July 2001 - modeller_usage

Error using MALIGN3D
by Michael Buck 24 Jan '02

24 Jan '02

MALIGN3D Top files which worked well using Modeler 4 are giving me this error : fndatmi_284E> Beginning atom index for a residue out of bounds: 0 0 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I am using the following script # MALIGN3D READ_ALIGNMENT FILE = 'pair.aa' SET ATOM_FILES = '1.pdb' '2.pdb' SET FIT_ATOMS = 'CA' MALIGN3D GAP_PENALTIES_3D= 0 2.0, WRITE_FIT = on, WRITE_WHOLE_PDB = off If anybody has seen this problem, please help. Thank you Michael Buck ************************************************ Michael Buck NCSU Genetics mjbuck(a)unity.ncsu.edu Phone (919)515-5759 Fax (919)515-3355 http://www4.ncsu.edu/~mjbuck *************************************************

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modeller on beowulf
by Oliver Hucke 16 Jul '01

16 Jul '01

Dear modeller users/developers, we have started to plan a small beowulf cluster for biomolecular simulation and intend to use modeller on this cluster. Has anybody experience with running modeller on such an architecture? Do you have hints that might help us with the design of the cluster? One more specific question: do you know about a freely available software with the capabilities of the CLUSTOR/EnFuzion package which is quite expensive? Any help is very much appreciated. Kind regards, Oliver -- ______________________________________ Oliver Hucke Inst. fuer Physikalische Chemie II Universitaet Freiburg Albertstr. 23a D-79104 Freiburg Tel. : +49-761-203-5130 (/-6179) Fax. : +49-761-203-6189 email: hucke(a)uni-freiburg.de ______________________________________

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Clashes in a model
by Dr Nicolas Le Novere 16 Jul '01

16 Jul '01

Dear users, I made a quite unusual model, with three structures as templates, linked by tethers which (presumably) do not present any secondary structures: >P1;tempA structureX:tempA:1::10::::: aaaaaaaaaa------------------------------ >P1;tempB structureX:tempB:1::10::::: ---------------bbbbbbbbbb--------------- >P1;tempC structureX:tempC:1::10::::: ------------------------------cccccccccc >P1;model sequence:model:::::::: aaaaaaaaaaTTTTTbbbbbbbbbbTTTTTcccccccccc Everything's fine, except that in the final model one tether cross directly through the domain C! It is already the case in the file .ini and that seems related to the initial relative positions of the three templates. Is it supposed to occur? Any idea how to fix that? Regards, -- Dr Nicolas Le Novère http://www-alt.pasteur.fr/~lenov Dpt of Zoology, Univ of Cambridge, Downing street, Cambridge CB2 3EJ, UK tel: +44 1223 336623 fax: +44 1223 336676 e-mail: nl223(a)cus.cam.ac.uk

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Modelling a dimer
by Pedro A Reche Gallardo 09 Jul '01

09 Jul '01

Hi all, I am trying to model a heterodimer (AB) from a known homodimer template (AA). I know how to model monomers, but no dimers. Any suggestion will be wellcomed, and it will be great if I could get an example showing how this thing is done. Regards, Pedro -- *************************************************************************** PEDRO a. RECHE gallardo, pHD TL: 617 632 3824 Scientist, Mol.Immnunol.Foundation, FX: 617 632 3351 Dana-Farber Cancer Institute, EM: reche(a)research.dfci.harvard.edu Harvard Medical School, URL: http://www.reche.org 44 Binney Street, D610C, Boston, MA 02115 ***************************************************************************

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