Re: [modeller_usage] beta-sheets and alpha-helixes

[Modeller Caretaker <>]

Matthias Negri wrote:
> my name is Matthias and I'm a PhD Student at University of Saarland. 
> I'm trying to model a cypP450 with modeller7v7 by defining the secondary
> structure (alpha, sheet..) in the special_restraints ROUTINE, but I
> still get error messages and the job is broken up!
>
> That's the error message I got:
> "Dynamically allocated memory at         amaxseq [B,kB,MB]:     39334681
>   38412.773    37.512
> TOP_________>   169  174 CALL ROUTINE = 'special_restraints'
>
> TOP_________>   170  479 SET ADD_RESTRAINTS = ON
>
> TOP_________>   171  480 MAKE_RESTRAINTS RESTRAINT_TYPE = 'ALPHA',
> RESIDUE_IDS = ';
>                       228:A' '253:A'
>
> assgn___215E> Dynamic memory allocation failed.
>               Routine, variable, status:  vars%val         1
> recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1"

Odd - that looks like a bug; looks like memory corruption has occurred here.

> 1.Can you tell me what the reason for failing is?
> 2.Further, does modeller8.1 resolve this problem (if there is a bug in
> mod7v7?)!

I can't really tell what the problem is unless you send me your complete 
input files. The problem is most likely fixed in 8v1 though, as that 
part of the code did see some changes between 7v7 and 8v1.

> TOP_________>   202  256 PICK_RESTRAINTS ADD_RESTRAINTS = OFF
>
> nselat__596E> Atom index is out of range (iatm,natm):     7458     7457
> recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1
>
> Dynamically allocated memory at          finish [B,kB,MB]:     39111561   "
> What's the reason for, where I do mistakes?

This means that you have restraints which refer to non-existent atoms, 
but I can't tell why that's happening without seeing your inputs.

	Ben Webb, Modeller Caretaker
--
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