[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[modeller_usage] Modeller cant find .seq file

To:
Subject: [modeller_usage] Modeller cant find .seq file
From: Esben Jannik Bjerrum <>
Date: Fri, 6 Feb 2004 13:26:10 +0100
Reply-to:

Dear fellow modeller users

I'm new to modeller and have some trouble to get it running. itcant find the blbp.seq file. I've tried to switch to uppercasefilenames, but in vain. below is the output from the terminal session.


I'm running on linux mandrake 9.2

Hope you have ideas about what is wrong

Esben

[esben@computer tut3]$ ls
blbp.seq  BLBP.seq  BLBP.SEQ  search.log  search.top  search.top~

[esben@computer tut3]$ cat blbp.seq

P1;blbp

sequence:blbp::::::::
VDAFCATWKLTDSQNFDEYMKALGVGFATRQVGNVTKPTVVIISQEGGKVVIRTQCTFKNTEINFQLGEEFEE
TSIDDRNCKSVVRLDGDKLIHVQKWDGKETNCTREIKDGKMVVTLTFGDIVAVRCYEKA*

[esben@computer tut3]$ cat search.top
SET OUTPUT_CONTROL = 1 1 1 1 2
SET SEARCH_RANDOMIZATIONS = 10
SEQUENCE_SEARCH FILE = ´blbp.seq´, ALIGN_CODES = ´blbp´

[esben@computer tut3]$ modeller search.top

[esben@computer tut3]$ cat search.log

                        MODELLER 6v2, 17 Feb 2002

    PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS


                    Copyright(c) 1989-2002 Andrej Sali
                           All Rights Reserved

                           Written by A. Sali
         with help from A. Fiser, R. Sanchez, M.A. Marti-Renom,
                  B. Jerkovic, A. Badretdinov, F. Melo,
                      J.P. Overington & E. Feyfant
                  Rockefeller University, New York, USA
                    Harvard University, Cambridge, USA
                Imperial Cancer Research Fund, London, UK
            Birkbeck College, University of London, London, UK

Kind, OS, HostName, Kernel, Processor: 4, Linux computer.dfuni.dk2.4.22-10mdksmp i686

Date and time of compilation         : 07/05/2002 17:30:36
Job starting time (YY/MM/DD HH:MM:SS): 2004/02/06  13:17:35.587


