Dear Bhavik,

If you still have not resolved your issue vis-a-vis the modeling of dimeric protein, please have a look @ http://structuropedia.org (which is an interface to MODELLER).

Structuropedia automizes such model building with user opting to either upload his(er) own dimer template or defaulting to an automatic template selection with Blast search. Have a look at it. It could help you trouble-shoot your issue as it will also provide you with an alignment file so that you can see how MODELLER handles dimeric structures.

With warmest regards,

AMJAD FAROOQ PhD DIC | Associate Professor
Dept of Biochemistry, University of Miami School of Medicine
Location: Gautier Building, Suite 217
Address: 1011 NW 15th Street #217, Miami , FL 33136, USA
Contact: amjad@farooqlab.net | 305-243-2429
Labpage: farooqlab.net | structuropedia.org

On Mon, May 25, 2015 at 12:10 PM, Bhavik Sawhney <bhavik@cdfd.org.in> wrote:

Dear Sir,
This is your post regarding modelling of the dimer protein on dimeric template. I have done the required changes in the ali file (alignment file), do I need to change the PAP file also, because I am getting following error while running Script 4 : Number of residues in the alignment and the pdb files are different.
With Regards,
Bhavik

Hi,

If you have a dimer as template and want to model a dimer with the same
organisation, you just need to include a "/" character as chain breaker in
the alignment file (between your 2 monomers).

I join an exemple of alignment for a dimer.

On Thu, 12 Jun 2003, Difei Wang wrote:

> Hi, All
>
> I am wondering if it is possible to model a dimer structure from a dimer
> template.
> I can not find anything in the manual. I tried to model each of them first and
> then
> put them together. However, I am not sure it is good or not for the packing in
> the
> contact region. Thanks for your help.
>
> Difei
>
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