[modeller_usage] Terminal patching (acetylation/amidation) in Modeller 7.7

["Niels Johan Christensen" <>]

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