Status of dynamic memory allocation in routine: amaxseq

Variable T L1 U1 L2 U2 L3 U3 SizeBytes

---------------------------------------------------------------------------

iseqdb I 1 1 14nseqdb I 1 1 14seqdb S 1 1 1 1 14codep S 1 1 120ialn2 I 1 1 1 3 312nresn2 I 1 3 312irestypn2 I 1 1 1 3 312invaln2 I 1 1 1 3 312nsegmn2 I 1 3 312iress1n2 I 1 30 1 3 90360iress2n2 I 1 30 1 3 90360resol2 R 1 3 312rfactr2 R 1 3 312caln2 S 1 1 1 3 33ccaln2 S 1 1 1 3 33alnchn2 S 1 2 1 3 66prottyp2 S 1 3 3240source2 S 1 3 3240range2 S 1 2 1 3 630name2 S 1 3 3240segidn2 S 1 30 1 3 901800codein2 L 1 3 312iattmod I 1 50 50200iatmgrp I 1 220 220880grpatm S 1 50 50250attmod S 1 220 2201980var R 1 3 1 16 48192pdf R 1 3 1 50 150600ientry I 1 4 416jentry I 1 4 416nentries I 1 1 14iar I 1 1 14jar I 1 1 14kar I 1 1 14lar I 1 1 14b1ic R 1 1 14b2ic R 1 1 14t1ic R 1 1 14t2ic R 1 1 14pic R 1 1 14tar L 1 1 14xmin R 1 1 14ymin R 1 1 14zmin R 1 1 14ialn I 1 1 1 3 312nresn I 1 3 312irestypn I 1 1 1 3 312invaln I 1 1 1 3 312nsegmn I 1 3 312iress1n I 1 30 1 3 90360iress2n I 1 30 1 3 90360resol R 1 3 312rfactr R 1 3 312alnacc R 1 1 14prof R 1 1 1 4 416gapdst R 1 3 1 3 936caln S 1 1 1 3 33ccaln S 1 1 1 3 33alnchn S 1 2 1 3 66prottyp S 1 3 3240source S 1 3 3240range S 1 2 1 3 630name S 1 3 3240segidn S 1 30 1 3 901800atmfull S 1 3 3768codein L 1 3 312iresatmn I 1 1 1 3 312natmn I 1 3 312iatmr1n I 1 1 1 3 312idih I 1 1 1 9 1 3 27108idihc I 1 1 1 9 1 3 27108iglbsim I 1 3 1 3 936isstruc I 1 1 1 3 312neigh I 1 1 1 3 312ineigh I 1 50 1 1 1 3 150600iresol I 1 3 312indats2n I 1 2 1 1 1 3 624imnchw I 1 1 1 3 312iacont I 1 3 312idsta1 I 1 1 1 3 312idsta2 I 1 1 1 3 312fractglsim R 1 3 1 3 936xn R 1 1 1 3 312yn R 1 1 1 3 312zn R 1 1 1 3 312dih R 1 1 1 9 1 3 27108acc R 1 1 1 3 312bison R 1 1 1 3 312curvn R 1 1 1 3 312atmnamn S 1 1 1 3 312resnumn S 1 1 1 3 315resnamn S 1 1 1 3 312chainn S 1 1 1 3 33accepts L 1 3 312memrange S 1 2 1 6 1 3 3636memalnchn S 1 2 1 6 1 3 3636mematmfull S 1 6 1 3 184608iatc I 1 5 1 1 520natc I 1 1 14iata I 1 3 1 1 312iatd I 1 4 1 1 416iatb I 1 2 1 1 28iati I 1 4 1 1 416resseg S 1 1 14iatmr1 I 1 1 14iattyp I 1 1 14iresatm I 1 1 14iatta I 1 1 14indats I 1 1 1 3 312irestyp I 1 1 14idihres I 1 4 1 9 1 1 36144natngh I 1 1 14radii R 1 1 14charge R 1 1 14x R 1 1 14y R 1 1 14z R 1 1 14biso R 1 1 14vx R 1 1 14vy R 1 1 14vz R 1 1 14atmacc R 1 1 14resnam S 1 1 14atmnam S 1 1 14resnum S 1 1 15chain S 1 1 11picres L 1 1 1 3 312picatm L 1 1 1 3 312katmr1 I 1 1 14kresatm I 1 1 14krestyp I 1 1 14x2 R 1 1 14y2 R 1 1 14z2 R 1 1 14charg2 R 1 1 14biso2 R 1 1 14radii2 R 1 1 14atm2nam S 1 1 14res2nam S 1 1 14chain2 S 1 1 11res2num S 1 1 15dvx R 1 1 14dvy R 1 1 14dvz R 1 1 14pdbfil S 1 16331 163312090368pdblst S 1 16331 1633181655indatm I 1 1 14itcsr I 1 7 1 1 728iatm I 1 1 14ipcsr I 1 1 14indatt I 1 1 14itacsr I 1 7 1 1 728iatt I 1 1 14ipacsr I 1 1 14iapairs I 1 2 1 1 28iarsr2 I 1 50 1 50 250010000iarsr I 1 50 50200indcsr I 1 1 14pcsr R 1 1 14pacsr R 1 1 14iatsym1 I 1 1 14iatsym2 I 1 1 14wghsym R 1 1 14

Dynamically allocated memory at amaxseq [B,kB,MB]: 22004832148.909 2.099

TOP_________>     2    2 SET SEARCH_RANDOMIZATIONS = 10

TOP_________> 3 3 SEQUENCE_SEARCH FILE = ´BLBP.SEQ´, ALIGN_CODES= ´BLBP´


fullfn__230E> File not found:  ´BLBP.SEQ´
             Directories:
             Extensions :  :.chn
             Prefixes   : nothing, pdb
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

Dynamically allocated memory at finish [B,kB,MB]: 22004832148.909 2.099Starting time : 2004/02/0613:17:35.587Closing time : 2004/02/0613:17:36.236

Total CPU time [seconds]                                 :       0.65
[esben@computer tut3]$

Prev by Date: [modeller_usage] RE: RE:
Next by Date: RE: [modeller_usage] Modeller cant find .seq file
Previous by thread: [modeller_usage] RE: RE:
Next by thread: RE: [modeller_usage] Modeller cant find .seq file
Index(es):
- Date
- Thread