Dear all,
First of all, thanks to Ben Webb for answering my question regarding acetylation in MODELLER 8.1.
Now, I would like to do the same thing in MODELLER 7.7, but mod7v7.exe error terminates when I run my script. I have included my script and excerpt from the .log file below.
It is rather peculiar that the .log says:
''Atom index is out of bounds: 708 706'',
since these indices are indeed present in the .ini file. What goes wrong?
Thank you.
Best Regards,
Niels Johan Christensen
>>> My script <<<
------------------------------------------------------
INCLUDE
SET PATCH_DEFAULT = off
SET ALNFILE = 'VaLd-TRIL16C-HAND.PIR'
SET KNOWNS = 'merged.pdb'
SET SEQUENCE = 'TRIL16C'
SET STARTING_MODEL = 1
SET ENDING_MODEL = 5
CALL ROUTINE = 'model'
STOP
SUBROUTINE ROUTINE = 'special_patches'
PATCH RESIDUE_TYPE='ACE', RESIDUE_IDS='1:'
PATCH RESIDUE_TYPE='CT2', RESIDUE_IDS='30:'
RETURN
END_SUBROUTINE
-------------------------------------------------------
>>> The .LOG file <<<<
getprog_531W> ROUTINE redefined: special_patches
check_ali___> Checking the sequence-structure alignment.
Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
delete__443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 6869 6678
csrrng__299E> Atom index is out of bounds: 708 706
recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1