Despite its better use of memory, it seems that "array too small" occurs
in 8v0 also. I used the following top file and a pdb file containing 70
residues and 2 calciums. After calculating the 5 loop models, it read in
the models for clustering. Then it started to do the clustering, with
the following log file (I've just included the part pertaining to the
clustering. The optimizing of the loops went OK). As you can see, MBNDPF
needed to be increased. I tried SET MAXRES = 5000, which isn't supported
any more, and SET TOPOLOGY_MODEL = 1, which didn't change anything. What
can be done?
MBNDPF is the maximum number of parameters in a parameter file, and it
cannot be increased in any released version of Modeller. 8v0 does remove
many limits, but not all of them. Did you edit toplib/par.lib to add new
parameters? If so, you will need to delete some unused parameters so
that MBNDPF is not exceeded.
MAXRES isn't supported any more because all of the limits which it
controlled no longer exist. Even if you could set it, it wouldn't change
anything. TOPOLOGY_MODEL merely selects which set of VDW radii to use.
Your only option with 8v0 or earlier is to edit the parameter file.
Alternatively, Modeller 8v1 will be released this month, and this
removes most remaining limits, including MBNDPF.