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

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-----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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