I had not done anything with par.lib, but I followed your suggestion and
edited it, removing things I wasn't using. I got rid of all the heme and
nucleic acid parameters, and this finally got rid of the MBNDPF error,
only to replace it with another concerning MANGPF (see below)! Any more
ideas?
Thanks for your attention.
John Penniston
Modeller Caretaker wrote:
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
transfe_505_> MODEL is an average of the largest cluster: 1.5000
openf5__224_> Open 14 UNKNOWN SEQUENTIAL nmemb.dat
openf5__224_> Open 16 UNKNOWN SEQUENTIAL occupancy.dat
trfxyz___> The largest cluster occupancy:
Template -1, occupancy: 1 71
Template -1, occupancy: 2 68
Template -1, occupancy: 3 68
transfe_511_> Number of templates for coordinate transfer: 3
After transfering coordinates of the equivalent template
atoms,
there are defined, undefined atoms in MODEL: 544 0
TOP_________> 390 652 WRITE_MODEL FILE = 'cluster.ini'
openf5__224_> Open 14 UNKNOWN SEQUENTIAL cluster.ini
wrpdb2__568_> Residues, atoms, selected atoms: 72 544 544
TOP_________> 391 653 READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib'
openf5__224_> Open 11 OLD SEQUENTIAL
${MODINSTALL8v0}/modlib\/top_heav.lib
read_to_681_> topology.submodel read from topology file: 3
openf5__224_> Open 11 UNKNOWN SEQUENTIAL
${MODINSTALL8v0}/modlib/models.lib