Forwarded to modeller_usage by the list owner

------ Forwarded Message From: luciana@org.chemie.tu-muenchen.de Date: Fri, 11 Apr 2003 17:18:33 +0200 (CEST) To: modeller-care@salilab.org 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 -----