Re: [modeller_usage] How to incorporate NAD and water in my model
To: deepti <>,
Subject: Re: [modeller_usage] How to incorporate NAD and water in my model
From: Joel Tyndall <>
Date: Thu, 15 Mar 2007 11:27:59 +1300
Hi Deepti,
I recently looked at a similar complex that included ATP and Mg. You can
add a # to your alignment file for NAD. See the response to my post
below (just replace ATP with NAD).
Cheers
J
Hi Joel
Have you tried to include an @ in your alignment file?according to restyp.lib (in mollib directory) it should correspond to ATP. I dont know how about the quality of the parameters are, but its a starter. And theres a starter for tweaking in top_heav.lib. If theres no ATP (or similat molecule) in you template You'll need to add some constraints to some atoms between your protein and ATP to restrict it to a position near the binding site.
Happy Modelling
Esben Bjerrum
deepti wrote:
Dear Modeller caretakers,
I am trying to construct a model for a protein having a known
structure for the purpose of learning Modeller.
The pdb structureis in form of protein-NAD adduct. My aim is to build
a similar model.
Using the templates I have built a model, please tell me how to
incorporate NAD and water in my model. I have read the manual 'faq' ,
but am confused how to change my alignment (including '.' for BLK
residues and 'w' ). How do I change the template pdb files for this?
How do I make my own restraint file?
My alignment file is(generated by align2d.py):-
>P1;1qsgA
structureX:1QSG.pdb: 2 :A: 259 :A:undefined:undefined:-1.00:-1.00
GFLS-GKRILVTGVASKLSIAYGIAQAMHREGAELAFTYQND--KLKGRVEEFAAQLGSDIVLQCDVAEDASIDT
I got a lesser objective function while using the alignment generated
by clustalw. Which would be a better option?
Also please suggest me ways to further refine my model so as to make
it almost like the pdb structure.