Hi, Michael,
The problem was with the format of the alignment file (you need to say
the entries are "structure", not "sequence", if you wish MODELLER to
read a structure file), and the second field in the second line of an
entry needs to be either the PDB file name or its root (see below). The
format of the alignment file is described in the manual ...
Happy modeling, Andrej
>P1;1
structure:1: : : : : : : : :
KRAHHNALERRRRDHIKESFTNLREAVP--TLK--GE--KASRAQILKKTTECIQTM*
>P1;2
structure:2: : : : : : : : :
AREQHNALERRRRDNIKDMYTSLREVVP--DAN--GERVQASRAVILKKAIESIEKG*
--
Andrej Sali, Associate Professor
The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399
tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540
e-mail ; http://salilab.org
-----Original Message-----
From:
[">mailto:] On Behalf Of
Michael Buck
Sent: Monday, January 24, 2000 9:06 AM
To:
Subject: Error using MALIGN3D
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
Phone (919)515-5759
Fax (919)515-3355
http://www4.ncsu.edu/~mjbuck
*************************************************