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
