Re: [modeller_usage] Modelling a protein loop close to DNA .....
To: Sergio Garay <>
Subject: Re: [modeller_usage] Modelling a protein loop close to DNA .....
From: Modeller Caretaker <>
Date: Wed, 13 Apr 2011 12:00:08 -0700
Cc:
On 4/13/11 4:09 AM, Sergio Garay wrote:
I have obtained a reasonably good model of protein dimer close to a DNA
molecule just copying the DNA template into my target. But now I want to
refine a protein loop close to DNA molecule but taking into account all
"real" interactions between the atoms of my protein and DNA.
The only "real" interactions Modeller can model with DNA or RNA are van
der Waals and stereochemistry (and electrostatics if you turn it on).
But in practice this is not sufficient to maintain the correct DNA
structure - it will unravel.
At the
moment I was not able to make modeller to recognize my target dna bases.
It should be able to read them in just fine - what problem are you
encountering?
So, my question is: if the ordering of the DNA base atoms in my pdb
record are different to the one in top_heav.lib, Should I change it in
my pdb or Should I rewrite the top in order to it matches with that of
pdb file.
Neither - they don't need to be in the same order.
I also changed my alignment in order to the bases can be recognized:
Looks fine to me, but when refining an existing PDB file, the alignment
isn't used. All non-loop regions will stay fixed, so it would make
little difference whether you treat DNA as a "real" residue or use a BLK
- the only interactions considered are van der Waals.