Fwd: modeller top files

[Bozidar Yerkovich <bozidar AT piano.rockefeller.edu>]

from one of our fellow MODELLERs... Can anyone help?
B..
----------  Forwarded Message  ----------

Subject: modeller top files
Date: Fri, 12 Jul 2002 12:17:13 +0100
From: "Rosh Karunaratne" <HIDDEN>
To: bozidar AT salilab.org

thanks for your help last week
Ive been reading through the online modeller manual (version6) and am having
trouble creating the 'right' top file for my ali file that I have created.
Below are two of the examples i have tried (both using the modeller manual)
but when I run procheck on the last *.B9999 file I get heavy violations and
bad contatcs between atoms.
All I am interested in is creating the 'best model' within least violations
etc
Is there a pre-prepared top file that you know of that will do this task?

Thanks for your help
Rosh

INCLUDE #rho1

SET ALNFILE  = 'name.ali'
SET HETATM_IO = on
SET KNOWNS   = '1abc'
SET SEQUENCE = '123456'
SET ATOM_FILES_DIRECTORY = '/d/d120/u/fkaru01/'
SET STARTING_MODEL = 1
SET ENDING_MODEL = 1
SET DO_LOOPS = '1'
SET LOOP_STARTING_MODEL =1
SET LOOP_ENDING_MODEL= 25
SET LOOP_MD_LEVEL = 'refine_5'
CALL ROUTINE = 'model'

or

SET ALNFILE = 'name.ali'
SET KNOWNS = '1abc'
SET SEQUENCE = '123456'
SET ATOM_FILES_DIRECTORY = '/d/d120/u/fkaru01/'
SET STARTING_MODEL = 2
SET ENDING_MODEL = 2

CALL ROUTINE = 'very_fast'
CALL ROUTINE = 'model'






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