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:
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# 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'
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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
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is there anybody who could explain me what I have to change ??
thank you!
Steffi