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:]
Sent: Saturday,
January 31, 2004 5:59 AM
To:
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 .