On Thu, Jul 22, 2004 at 11:08:44AM -0500, Evans Adolfo Tapia wrote:
> I'm using modeller lately, and I haven't had any problems while predicting
> the tertiary structure of a target using in the multiple alignment
> sequences with pdb files.
>
> Now that I'm trying to use, only CA files I receive this message and
> obviously Modeller stops the execution...
>
> > Array too small. Increase MPRMCNS
> > current maximum, current need: 1393200 1393224
>
> Do you know if this is a parameter I can increase? or what can be causing
> the error.
This error means that Modeller has run out of space for restraint
parameters. It guesses the dimension for the restraints array from the
number of residues in your system - presumably you have more restraints
per residue than it's expecting. You cannot increase this parameter
directly, but you can increase Modeller's maximum number of residues to
give a correspondingly larger number of restraints - just add
SET MAXRES = 5000
before you read in your PDB files. You may have to tweak this number to
use memory most efficiently.
Note also that Modeller's guess depends on your topology model. It
allocates memory for roughly 400 restraint parameters per atom, and in
turn in the default topology model (3) it assumes roughly 12 atoms per
residue. If you're building an all-atom model, then make sure you have
SET TOPOLOGY_MODEL = 1
to tell Modeller this - then it'll assume roughly 20 atoms per residue.
Ben Webb, Modeller Caretaker
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