Modeller Caretaker wrote:

mailto:modeller_usage@salilab.org

> Anshul Awasthi wrote: > >> 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 suggest that you use the latest version, Modeller 8v2, instead. Not > only does it incorporate a number of bug fixes, but it gives more > informative diagnostics for problems like this one. It will read old > TOP scripts just fine, provided they have the .top file extension. > >> 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/* > > > > The final / is unnecessary here, since nothing follows the ion. > >> ================================================================== >> But when I run the modeller i get an error message stating "SEQUENCE >> DIFFERENCE BETWEEN ALIGNMENT AND 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 > > > > Your PDB file appears to have an UNK residue rather than a Zn atom > here. It's hard to say what your problem might be, as I'm guessing > your PDB is modified from code 1wvr (since the A chain continues to > residue 221, and the ion is cadmium, not zinc). > > If your problem continues, send me your full input files, and I'll > take a look. > > Ben Webb, Modeller Caretaker

Dear Ben, I was able to run the programme and got a model with Zn ion. But I was only able to do it without adding the restraints to the His residues and the Zn ion. But when I put the following subroutine at the end of my .top file, I get an error.

SUBROUTINE ROUTINE = 'special_restraints' SET ATOM_IDS 'NE2:420' 'ZN2:1436' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0.1 SET ATOM_IDS 'NE2:892' 'ZN2:1436' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0.1 RETURN END_SUBROUTINE

Following is the last portion of the log file with the error;

TOP_________> 231 199 MAKE_RESTRAINTS

make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 19104 19104 make_re_423_> Number of previous, current selected restraints: 18913 18913 TOP_________> 232 200 DELETE_ALIGNMENT

TOP_________> 233 201 RETURN

TOP_________> 234 165 CALL ROUTINE = 'special_restraints'

TOP_________> 235 810 SET ATOM_IDS 'NE2:420' 'ZN2:1436'

TOP_________> 236 811 ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0; .1

add_res_442E> One or more atoms absent from MODEL: NE2:420 ZN2:1436 top_error__E> ERROR_STATUS >= STOP_ON_ERROR: 1 1

The number of the residues I have used correspond to the modeller numbering system (*.ini file). I am not sure about the RESTRAINT_PARAMETERS I have put in the subroutines as I have duplicated it from one of the earlier posts. I tried to know more about them from the manual but could not understand. I shall be glad if you could also explain the meaning of various fields being used in the parameters.

With regards, Anshul