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