Re: [modeller_usage] How to incorporate NAD and water in my model

[Joel Tyndall <joel.tyndall AT otago.ac.nz>]

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
> MFAELGKVWPKFDGFVHSIGFAPGDQLDGDYVNAVTREGFKIAHDISSYSFVAMAKACRSMLNPGSALLTLSYLG 
>
> AERAIPNYNVMGLAKASLEANVRYMANAMGPEGVRVNAISAGPIRTLAASGIK--------DFRKMLAHCEAVTP
> IRRTVTIEDVGNSAAFLCSDLSAGISGEVVHVDGGFSIAAMNEL*
>
> >P1;1eny
> sequence:1eny:    : :    : ::: 0.00: 0.00
> AGLLDGKRILVSGIITDSSIAFHIARVAQEQGAQLVLTGFDRLRLIQRITDRLPAKAPLLELDVQNEEHLASLAG
> RVTEAIGAGNKLDGVVHSIGFMPQTGMGINPFFDAPYADVSKGIHISAYSYASMAKALLPIMNPGGSIVGMDFDP
> S-RAMPAYNWMTVAKSALESVNRFVAREAGKYGVRSNLVAAGPIRTLAMSAIVGGALGEEAGAQIQLLEEGWDQR
> 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 
> <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/1050715198@Middle5/1120029_1114336/1119254/1?PARTNER=3&OAS_QUERY=null%20target=new%20> 
>
>
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--
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin 9054
New Zealand                     

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