I have found that the problem mentioned by  Tom Lee about modelling loops only occurs for
the MSI version of MODELLER and not the academic version. I get around the problem by
putting the following in the TOP file.:

INCLUDE
DEFINE_STRING VARIABLES = LOOP_CSRFILE LOOP_INI_MODEL
SET SEQUENCE              = 'aaa'
SET MODEL                 = 'aaa.pdb'     # initial model of the target
    :
    :
 

The define_string... line is the only line to be added.
I can't remember how I trouble-shot the problem as I fixed it a month ago.

I believe this will fix Dr Lee's problem.

Regards
Rob

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Robert Jorissen

Ludwig Institute for Cancer Research
P.O. BOX 2008, Royal Melbourne Hospital
Parkville, Victoria 3050, Australia

phone: ++61-3-9341-3155
fax:   ++61-3-9341-1938

e-mail: Robert.Jorissen@ludwig.edu.au
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