Absolutely! You have the solution right there! Account for the missing residue numbers of Mg/ATP in the alignment file. Modeller reads a PDB file as specified in the alignment format – so if you include more residues in the template, you have to alter the PIR format fields to tell the program to read them in from the PDB file first.

Eswar.

---

Eswar Narayanan, Ph.D

Mission Bay Genentech Hall
600 16th Street, Suite N474Q
University of California, San Francisco
San Francisco, CA 94143-2240 (CA 94158 for courier)

Tel +1 (415) 514-4233; Fax +1 (415) 514-4231

http://www.salilab.org/~eashwar

-----Original Message-----
From: SLN Prasad Reddy [mailto:sreeyapu@rediffmail.com]
Sent: Thursday, February 05, 2004 6:31 AM
To: Eswar Narayanan
Subject: Re: RE:

  Sir,
      I have given a mail a week back regarding modelling of hetero atoms along with main protein. You suggested me to check the number of residues in pdb file of template and .ali file. I checked it and it is same. I used fallowing .top file for modelling ( i am using modeller6v2 for windows nt)



INCLUDE                            # Include the predefined TOP routines
SET ALNFILE  = 'fi.ali'            # alignment filename
SET KNOWNS  = 'Tem11'              # codes of the templates
SET SEQUENCE = 'tar1'              # code of the target
SET MODEL_TOPOLOGY = 1 SET HYDROGEN_IO = off, HETATM_IO = on, WATER_IO = off
SET TOPLIB = ${LIB}/top.lib
SET PARLIB = ${LIB}/par.lib
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


              Still the logfile is showing the number of residues in Pdb file of template and .ali are different and it also indicating the .ali file consists of 253 atoms and pdb file of template is having 251 ( The number of atoms present in my protein  and template is 251 excluding heteroatoms.)So programme may be recognising Mg($) and ATP(@) in .ali file and not doing so with pdb dile of template. Kindly suggest me solution .

              Is the top file (above) i am using is a correct one for modelling hetatms. 


Thank you

With regards

Prasad.







On Sat, 31 Jan 2004 Eswar Narayanan wrote :
>Prasad,
>
>
>
>The error message tells you exactly what the problem is. The number of
>residues in the alignment and PDB files are different. There are more or
>less residues in the alignment than what is read in from the PDB file.
>
>
>
>Eswar.
>
>
>
>---
>
>Eswar Narayanan, Ph.D
>
>Mission Bay Genentech Hall
>600 16th Street, Suite N474Q
>University of California, San Francisco
>San Francisco, CA 94143-2240 (CA 94158 for courier)
>
>Tel +1 (415) 514-4233; Fax +1 (415) 514-4231
>
>http://www.salilab.org/~eashwar
>
>-----Original Message-----
> From: SLN Prasad Reddy [mailto:sreeyapu@rediffmail.com]
>Sent: Saturday, January 31, 2004 5:59 AM
>To: eashwar@salilab.org
>Subject:
>
>
>
>
>  Sir,
>        I am struggling in modeling a protein with ligand (ATP) and metal
>atom (Mg). I am requesting you to help me in this regard.
>
>        My  problem : I want to model a protein with ligand and metal ion.
>The template I have chosen  is a crystal structure having both lignad and
>metal atom. I tried with procedure given  in the FAQ's question #16 of
>Modeller6v2 manual . I found symbols for ATP and Mg form restyp.lib  of
>Modeller 6v2 and incorporated at the end of the alignment like  following
>
> >P1;templ1 structureX:templ1:1::10::
>FAYVI/.$@*
> >P1;targ1 sequence:targ1:1::8::
>-GWIV/.$@*
>
>
>The top file is :
>
>INCLUDE
>SET OUTPUT_CONTROL = 1 1 1 1 1
>SET ALNFILE = 'fi.ali'
>SET KNOWNS = 'temp11'
>SET SEQUENCE = 'targ1'
>SET HETATM_IO = on
>CALL ROUTINE = 'model'
>
>
>But I am getting a log file as fallows
>
>TOP_________>  105  705 SET ALNFILE = 'fi.ali'
>
>TOP_________>  106  706 SET KNOWNS = 'temp11'
>
>TOP_________>  107  707 SET SEQUENCE = 'targ1'
>
>TOP_________>  108  708 SET HETATM_IO = ON
>
>TOP_________>  109  709 CALL ROUTINE = 'model'
>
>TOP_________>  110  399 CALL ROUTINE = 'getnames'
>
>TOP_________>  111  509 STRING_IF STRING_ARGUMENTS = MODEL 'undefined',
>OPERATION;
>                      = 'EQ', THEN =    'STRING_OPERATE OPERATION =
>CONCATENA;
>                      TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL'
>
>TOP_________>  112  510 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined',
>OPERATI;
>                      ON = 'EQ', THEN =    'STRING_OPERATE OPERATION =
>CONCATE;
>                      NATE, STRING_ARGUMENTS = SEQUENCE .rsr,  RESULT =
>CSRFILE;
>                      '
>
>TOP_________>  113  511 STRING_OPERATE OPERATION = 'CONCATENATE',
>;
>                        STRING_ARGUMENTS = SEQUENCE '.sch',  RESULT =
>SCHFILE
>
>TOP_________>  114  512 STRING_OPERATE OPERATION = 'CONCATENATE',
>;
>                        STRING_ARGUMENTS = SEQUENCE '.mat',  RESULT =
>MATRIX_FI;
>                      LE
>
>TOP_________>  115  513 SET ROOT_NAME = SEQUENCE
>
>TOP_________>  116  514 RETURN
>
>TOP_________>  117  400 CALL ROUTINE = 'homcsr'
>
>TOP_________>  118  106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS
>SEQUE;
>                      NCE
>
>
>Dynamically allocated memory at        amaxseq [B,kB,MB]:      2205269
>2153.583    2.103
>openf5__224_> Open      11  OLD  SEQUENTIAL  fi.ali
>
>Dynamically allocated memory at        amaxbnd [B,kB,MB]:      5865109
>5727.646    5.593
>openf5__224_> Open      11  OLD  SEQUENTIAL  fi.ali
>read_al_374_> Non-standard residue type,position,sequence:  $              1
>read_al_374_> Non-standard residue type,position,sequence:  @              1
>read_al_374_> Non-standard residue type,position,sequence:  $            2
>read_al_374_> Non-standard residue type,position,sequence:  @            2
>
>Read the alignment from file      : fi.ali
>Total number of alignment positions:
>
>  #  Code        #_Res #_Segm PDB_code    Name
>----------------------------------------------------------------------------
>---
>  1      temp11        1        temp11
>  2      targ1          1        targ1
>TOP_________>  119  107 CHECK_ALIGNMENT
>
>check_a_343_> >> BEGINNING OF COMMAND
>openf5__224_> Open      11  OLD  SEQUENTIAL  ./temp11.pdb
>rdabrk__290E> Number of residues in the alignment and  pdb files are
>different:
>              For alignment entry:        1
>recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1      1
>
>Dynamically allocated memory at          finish [B,kB,MB]:      5865109
>5727.646    5.593
>Starting time                                            : 2000/08/03
>19:06:47.190
>Closing time                                            : 2000/08/03
>19:06:52.888
>Total CPU time [seconds]                                :      0.00
>
>
>                              Kindly suggest me a solution to my problem.
>
>
>Thanking you
>
>
>With regards
>
>Prasad .
>
>
>
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