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.
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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 . > > > > http://clients.rediff.com/signature/track_sig.asp >