[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

bad pdb file error



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