[modeller_usage] Protein + Metal Ion

[Anshul Awasthi <>]

Dear Modeller users,

I am trying to model the structure of  a protein that contains Zn ion in 
the active site, using modeller 7v7. For the modeling purpose I am using 
5 templates and one of them contains 2 His residues coordinated with Zn 
ion, and these residues are conserved among all the templates and the 
target sequence.

I have included these lines in my top file


SET HETATM_IO             = on

SUBROUTINE ROUTINE        = 'special_restraints'
SET ATOM_IDS 'NE2:493' 'ZN:1422'
SET ATOM_IDS 'NE2:921' 'ZN:1422'
ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0.1
RETURN
END_SUBROUTINE
==================================================================

I have put /z* at the end of the alignment file as follows:

P1;1WVR
structureX:1WVR:   9 :A: 181 :::::
PRKPEIQNEIIDLHNSLRRSVN------------PTASNMLKMEWYPEAAANAERWAYRCIESHSSRDSRVIGG-
---IKCGENIYMAT-----YPAKWTDIIHAWHGEYKDFKYGVGAVPSD----AVIGHYTQIVWYKSYRAGCAAAY
CPSSKYS------YFYVCQYCPAGNIIGKTATPYKSGPPCGDCP-SD-C-DN--GLCTN/z/*
==================================================================
But when I run the modeller i get an error message stating "SEQUENCE 
DIFFERENCE BETWEEN ALIGNMENT AND  PDB "

Following is the portion of the generated log file:

read_al_374_> Non-standard residue type,position,sequence:  z      
210        2

Read the alignment from file       : templates.ali
Total number of alignment positions:   210

#  Code        #_Res #_Segm PDB_code    Name
------------------------------------------------------------------------------- 

1       1RC9     173      1        1RC9
2       1WVR     174      2        1WVR
3       1XX5     173      1        1XX5
4       1U53     186      1        1U53
5       1QNX     170      1        1QNX
6      GLiPR     181      1       GLiPR
TOP_________>   137  113 STRING_IF STRING_ARGUMENTS = TOP_VERSION 
'accelrys', OPER;
                   ATION = 'ne', THEN = 'GO_TO __ACCELRYS1'

TOP_________>   138  117 CHECK_ALIGNMENT

check_a_343_> >> BEGINNING OF COMMAND
openf5__224_> Open       11  OLD  SEQUENTIAL  ./1RC9.pdb
openf5__224_> Open       11  OLD  SEQUENTIAL  ./1WVR.pdb
rdabrk__291E> Sequence difference between alignment and  pdb :

STRUCTURE RES_IND  ALN_ITYP  ALN_RES  X_ITYP  X_RES  -----*-----
        2     174        30     ZN2       24   UNK   GLCTNz  
rdabrk__288W> Protein not accepted:        2
openf5__224_> Open       11  OLD  SEQUENTIAL  ./1XX5.pdb
openf5__224_> Open       11  OLD  SEQUENTIAL  ./1U53.pdb
openf5__224_> Open       11  OLD  SEQUENTIAL  ./1QNX.pdb
check_a_337E> Structure not read in:        2
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1
=================================================================================== 


Can anyone suggest where things might be going wrong?

With regards,
Anshul