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 :::::
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
.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.