Re: [modeller_usage] How to incorporate NAD and water in my model
To: , ,
Subject: Re: [modeller_usage] How to incorporate NAD and water in my model
From: "Charlie Allerston" <>
Date: Thu, 15 Mar 2007 15:07:40 +0000
Do you have to use the modeller alignment script? I have been using ebi
software to create a .pir file.
After reading the modeller files and tutorials i am still at a loss as to
how to use these 'blk' characters. I am trying to get a molecule of fad
that is present in my template into my model.
From: Joel Tyndall <>
To: deepti <>,
Subject: Re: [modeller_usage] How to incorporate NAD and water in my model
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
> APIGWNMKDATPVAKTVCALLSDWLPATTGDIIYADGGAHTQLL*
>
>
>
>
> 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.
>
>
> Thanks and Regards,
> Deepti
>
>
>
> dreams
>
>
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--
Joel Tyndall, PhD
Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin 9054
New Zealand
Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti 9054
Aotearoa
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Fax / Waeawhakaahua +64 3 4797034
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