, all the *.V* files are generated in the directory where the perl script launching modeller is and not in the directory where the top file actually is. What is the equivalent for these files ? Thanks in advance, Antoine

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loop modelling
by nurul bahiyah 08 Jan '04

08 Jan '04

i need help on loop prediction, templates for loop regions can be found by scanning the whole PDB for segments that fit on the two core regions spanning the loop right, my question is.. how would i do that, i would like to try scanning the PDB for loop regions, but i dont know how..

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Fwd: FW: Modeller
by Modeller Caretaker 05 Jan '04

05 Jan '04

----- Forwarded message from David Farrell <farrelld(a)ohsu.edu> ----- Dear Dr. Sali, I need some advice on some molecular modeling experiments. We have a fibrinogen peptide, VRPEHPAETEY(SO3)DSLY(SO3)PEDDL, which binds to thrombin exosite II, and we would like to use "Dock" to get an idea of the contacts between the peptide and thrombin. The problem is that although there are many solved crystal structures for thrombin, there is no published structure for the peptide. Could Modeller give predictions for the conformation of the peptide that we could then use in Dock? Or is it more likely that this short peptide is mostly a random coil that assumes an induced-fit conformation upon binding to thrombin? If so, is there any other approach to predict the structure of the bound peptide in silico? Sincerely, David Farrell David H Farrell, PhD Associate Professor Dept of Pathology, L113 Oregon Health & Science University 3181 SW Sam Jackson Park Rd Portland, OR 97239 503-494-8602 503-494-2025 FAX E-mail: farrelld(a)ohsu.edu http://www.ohsu.edu/pathology/FacultyOHSUFarrell.htm ----- End forwarded message -----

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