John Penniston wrote: > 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.
Ben Webb, Modeller Caretaker