hello,
I would like to do another modeling procedure with two of my recent models
as templates, so all the three sequences (2 structures, 1 sequence) in the
aln-file are identical.
to make a structural alignment of the 2 models I have used the command
MALIGN with the following .top-script:
----------------------------------
# Read the sequences of structures from the specs in SEGFILE:
READ_ALIGNMENT FILE = 'x.ali', ALIGN_CODES = 'all'
# do a multiple sequence alignment of structures:
MALIGN GAP_PENALTIES_1D = -600 -400
# do a multiple structural alignment of structures:
MALIGN3D GAP_PENALTIES_3D = 0.0 3.0, WRITE_FIT = ON, WRITE_WHOLE_PDB = OFF,
FIT_ATOMS = 'CA'
# align the last sequence with the fixed alignment of structures:
ALIGN GAP_PENALTIES_1D = -600 -400
# write the alignment to a file ALNFILE
WRITE_ALIGNMENT FILE = 'out.aln', ALIGNMENT_FORMAT = 'ALN'
------------------------------------------------------------
after a few seconds the run stops with the following message in the log-file:
---------------------------------------------------------------------------
Multiple dynamic programming alignment (MALIGN):
Residue-residue metric : ${MODINSTALL6v2}/modlib//as1.sim.mat
ALIGN_BLOCK : 1
Gap introduction penalty: -600.0000
Gap extension penalty : -400.0000
Length of alignment : 358
fndatmi_284E> Beginning atom index for a residue out of
bounds: 0 0
recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
-----------------------------------------------------------------
is there anybody who could explain me what I have to change ??
thank you!
Steffi
