Subject: Re: [modeller_usage] Protein-DNA loop model
From: Modeller Caretaker <>
Date: Thu, 17 Nov 2011 08:33:55 -0800
Cc:
On 11/17/11 1:23 AM, Rubben Torella wrote:
My first problem is that MODELLER does not support DNA
Sure it does - you can use the '.' residue type just like a ligand to
copy the DNA from the template directly into the model. Modeller will
automatically add restraints on it to keep it rigid.
I use the options _a.md_level= None_ to keep the rest of the protein
fixed
md_level only controls the level of MD refinement, not all of the
optimization. If you set it to None, the model will still be optimized
with CG. If you don't want it to move at all, see
http://salilab.org/modeller/9.10/manual/node23.html
I have another problem now: I have a very long loop to build (35 aa)
and using these two commands, MODELLER create a very strange hairpin
loop to connect these two positions. I know which will be the correct
structure of this loop because I have a similar protein that present
this loop
In that case you should probably align that other protein with your
model in the loop region. Modeller is unlikely to successfully model a
35aa loop without a template - the conformational space is just too large.
Ben Webb, Modeller Caretaker
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