- modeller_usage - salilab.org

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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help!
by nick jones 05 Jan '04

05 Jan '04

I have a problem with modeller. I am new to the program and I couldnt find a manual for modeller usage in a command prompt. If anyone has a manual for modeller usage in MS-DOS command prompt or knows how to open pdb files from it please help! --------------------------------- Do you Yahoo!? New Yahoo! Photos - easier uploading and sharing

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Gaps in pdb file
by MacFarlane, Amanda J. 22 Dec '03

22 Dec '03

Dear Modellers, I'm relatively new to Modeller, and I have a question which I hope has an easy answer. Whenever the pdb file for a solved structure has a gap in the residue numbers (so, for instance, it jumps from residue 300 to 315), I get an error saying that the number of residues in the alignment file and the pdb file are different. How can I fix this problem? Thanks! Amanda MacFarlane Amanda MacFarlane Autoimmune Disease Group/Diabetes Ottawa Health Research Institute Lab N1 Box 221 501 Smyth Road Ottawa ON K1S 5B7

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About rotamers ?
by Mickael Krzeminski 18 Dec '03

18 Dec '03

Hi! I have never read something about rotamers... I would like to know wether MODELLER6v2 cares about rotamers ? And if yes, what method (I should say 'library') is used in this case ? Best resgards, Mickaël

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simple question
by Michael Grabe 15 Dec '03

15 Dec '03

dear modellers, I want to make a 3 A harmonic distance restraint between these two atoms: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ATOM 464 CD GLU 56 -7.029 6.474 8.483 1.00130.43 1SG 465 ...... ATOM 545 CZ ARG 66 -13.040 -0.756 16.131 1.00255.28 1SG 546 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% But for the life of me, I can't get the syntax right inside the special_restraints subroutine. Can someone help me out? -Michael ------------------------------------------------------------------------ -------------------------- Michael Grabe, Ph.D. Post-doctoral Fellow Howard Hughes Medical Institute University of California, San Francisco 533 Parnassus Ave. San Francisco, CA 94143 mgrabe(a)itsa.ucsf.edu tel: ++ 415.476.6585 http://itsa.ucsf.edu/~mgrabe

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Max templates
by Jenny.Carmichael＠csiro.au 14 Dec '03

14 Dec '03

Dear modellers, Just a quick question, is there a maximum number of templates that it is possible to use, say 40, 50 or 60 for example, derived from NMR structure files. JennyC

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online interface
by rathankar rao 04 Dec '03

04 Dec '03

hi 1. are there any commands to check the intermolecular contacts incase of a macromolecule.plz explain. if webinterface is present plz give the URL 2. DOES Modeller has online interface N.Rathankar Assistant Proffessor in physics Madanapalle Institute of Technological Sciences (MITS). INDIA WEBSITE: http://www.geocities.com/rathankar/ --------------------------------- Do you Yahoo!? Free Pop-Up Blocker - Get it now

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Re: [modeller_usage] Upper limit distance restraint
by Thorsten Schweikardt 04 Dec '03

04 Dec '03

Hello Miha, you have to include a user distance-restraint, the concerning chapter in the manual about these restraints and the parameters used is named "2.5 Calculation of spatial restraints". There is also the FAQ at http://salilab.org/modeller/FAQ.html, open it and look for "I want to add my own restraints". This is an example (to be inserted in your .top file): ... [rest of your .top-file...] CALL ROUTINE = 'model' SUBROUTINE ROUTINE = 'special_restraints' SET ATOM_IDS = 'CA:25' 'CA:187' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 10.0 1.0 SET ADD_RESTRAINTS = off RETURN END_SUBROUTINE I hope this helps you getting started. Best wishes and happy modelling, Thorsten Schweikardt Molecular Biophysics Mainz, Germany > > -----Ursprüngliche Nachricht----- > > Von: Miha Pavsic [mailto:miha.pavsic@ijs.si] > > Gesendet: Mittwoch, 3. Dezember 2003 10:54 > > An: modeller_usage(a)salilab.org > > Betreff: [modeller_usage] Upper limit distance restraint > > > > > > Hello Modeller users, > > > > I am looking for a way to specify upper limit distance restraint > > between CA atoms of two residues (eg., max 10 A between CA:25 and > > CA:187). Can someone please give me an example of doing this? > > > > Regards, > > Miha Pavsic > > >

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RE: [modeller_usage] GTP RTF
by Eswar Narayanan 03 Dec '03

03 Dec '03

It's a modified version of CHARMM-22 for the topology libraries. Eswar. --- Eswar Narayanan, Ph.D Mission Bay Genentech Hall 600 16th Street, Suite N474Q University of California, San Francisco San Francisco, CA 94143-2240 (CA 94158 for courier) Tel +1 (415) 514-4233; Fax +1 (415) 514-4231 http://www.salilab.org/~eashwar > -----Original Message----- > From: devary(a)jct.ac.il [mailto:devary@jct.ac.il] > Sent: Wednesday, December 03, 2003 10:28 AM > To: Eswar Narayanan > Subject: RE: [modeller_usage] GTP RTF > > thank you for the help please tell me which version of charmm > modeller is using > yoram > > > Quoting Eswar Narayanan <eashwar(a)salilab.org>: > > > Please check $MODINSTALLXvX/modlib/top_heav.lib. > > > > Best > > Eswar. > > > > --- > > Eswar Narayanan, Ph.D > > Mission Bay Genentech Hall > > 600 16th Street, Suite N474Q > > University of California, San Francisco > > San Francisco, CA 94143-2240 (CA 94158 for courier) > > Tel +1 (415) 514-4233; Fax +1 (415) 514-4231 > > http://www.salilab.org/~eashwar > > > > > -----Original Message----- > > > From: modeller_usage-bounces(a)salilab.org [mailto:modeller_usage- > > > bounces(a)salilab.org] On Behalf Of devary(a)jct.ac.il > > > Sent: Wednesday, December 03, 2003 12:26 AM > > > To: modeller_usage(a)salilab.org > > > Subject: [modeller_usage] GTP RTF > > > > > > Dear Sir I am trying to build a model with GTP can you pls > > > tell were can I find parameters for GTP or you have it somewhere > > > yoram > > > > > > _______________________________________________ > > > modeller_usage mailing list > > > modeller_usage(a)salilab.org > > > http://salilab.org/mailman/listinfo/modeller_usage > > > > _______________________________________________ > > modeller_usage mailing list > > modeller_usage(a)salilab.org > > http://salilab.org/mailman/listinfo/modeller_usage > >

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GTP RTF
by devary＠jct.ac.il 03 Dec '03

03 Dec '03

Dear Sir I am trying to build a model with GTP can you pls tell were can I find parameters for GTP or you have it somewhere yoram

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