Forwarded to modeller_usage by the list owner
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From:
Date: Fri, 11 Apr 2003 17:18:33 +0200 (CEST)
To:
Subject: Fwd: problem with modeller6v2,(.pdb attached)
hi everybody,
I am a new user of modeller6v2. I am trying to build a bidomain protein
(avb5) I
have the xray structure of one very similar(avb3), they have one subunit in
common while the b is different.I could build just the b5 and assemble it
with
the av, but I want to build the two subunit together as in the next step I
want
to include the ligand which bind in the interface between the two subunits,
this
because i want to model a big loop which is upon the binding site and I
think
that the presence of the ligand could help the refinement of the loop in a
proper conformation as this loop is responsible for the specificity.
I followed the example which you give in the case you want to build a
chimera
protein so my allingment is :
>P1;1L5G_Av_aa1-437
structureX:1L5G_Av_aa1-437.pdb:1::437::::0.00:0.00
FNLDVDSPAEYSGPEGSYFGFAVDFFVPSASSRMFLLVGAPKANTTQPGIVEGGQVLKCDWSSTRRCQPIEFDATG
NRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQEREPVGTCFLQDGTKTVEYAPCRSQDIDADGQ
GFCQGGFSIDFTKADRVLLGGPGSFYWQGQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAV
GDFNGDGIDDFVSGVPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLFMDRG
SDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAIAAPYGGEDKKGIVYIFNGRS
TGLNAVPSQILEGQWAARSMPPSFGYSMKGATDIDKNGYPDLIVGAFGVDRAILYRA-------------------
----------------------------------------------------------------------------
----------------------------------------------------------------------------
---------------------------------------------------------------------------*
>P1;1L5G_B3_aa109-352
structureX:1L5G_B3_aa109-352.pdb:109::352::::0.00:0.00
----------------------------------------------------------------------------
----------------------------------------------------------------------------
----------------------------------------------------------------------------
----------------------------------------------------------------------------
----------------------------------------------------------------------------
---------------------------------------------------------DYPVDIYYLMDLSYSMKDD
LWSIQNLGTKLATQMRKLTSNLRIGFGAFVDKPVSPYMYISPPEALENPC--YDMKTTCLPMFGYKHVLTLTDQVT
RFNEEVKKQSVSRNRDAPEGGFDAIMQATVCDEKIGWRNDASHLLVFTTDAKTHIALDGRLAGIVQPNDGQCHVGS
DNHYSASTTMDYPSLGLMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTTVGVLSMDSSNVLQLIVDAYGKIR*
>P1;integrin_beta5
sequence::::::SEQ::0.00:0.00
FNLDVDSPAEYSGPEGSYFGFAVDFFVPSASSRMFLLVGAPKANTTQPGIVEGGQVLKCDWSSTRRCQPIEFDATG
NRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQEREPVGTCFLQDGTKTVEYAPCRSQDIDADGQ
GFCQGGFSIDFTKADRVLLGGPGSFYWQGQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAV
GDFNGDGIDDFVSGVPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLFMDRG
SDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAIAAPYGGEDKKGIVYIFNGRS
TGLNAVPSQILEGQWAARSMPPSFGYSMKGATDIDKNGYPDLIVGAFGVDRAILYRADYPVDLYYLMDLSLSMKDD
LDNIRSLGTKLAEEMRKLTSNFRLGFGSFVDKDISPFSYTAP-RYQTNPCIGYKLFPNCVPSFGFRHLLPLTDRVD
SFNEEVRKQRVSRNRDAPEGGFDAVLQAAVCKEKIGWRKDALHLLVFTTDDVPHIALDGKLGGLVQPHDGQCHLNE
ANEYTASNQMDYPSLALLGEKLAENNINLIFAVTKNHYMLYKNFTALIPGTTVEILDGDSKNIIQLIINAYNSIR*
****the .top is the model-default, just to try the alignment, I have in
mind to modify it for the loop refinement.
# Homology modelling by the MODELLER TOP routine 'model'.
INCLUDE # Include the predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to produce a large log file
SET ALNFILE = 'beta5.ali' # alignment filename
SET KNOWNS = '1L5G_Av_aa1-437''1L5G_B3_aa109-352' # codes of the
templates
SET SEQUENCE = 'integrin_beta5' # code of the target
SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom
files
SET STARTING_MODEL= 1 # index of the first model
SET ENDING_MODEL = 1 # index of the last model
# (determines how many models to
calculate)
CALL ROUTINE = 'model' # do homology modelling
******the file in the directory are:
1L5G_Av_aa1-437.pdb integrin_beta5.ini
1L5G_B3_aa109-352.pdb integrin_beta5.rsr
WBLOGFILE integrin_beta5.sch
beta5.ali model-default.log
integrin_beta5.D00000001 model-default.top
integrin_beta5.V99990001
*********my problem is that the calculation stops giving a core :
lib-4190 : UNRECOVERABLE library error
A numeric input field contains an invalid character.
Encountered during a list-directed READ from an internal file (character
variable)
IOT Trap
/usr/people/luci/bin/modeller6v2/bin/mod6v2[38]: 21472 Abort(coredump)
******in the .log you find no error:
itacsr I 1 7 1 10 70 280
iatt I 1 10 10 40
ipacsr I 1 10 10 40
iapairs I 1 2 1 1 2 8
iarsr2 I 1 50 1 50 2500 10000
iarsr I 1 50 50 200
indcsr I 1 128340 128340 513360
pcsr R 1 2566800 2566800 10267200
pacsr R 1 10 10 40
iatsym1 I 1 8556 8556 34224
iatsym2 I 1 8556 8556 34224
wghsym R 1 8556 8556 34224
Dynamically allocated memory at amprmcns [B,kB,MB]: 29049215
28368.375 27.703
openf5__224_> Open 11 OLD SEQUENTIAL integrin_beta5.rsr
openf5__224_> Open 11 OLD SEQUENTIAL integrin_beta5.rsr
***it seem like the template .pdb are wrong, but I can't find any error in
them,
the strange thing is that with the same pdb input once the calculation
finished
giving one subunit well superimposable, the other subunit not, so I thouth
that
it might due to an error in the alignment of the second subunit so i have
done
again the alignment and this time I get the core...what happen? is my
protein
too big? in total it is made up by around 700 aa, sometime the calculation
works and sometime not. very often I got the same core also when i model
only
one subunit, I really don't understand on what depends.
Previouly, I used the version4 for building only one subunit but I never had
this
problem, every thing went rigth with the version4, if I use the same
directory
which was successful with version4 it fails with version 6v2. is it possible
that this is a problem of this last version?
thanks in advance and sorry if I bother you
----- End forwarded message -----
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