starting with 6v1 - modeller_usage

2 May 2002


      Hi,
I am new user of Modeller and as a test I took input files (see bellow)
from a friend which were successfully run with version 5. After a few
minutes of computing here is the message I get in the logfile:
------------------------------------------------------------------------------------
Initial value of energy before optimization       :       15011.7158
Current energy                                    :       14658.3125
Symmetry term within energy                       :           0.0000
Optimizer exit status                             :        0
Number of iterations                              :       67
Number of calls to energy function                :      139
Number of updates of dynamic contacts             :        8
Number of non-updates of dynamic contacts         :      132
Final maximal atomic shift                        :    0.007
act10___551E> No such routine:
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1
Dynamically allocated memory at          finish [B,kB,MB]:    
17362145   16955.219    16.558
Starting time                                            : 2002/05/02 
10:09:43.976
Closing time                                             : 2002/05/02 
10:14:02.653
Total CPU time [seconds]                                 :       0.00
------------------------------------------------------------------------------------
The PDB files come from the PDB server. Is there any problem in the
input file ?
Thanks for any help or suggestion
Laurent
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
@ Laurent TROXLER @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@/@@/@@/@@@@  
  UPR 9022 CNRS, Réponse Immunitaire et          /  /  /  \
       Développement chez les Insectes          / // // /\ \
  Institut de Biologie Moléculaire et Cellulaire\ / // // /
  15 rue René Descartes                          \ /\ /\ /
  67084 Strasbourg Cedex - FRANCE                /\ /\ /\ \
  E-mail: L.Troxler@ibmc.u-strasbg.fr           / // // /\ \
  Tel   : (33) 03 88 41 70 07                   \ / // // / 
@ Fax   : (33) 03 88 60 69 22 @@@@@@@@@@@@@@@@@@@@@/@@/@@/@@@
""""""""""""""""""""""""""""""""""""""""""""""""""/""/""/""""
-- 

input.top:
------------------------------------------------------------------------------------
INCLUDE
#SET OUTPUT_CONTROL = 1 1 1 1 2
SET DIRECTORY = 'model2_dir'
SET ATOM_FILES_DIRECTORY = 'model2_dir'
SET OUTPUT_DIRECTORY = 'model2_dir'
SET PDB_EXT = '.pdb'

SET ALNFILE = 'easter2.pir'
SET KNOWNS =  '1QRZ' '1DST' '1FIW' '1AUT'
SET SEQUENCE = 'east'

SET MD_LEVEL = 'refine1'
SET OUTPUT = 'long' 
CALL ROUTINE = 'model'
------------------------------------------------------------------------------------

input.pir
------------------------------------------------------------------------------------
>P1;1QRZ
structureX:1QRZ :  546:A:  791:A:undefined:undefined:-1.00:-1.00
-----------------------FDCGKPQVE-----------------------PKKCP
GRVVGGCV----AHPHSWP-W----------QVSLRTRFG----QHFCGGTLISPEWVLT
AAHCLEK---------SPRPSSYKVILGAHQEV---------------------------
----NL------------EPHVQEIEVS---RLFLEPTR-----------KDIALLKLSS
PAVITD------KVIPACLP---SPNYMVA-DRTECFITGWGETQGTFGAG------LLK
EAQLPVIENKVCNR--------YEFLNGRVQSTELCAGHL-AGGTDSCQGDSGGPLVCFE
KDK----YILQGVTSWG-LGCARPNKPGVYVRVSRFVTWIEGVLR-NN------------
--------------------------*
>P1;1DST
structureX:1DST :  16: :  243: :undefined:undefined:-1.00:-1.00
------------------------------------------------------------
--ILGGRE----AEAHARP------------YMASVQLNG----AHLCGGVLVAEQWVLS
AAHCLE----------DAADGKVQVLLGAHSLS---------------------------
----QP------------EPSKRLYDVL---RAVPHPDYQPDTI-----DHDLLLLQLSE
KATLGP------AVRPLPWQ---RVDRDVA-PGTLCDVAGWGIVNHAGRRPD-----SLQ
HVLLPVLDRATCNR--------RTHHDGAITERLMCAE---SNRRDSCKGDSGGPLVCG-
-------GVLEGVVSWGSRVCGNRKKPGIYTRVASYAAWIDSVLA---------------
--------------------------*
>P1;1FIW
structureX:1FIW :  16:A:  254:A:undefined:undefined:-1.00:-1.00
------------------------------------------------------------
--IIGGQD----AAHGAWPWM-------VSLQIFTYHNNR---RYHVCGGSLLNSQWLLT
AAHCFRI---------KKKVTDWRLIFGAKEVEWG-------------------------
--TNKPV-----------KPPLQERYVE---KIIIHEKYSASSE-----ANDIALMKITP
PVTCGH------FIGPGCLP---QFRAGPPRVPQTCWVAGWGFLQENARRTSP----MLQ
EARVDLIDLGLCNS--------TRWYNGRIRSTNVCAGYP-EGKIDTCQGDSGGPLMCKD
SAEN--SYVVVGITSWG-VGCARAKRPGVYTSTWSYLNWIASKIGSTAVHMIQLPT*
>P1;1AUT
structureX:1AUT :  17:C:  244:C:undefined:undefined:-1.00:-1.00
------------------------------------------------------------
---IDGKM----TRRGDSP-W----------QVVLLDSKK----KLACGAVLIHPSWVLT
AAHCMD------------ESKKLLVRLGEYDLR---------------------------
----RW------------EKWELDLDIK---EVFVHPNYSKSTT-----DNDIALLHLAQ
PATLSQ------TIVPICLPDSGLAERELNQAGQETLVTGWGYHSSREKEAKRNRTFVLN
FIKIPVVPHNECSE----------VMSNMVSENMLCAGIL-GDRQDACEGDSGGPMVASF
HG----TWFLVGLVSWG-EGCGLLHNYGVYTKVSRYLDWIHGHIRD--------------
----------------*
>P1;east 
sequence::::::::0.00: 0.00
------------------------------------------------------------
---YGGMK----TKIDEFPWM----------ALIEYTKSQG-KKGHHCGGSLISTRYVIT
ASHCVNG------KALPTDWRLSGVRLGEWDT----------------------------
--NTNPDCEVDVRGMKDCAPPHLDVPVE---RTIPHPDYIPASK---NQVNDIALLRLAQ
QVEYTD------FVRPICLP-LDVNLRSATFDGITMDVAGWGKTEQLSASN------LKL
KAAVEGSRMDECQN-------VYSSQDILLEDTQMCAG-G-KEGVDSCRGDSGGPLIGLD
TNKVNTYYFLAGVVSFGPTPCGLAGWPGVYTLVGKYVDWIQNTIES--------------
--------------------------*

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