FW: top file problem

28 Jun 2003


      Forwarded by list-owner:
------ Forwarded Message
From: "truename" yb_108@yeah.net
Date: Sat, 28 Jun 2003 17:48:51 +0800 (CST)
To: "modeller care" modeller-care@salilab.org
Subject: Re: your modeller question
Dear Ursula Pieper:
Thank you for your reply!
How ever both the sequence that I used to align and pdb file are from the
PDB.They are exactly corrospondent file for the same protein.
The content of p.top are as following
___________________________________________________________________________
# Very fast homology modelling by the MODELLER TOP routine 'model'.
INCLUDE                             # Include the predefined TOP routines
SET ALNFILE  = 'Together2.ali'      # alignment filename
SET KNOWNS   = '1DBG_A' '1AIR_'              # codes of the templates
SET SEQUENCE = 'T0101'               # code of the target
SET ATOM_FILES_DIRECTORY = './:../1DBG_A 1AIR_' # directories for input atom
files
SET STARTING_MODEL = 2
SET ENDING_MODEL = 2
SET OUTPUT_CONTROL = 1 1 1 1 2
# SET OUTPUT = 'LONG'
SET FINAL_MALIGN3D = 1
CALL ROUTINE = 'very_fast'          # prepare for extremely fast
optimization
CALL ROUTINE = 'model'              # do homology modelling
___________________________________________________________________________
and my p.aln file are as follwing
___________________________________________________________________________
>P1;1DBG_A
structureX:1DBG_A:1    : :506  : : : : :
----MKMLNKLAGYLLPIMVLLNVAPCLGQVVASNETLYQVVKEVKPGGLVQIADGTY--
-----KDVQLIVSNSGKSGLPITIKALNPGKVFFTGDAKVELRGEHLILEGIWFKDGNRA
IQAWKSHGPGLVAIYGSYNRITACVFDCFDEANSAYITTSLTEDGKVPQHCRIDHCSFTD
KITFDQVINLNNTARAIKDGSVGGPGMYHRVDHCFFSNPQKPGNAGGGIRIGYYRNDIGR
CLVDSNLFMRQDSEAEIITSKSQENVYYGNTYLNCQGTMNFRHGDHQVAINNFYIGNDQR
FGYGGMFVWGSRHVIACNYFELSETIKSRGNAALYLNPGAMASEHALAFDMLIANNAFIN
VNGYAIHFNPLDERRKEYCAANRLKFETPHQLMLKGNLFFKDKPYVYPFFKDDYFIAGKN
SWTGNVALGVEKGIPVNISANRSAYKPVKIKDIQPIEGIALDLNALISKGITGKPLSWDE
VRPYWLKEMPGTYALTARLSADRAAKFKAVIKRNKEH*
>P1;T0101
sequence:T0101:1    : :400  : : : : :
ADCSSDLTSGISTKRIYYVAPNGNSSNNGSSFNAPMSFSAAMAAVNPGELILLKPGTYTI
PYTQGKGNTITFNKSGKDGAPIYVAAANCGRAVFD----------FSFPDSQWVQAS---
--------------YGFYVTGDYWYFKGVEVTRAGYQGAYVIGSHNTFENTAFHHN----
----------RNTGLEINNG--GSYNTVINSDAYRNYDPKKNGSMADGFGP-KQKQGPGN
RFVGCRAWENSDDGFDLFDS--PQKVVIENSWAFRNGINYWNDSAFAGNGNGFKLGGNQA
VGN-------HRITRSVAFGNVSKGFDQNNNAGGVT---------------VINNTSYKN
GINYGFGSNVQSGQK----------------------HYFRNNVSLSASVTVSNADAKSN
SWDTGPAASASDFVSLDTSL------------------------ATVSRDNDGTLPETSL
FRLSANSKLINAGTKESNISYSGSAPDLGAFERN---*
>P1;1AIR_
structureX:1AIR_:1    : :353  : : : : :
---------ATDTGGYAATAGGNVTGAVSKTATSMQDIVNIIDAARLDANGKKVKG----
-----GAYPLVITYTGNEDSLINAAAAN--------------------ICGQWSKDPRG-
--------------VEIKEFTKGITIIGANGSSANFGIWIKKSSDVVVQNMRIGYLPGG-
----------AKDGDMIRVD--DSPNVWVDHNELFAANHECDGTPDN-----------DT
TFESAVDIKGASNTVTVSYN-----YIHGVKKVGLDGSSSSDTGRNITYHHNYYNDVNAR
LPLQ-------RGGLVHAYNNLYTNITGSGLNVRQN------------------GQALIE
NNWFEKAINPVTSRY--------------------------DGKNFGTWVLKGNNITKPA
DFSTYSITWTADTKPYVNAD---------------------------SWTSTGTFPTVAY
N----YSPVSAQCVKDKLPGYAGVGKNLATLTSTACK*
___________________________________________________________________________
Best Regards
YeBin
Error message:
> However, some difficulties confronted me during my first project of
> protein modelling. Do you lend me a hand to solve it?
> The error messages are as following:
> ________________________________________________
> rdpir____648E>Alignment sequence not found in PDB file:      1  ./1AIR.atm
> recover_____E>ERROR_STATUS >=STOP_ON_ERROR:         1      1
> 
> And p.top and p.ali are included in the attachment
> 
> Thanks a lot!
> Best regards
> 
> YeBin
> 
> 
> ------ End of Forwarded Message
>

Modeller Care

tags (0)

participants (1)