Dear all,
I'm trying to model a protein including a cofactor, but get an error message pointing towards problems in the alignment and/or pdb file. Modelling without cofactor (i.e. removing "/." from the alignment file) works fine. I can't figure out what causes the problem.
Any help will be appreciated, please see the files below.
Thanks in advance,
ralf
xxx.log: <snip> TOP_________> 120 106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153.583 2.103 openf5__224_> Open 11 OLD SEQUENTIAL xxx.ali openf5__224_> Open 13 OLD SEQUENTIAL ./yyy.pdb Dynamically allocated memory at amaxbnd [B,kB,MB]: 9440821 9219.552 9.003 openf5__224_> Open 11 OLD SEQUENTIAL xxx.ali openf5__224_> Open 13 OLD SEQUENTIAL ./yyy.pdb rdpir___648E> Alignment sequence not found in PDB file: 1 ./yyy.pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
xxx.top: INCLUDE SET OUTPUT_CONTROL= 1 1 1 1 1 SET ALNFILE = 'xxx.ali' SET KNOWNS = 'yyy' SET SEQUENCE = 'xxx' SET STARTING_MODEL = 20 SET ENDING_MODEL = 20 SET HETATM_IO = on CALL ROUTINE = 'model'
xxx.ali: >P1;xxx sequence:xxx:.:.:.:.:.:.:.:. VKNER/.* >P1;yyy structureX:yyy:.:.:.:.:.:.:.:. VKQER/.*
yyy.pdb: <snip> ATOM 3488 OXT ARG A 447 31.403 66.404 103.394 1.00 65.84 O TER 3489 ARG A 447 HETATM 3490 AP FAD 448 60.780 56.948 67.003 1.00 33.65 P <snip>
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