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

[modeller_usage] Modeller cant find .seq file

Dear fellow modeller users
I'm new to modeller and have some trouble to get it running. it cant find the blbp.seq file. I've tried to switch to uppercase filenames, 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.dk 2.4.22-10mdksmp 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 Size Bytes 
---------------------------------------------------------------------------
iseqdb I 1 1 1 4 nseqdb I 1 1 1 4 seqdb S 1 1 1 1 1 4 codep S 1 1 1 20 ialn2 I 1 1 1 3 3 12 nresn2 I 1 3 3 12 irestypn2 I 1 1 1 3 3 12 invaln2 I 1 1 1 3 3 12 nsegmn2 I 1 3 3 12 iress1n2 I 1 30 1 3 90 360 iress2n2 I 1 30 1 3 90 360 resol2 R 1 3 3 12 rfactr2 R 1 3 3 12 caln2 S 1 1 1 3 3 3 ccaln2 S 1 1 1 3 3 3 alnchn2 S 1 2 1 3 6 6 prottyp2 S 1 3 3 240 source2 S 1 3 3 240 range2 S 1 2 1 3 6 30 name2 S 1 3 3 240 segidn2 S 1 30 1 3 90 1800 codein2 L 1 3 3 12 iattmod I 1 50 50 200 iatmgrp I 1 220 220 880 grpatm S 1 50 50 250 attmod S 1 220 220 1980 var R 1 3 1 16 48 192 pdf R 1 3 1 50 150 600 ientry I 1 4 4 16 jentry I 1 4 4 16 nentries I 1 1 1 4 iar I 1 1 1 4 jar I 1 1 1 4 kar I 1 1 1 4 lar I 1 1 1 4 b1ic R 1 1 1 4 b2ic R 1 1 1 4 t1ic R 1 1 1 4 t2ic R 1 1 1 4 pic R 1 1 1 4 tar L 1 1 1 4 xmin R 1 1 1 4 ymin R 1 1 1 4 zmin R 1 1 1 4 ialn I 1 1 1 3 3 12 nresn I 1 3 3 12 irestypn I 1 1 1 3 3 12 invaln I 1 1 1 3 3 12 nsegmn I 1 3 3 12 iress1n I 1 30 1 3 90 360 iress2n I 1 30 1 3 90 360 resol R 1 3 3 12 rfactr R 1 3 3 12 alnacc R 1 1 1 4 prof R 1 1 1 4 4 16 gapdst R 1 3 1 3 9 36 caln S 1 1 1 3 3 3 ccaln S 1 1 1 3 3 3 alnchn S 1 2 1 3 6 6 prottyp S 1 3 3 240 source S 1 3 3 240 range S 1 2 1 3 6 30 name S 1 3 3 240 segidn S 1 30 1 3 90 1800 atmfull S 1 3 3 768 codein L 1 3 3 12 iresatmn I 1 1 1 3 3 12 natmn I 1 3 3 12 iatmr1n I 1 1 1 3 3 12 idih I 1 1 1 9 1 3 27 108 idihc I 1 1 1 9 1 3 27 108 iglbsim I 1 3 1 3 9 36 isstruc I 1 1 1 3 3 12 neigh I 1 1 1 3 3 12 ineigh I 1 50 1 1 1 3 150 600 iresol I 1 3 3 12 indats2n I 1 2 1 1 1 3 6 24 imnchw I 1 1 1 3 3 12 iacont I 1 3 3 12 idsta1 I 1 1 1 3 3 12 idsta2 I 1 1 1 3 3 12 fractglsim R 1 3 1 3 9 36 xn R 1 1 1 3 3 12 yn R 1 1 1 3 3 12 zn R 1 1 1 3 3 12 dih R 1 1 1 9 1 3 27 108 acc R 1 1 1 3 3 12 bison R 1 1 1 3 3 12 curvn R 1 1 1 3 3 12 atmnamn S 1 1 1 3 3 12 resnumn S 1 1 1 3 3 15 resnamn S 1 1 1 3 3 12 chainn S 1 1 1 3 3 3 accepts L 1 3 3 12 memrange S 1 2 1 6 1 3 36 36 memalnchn S 1 2 1 6 1 3 36 36 mematmfull S 1 6 1 3 18 4608 iatc I 1 5 1 1 5 20 natc I 1 1 1 4 iata I 1 3 1 1 3 12 iatd I 1 4 1 1 4 16 iatb I 1 2 1 1 2 8 iati I 1 4 1 1 4 16 resseg S 1 1 1 4 iatmr1 I 1 1 1 4 iattyp I 1 1 1 4 iresatm I 1 1 1 4 iatta I 1 1 1 4 indats I 1 1 1 3 3 12 irestyp I 1 1 1 4 idihres I 1 4 1 9 1 1 36 144 natngh I 1 1 1 4 radii R 1 1 1 4 charge R 1 1 1 4 x R 1 1 1 4 y R 1 1 1 4 z R 1 1 1 4 biso R 1 1 1 4 vx R 1 1 1 4 vy R 1 1 1 4 vz R 1 1 1 4 atmacc R 1 1 1 4 resnam S 1 1 1 4 atmnam S 1 1 1 4 resnum S 1 1 1 5 chain S 1 1 1 1 picres L 1 1 1 3 3 12 picatm L 1 1 1 3 3 12 katmr1 I 1 1 1 4 kresatm I 1 1 1 4 krestyp I 1 1 1 4 x2 R 1 1 1 4 y2 R 1 1 1 4 z2 R 1 1 1 4 charg2 R 1 1 1 4 biso2 R 1 1 1 4 radii2 R 1 1 1 4 atm2nam S 1 1 1 4 res2nam S 1 1 1 4 chain2 S 1 1 1 1 res2num S 1 1 1 5 dvx R 1 1 1 4 dvy R 1 1 1 4 dvz R 1 1 1 4 pdbfil S 1 16331 16331 2090368 pdblst S 1 16331 16331 81655 indatm I 1 1 1 4 itcsr I 1 7 1 1 7 28 iatm I 1 1 1 4 ipcsr I 1 1 1 4 indatt I 1 1 1 4 itacsr I 1 7 1 1 7 28 iatt I 1 1 1 4 ipacsr I 1 1 1 4 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 1 1 4 pcsr R 1 1 1 4 pacsr R 1 1 1 4 iatsym1 I 1 1 1 4 iatsym2 I 1 1 1 4 wghsym R 1 1 1 4
Dynamically allocated memory at amaxseq [B,kB,MB]: 2200483 2148.909 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]: 2200483 2148.909 2.099 Starting time : 2004/02/06 13:17:35.587 Closing time : 2004/02/06 13:17:36.236 
Total CPU time [seconds]                                 :       0.65
[esben@computer tut3]$