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
…
[View More]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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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,
…
[View More]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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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 …
[View More]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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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, …
[View More]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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