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
Niels Johan Christensen wrote: > 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.
The TOP script you show should work just fine in Modeller 8v1, so I'm not sure why you want to use 7v7 instead. It's possible that you're seeing a bug that's been fixed in 8v1; try it out with the latest version.
> 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?
I cannot reproduce your problem without seeing all of your input files.
Ben Webb, Modeller Caretaker