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