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.