Hello, I'm looking for any assistance anyone can offer with the following problem. I am attempting to create a model of a nitroreductase, and I'm getting the following error.
addatms_223E> Array too small. Increase MAXATM current maximum, current need: 2964 2965 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
The only reference to it in the archives that I have found, just notes it as a possible bug. I'm a fairly new user and am attempting to follow the manuals guidance on this. It appears to occur when I call GENERATE_TOPOLOGY SEQUENCE in the TOP file. My TOP file looks something like :
SET OUTPUT_CONTROL = 1 1 1 1 1 SET ATOM_FILES_DIRECTORY = './:../atom_files' READ_TOPOLOGY FILE='$(LIB)/top.lib' READ_PARAMETERS FILE='$(LIB)/par.lib' READ_MODEL FILE='1ICV' SEQUENCE_TO_ALI ATOM_FILES = '1ICV', ALIGN_CODES='1ICV' SEQUENCE_TO_ALI ADD_SEQUENCE=off, ATOM_FILES=ATOM_FILES '1ICV.ini',; ALIGN_CODES = ALIGN_CODES '1ICV-ini' GENERATE_TOPOLOGY SEQUENCE = '1ICV-ini' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ=off MAKE_RESTRAINTS RESTRAINT_TYPE='stereo' WRITE_MODEL FILE='1icv.ini'
The 1ICV file is a downloaded, unaltered pdb file. Any ideas as to what's happening?
On Thu, Aug 26, 2004 at 02:52:49PM +1200, firstname.lastname@example.org wrote: > Hello, I'm looking for any assistance anyone can offer with the following > problem. I am attempting to create a model of a nitroreductase, and I'm > getting the following error. > > addatms_223E> Array too small. Increase MAXATM > current maximum, current need: 2964 2965 > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
See also http://salilab.org/archives/modeller_usage/2004/msg00262.html. Modeller thinks you have 2964 atoms in your system, but you're ending up with more. Make sure you are setting the correct TOPOLOGY_MODEL (see the referenced post). If that doesn't work then you can work around the problem by manually setting MAXRES in your TOP script, also in the referenced post.
Ben Webb, Modeller Caretaker