Sorry for the bother, but I can't figure this out for the life of me...
I'm attempting to do a 2d alignment of the R2R3 region of AtTT2 with the
MYB 1MSF. However, when I try to run the align2d command (script below),
it says that I am using a malformed pdb file. I am certain that is not
the case, as I just recently got the file directly from the pdb. If
anyone could help me out with this, it would be much appreciated.
____
<every ATOM definition in the pdb file, same as below>
iup2crm_279W> IUPAC atom not found in topology library; residue type
index: C4 25
Possible reasons are a non-standard PDB file, or a new
residue/atom types.
Compare the offending residue in the PDB file with its
definition in the topology library.
fndatmi_285W> Number of residues <> number of atoms; atom code:
127 105 CA
fndatmi_285W> Number of residues <> number of atoms; atom code:
127 105 CA
openf5__224_> Open 11 OLD SEQUENTIAL
${MODINSTALL6v2}/modlib//as1.sim.mat
rdrrwgh_268_> Number of residue types: 20
dispers_247E> Internal error: 126 127
recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]:
5936909 5797.763 5.662
Starting time : 2003/05/08
17:50:17.028
Closing time : 2003/05/08
17:50:26.897
Total CPU time [seconds] : 0.00
_____
The .top:
SET OUTPUT_CONTROL 1 1 1 1 1
READ_TOPOLOGY FILE = '/home/osu3233/bin/modeller6v2/modlib/top_allh.lib'
READ_MODEL FILE = '1MSF'
SEQUENCE_TO_ALI ALIGN_CODES = '1MSF' ALIGN_CODES = '1MSF'
#GENERATE_TOPOLOGY SEQUENCE = '1MSF'
#SEQUENCE_TO_ALI ALIGN_CODES = '1MSF'
READ_ALIGNMENT FILE = 'test.ali', ALIGN_CODES = 'AtTT2', ADD_SEQUENCE = ON
ALIGN2D
WRITE_ALIGNMENT FILE='AtTT2-1msf.ali', ALIGNMENT_FORMAT='PIR'
WRITE_ALIGNMENT FILE='AtTT2-1msf.pap', ALIGNMENT_FORMAT='PAP'
Thanks,
Mike Kurtz