Dear Sir,

We are starting work with Modeller on the base of "Comparative protein structure modeling with Modeller: A practical approach".

We have a problem with work of the script 'compare.top'. We obtained the following message:

pntdp___252E> increase MAXRES or gap penalties.
recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1

When we removed 'MALIGN3D' command from the script it seems to work but execution of the next script 'align2d.top' looked as follows:

Dynamically allocated memory at         amaxseq [B,kB,MB]:      2200483    2148.
909     2.099
TOP_________>     2    2 READ_MODEL FILE = '1f88.pdb'

openf5__224_> Open 11 OLD SEQUENTIAL 1f88.pdb

Dynamically allocated memory at         amaxbnd [B,kB,MB]:     12194587   11908.
776    11.630
openf5__224_> Open       11 OLD SEQUENTIAL 1f88.pdb
rdatm___297_> Segments, residues, atoms:        2      643     5069
rdatm___298_> Segment:        1     1 A     1 A     2639
rdatm___298_> Segment:        2     1 B     1 B     2430
iatmcls_286W> MODEL atom not classified: ALA:OT1 ALA
iatmcls_286W> MODEL atom not classified: ALA:OT2 ALA
iatmcls_286W> MODEL atom not classified: ASN:OT1 ASN
TOP_________>     3    3 SEQUENCE_TO_ALI ALIGN_CODES = '1f88A'

TOP_________> 4 4 READ_ALIGNMENT FILE = 'korhum.ali', ALIGN_CODES = 'korh
um;
', ADD_SEQUENCE = ON

openf5__224_> Open 11 OLD SEQUENTIAL korhum.ali

Dynamically allocated memory at         amaxbnd [B,kB,MB]:     12227463   11940.
882    11.661
openf5__224_> Open       11 OLD SEQUENTIAL korhum.ali
read_al_374_> Non-standard residue type,position,sequence: /      339        1
read_al_374_> Non-standard residue type,position,sequence: /      645        1

Read the alignment from file : korhum.ali
Total number of alignment positions: 645

# Code        #_Res #_Segm PDB_code    Name
-------------------------------------------------------------------------------
1     korhum     643      3       1f88A undefined
TOP_________>     5    5 ALIGN2D

Dynamically allocated memory at         amaxbnd [B,kB,MB]:     24499233   23925.
031    23.364
align2d_276_> ALIGN_BLOCK changed to 1.
pdbnam__217W> Filename for PDB code not found: 1f88A
              Directories: ./
              Extensions :   :.atm:.pdb:.ent:.crd
rdabrk__288W> Protein not accepted:        1
mkapsa__293W> No TOPOLOGY_LIB is in memory. Use READ_TOPOLOGY to read one.
openf5__224_> Open       11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//as1.sim.m
at
rdrrwgh_268_> Number of residue types:       20
dispers_247E> Internal error:      642      643
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

Dynamically allocated memory at          finish [B,kB,MB]:     24499233   23925.
031    23.364
Starting time                                            : 2004/06/21 10:13:11.
753
Closing time                                             : 2004/06/21 10:13:15.
768
Total CPU time [seconds]                                 :       3.92

Please suggest what we did wrong.

Thank You.

Marcin Hus

Medical University in Lublin

Poland