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