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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Dr. Ralf Schmid
ICMB
The University of Edinburgh
Michael Swann Building 3.14
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