- modeller_usage - salilab.org

DOUBLE
by Delmiro Fernandez-Reyes 05 Sep '01

05 Sep '01

Hi It is possible to get code or the exec for mod_i486-linux-MAXSEQ=10_MAXRES=1000_DOUBLE instead of the SINGLE mod_i486-linux-MAXSEQ=10_MAXRES=1000.Z Also I am cofused because it is a web page of a release5 but the link to the software is the one of number 4? Delmiro -- Dr. Delmiro Fernandez-Reyes National Institute for Medical Research Division of Mathematical Biology The Ridgeway, Mill Hill, London NW7 1AA Tel: +44 020 89593666 ext. 2632 Tel: +44 020 89138711 Direct Fax: +44 020 89138545 http://mathbio.nimr.mrc.ac.uk/

1 0

problem with share libraries under linux 2.4.x
by Delmiro Fernandez-Reyes 04 Sep '01

04 Sep '01

Hi I just installed Modeller4 under linux kernel 2.4.x the only problem I have is executing > soft/modeller4/bin/mod4 model-default /soft/modeller4/bin/mod_i386-linux: error while loading shared libraries: /soft/modeller4/bin/mod_i386-linux: undefined symbol: acos check libs and it seems I have the right set of linked libs ldd -d mod_i386-linux /lib/libNoVersion.so.1 => /lib/libNoVersion.so.1 (0x40017000) libf2c.so.0 => /usr/lib/libf2c.so.0 (0x40034000) libc.so.6 => /lib/libc.so.6 (0x4004b000) /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000) Any ideas on this Delmiro -- Dr. Delmiro Fernandez-Reyes National Institute for Medical Research Division of Mathematical Biology The Ridgeway, Mill Hill, London NW7 1AA Tel: +44 020 89593666 ext. 2632 Tel: +44 020 89138711 Direct Fax: +44 020 89138545 http://mathbio.nimr.mrc.ac.uk/

1 0

Modelling a loop repeat
by Troy Wymore 29 Aug '01

29 Aug '01

Hello Modellers, I would like to restrain a loop that is repeated throughout my TARGET to have the same conformation as the first loop conformation where the alignment to the TEMPLATE is good. What is the easiest way to go about this? DEFINE_SYMMETRY? Any help would be much appreciated, Troy Wymore Biomedical Initiative Group Pittsburgh Supercomputing Center

2 1

[Fwd: Problems with heteroatoms (Zn)]
by Sirisha sunkara 27 Aug '01

27 Aug '01

Hi, I have this problem solved. I had a wrong representation of the Zn heteroatoms in my PDB file. It had to be annotated as ZN2 and not ZN, because that's how it's represented in the top_heav.lib file. Thanks to one of the modeller users who pointed this out to me - I'm sorry I forget his name. Regards, Sirisha Sunkara

2 1

Problems with heteroatoms (Zn)
by Sirisha sunkara 17 Aug '01

17 Aug '01

Hi, I'm trying to model a 283 aa long protein using Modeller4 with Zn heteroatom. The problem is Zn heteroatom does not show up in my output file. My template structure has a Zn Heteroatom in it. At this point I'm not interested in a model with hydrogens or water. I know people have had similar problems earlier and I also tried all the methods suggested in the archives of the mailing lists from 1998 and 1999. It still doesn't work. Has there been any update in the library files in Modeller5 for this? My model-segment.top file looks like this: INCLUDE # Include the predefined TOP routines SET ALNFILE = 'file.ali' SET KNOWNS = 'abc' SET SEQUENCE = 'gi_xxxxxxxx' SET ATOM_FILES_DIRECTORY = './:../atomfiles' SET TOPOLOGY_MODEL =3, HYDROGEN_IO = off, WATER_IO = off, HETATM_IO = on READ_PARAMETERS FILE = '$(LIB)/par.lib' READ_TOPOLOGY FILE= '$(LIB)/top_heav.lib' SET STARTING_MODEL= 4 SET ENDING_MODEL = 4 SET DYNAMIC_FLAG = 0 CALL ROUTINE = 'model' SUBROUTINE ROUTINE = 'select_atoms' PICK_ATOMS SELECTION_SEGMENT='1:' '283:', SELECTION_SEARCH='segment', ; PICK_ATOMS_SET=1, RES_TYPES='all', ATOM_TYPES='all', ; SELECTION_FROM='all', SELECTION_STATUS='initialize', SELECTION_STEP=1 RETURN END_SUBROUTINE I have Zn in my alignment files set up as XXX/z* in both template and query sequences. My template PDB file also has "only ZN" heteroatoms - I stripped out all other heteroatoms in my template PDB file just to make sure. What am I doing wrong? I appreciate all your help, Sirisha Sunkara

1 0

Modelling a loop repeat
by Troy Wymore 10 Aug '01

10 Aug '01

Hello Modellers, I would like to restrain a loop that is repeated throughout my TARGET to have the same conformation as the first loop conformation where the alignment to the TEMPLATE is good. What is the easiest way to go about this? DEFINE_SYMMETRY? Any help would be much appreciated, Troy Wymore Biomedical Initiative Group Pittsburgh Supercomputing Center

2 1

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 ______________________________________

2 1

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

2 1

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 ***************************************************************************

1 0

H Bond between GLU OE1 and ASP OD2
by Dr Nicolas Le Novere 27 Jun '01

27 Jun '01

Dear users, In a model I got with MODELLER, there is a potential hydrogen bond between oxygens of a glutamate and an aspartate (or the respective acids). However there is supposedly an important electrostatic repulsion. In the template the aspartate is replaced by a glycine. There is room for several of the glutamate conformers. Is it normal that MODELLER made the choice to keep the original conformer of the glutamate even with the unfavourable electrostatic environment? 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

2 1