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
Ben, 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 ${MODINSTALL8v0}/modlib/models.lib TOP_________> 392 654 READ_PARAMETERS FILE = '$(LIB)/par.lib'
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v0}/modlib/par.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v0}/modlib/par.lib rdparf__223E> Internal error: array too small: MANGPF current maximum, current need: 600 601 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]: 3236975 3161.108 3.087 Starting time : 2005/06/10 13:44:15.703 Closing time : 2005/06/10 13:45:52.828 Total CPU time [seconds] : 96.67
John Penniston wrote: > 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?
Well, it's the same thing again: while MBNDPF is the maximum number of bonds in the parameter file, MANGPF is the equivalent for angles. The solution is the same - you just need to attack the ANGLES parameters in par.lib this time. (There's also MDIHPF and MIMPPF, for dihedrals and impropers.)
Ben Webb, Modeller Caretaker
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John Penniston -
Modeller Caretaker