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:
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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