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--------------
--------------------------*
------------------------------------------------------------------------------------
