I try to model homedimer with few point mutations using hometrimer as a
template. In the alignment file I specified to use only chain A and
chain B from the template, but the out put dimer model has different
monomer-monomer interface than template. I used standard
script( http://salilab.org/modeller/9v4/manual/node28.html) and the
alignment file:
If this is your actual alignment file, then there are some problems with it:
1. The chain break character is a forward slash (/). You seem to be
using a backward slash (\). That won't work.
2. You don't have anything aligned with your second chain, so Modeller
will build a very poor model for that. What you have as your
alignment is something like:
aaaa/---- template 1
bbbb/---- template 2
XXXX/YYYY model
The result is that Modeller will use *both* of your templates to
model the first chain, but will have no homology information at all
for the second - so you'll essentially get an extended chain. If you
really want to build a dimer using two single chain templates, your
alignment should look something like:
aaaa/---- template 1
----/bbbb template 2
XXXX/YYYY model
This, however, is still not ideal (see point 3).
3. You have split your template 1EFA into two single chain templates.
Since Modeller has no way to tell that these two templates are
actually from the same PDB, it can't build distance restraints
between the two chains, and thus the interface will not be conserved.
In order to conserve the interface, you should use a single dimer
template rather than two monomer templates, i.e.
aaaa/bbbb template 1
XXXX/YYYY model
In your case, your alignment file would thus look like:
>P1;inv3HD
sequence:inv3HD:1:.: 331 ::MODELLING PROTEIN:undefined::
(sequence of A chain) / (sequence of B chain)
>P1;1EFA
structureX:1EFA:2:A: 329 :B:LAC REPRESSOR:undefined::
(sequence of A chain) / (sequence of B chain)
Note that in the header for the 1EFA template you now tell Modeller to
read from residue 2 in the A chain all the way through to residue 329 in
the B chain. Look at the alignment file that goes with that script I
pointed you to (twochain.ali, in examples/automodel/) for a working
example. Notice that both the template and the model are dimers.