------ Forwarded Message From: Tom Burghardt burghardt@mayo.edu Date: Thu, 28 Aug 2003 14:40:36 -0500 (CDT) To: Modeller Care modeller-care@salilab.org Subject: building a new residue

Dear Modellers,

I defined a new residue type following the instructions (a-d) of FAQ17 in the Modeller handbook. I did not do the last step (e) because I need to run the program first to see what needs to be done. To allow Modeller to recognize the new residue single letter code in the sequence file (FAQ17 part d) I modified the residue type library 'modlib/restyp.lib' with a new entry at the end of the file (index=142). When I run Modeller I get the message:

read_al_375E> Unknown residue type,position,sequence: U 84 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1

implying I guess that it does not recognize the one letter code I assigned my modified residue. Everything runs OK if I replace the modified residue with a BLK residue in the alignment file. My top file is below.

INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log SET ALNFILE = 'seq-sk_sk_T1_short_gly.ali' # alignment filename SET KNOWNS = '2tnx' # codes of the templates SET SEQUENCE = '2tns' # code of the target SET TOPOLOGY_MODEL = 3,HETATM_IO=ON SET TOPLIB = '${LIB}/top_heav.lib' SET PARLIB = '${LIB}/par.lib' READ_RESTYP_LIB RESTYP_LIB_FILE='${LIB}/restyp.lib' SET ATOM_FILES_DIRECTORY = './' # directories for input atom files SET STARTING_MODEL= 1 # index of the first loop model SET ENDING_MODEL = 1 # index of the last loop model CALL ROUTINE = 'model' # do homology modelling

Thanks

Tom Burghardt

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