------ Forwarded Message
From: Tom Burghardt <>
Date: Thu, 28 Aug 2003 14:40:36 -0500 (CDT)
To: Modeller Care <>
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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