[modeller_usage] problems with the MALIGN command

[Stefanie Offermann <>]

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