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Re: [modeller_usage] How to incorporate NAD and water in my model
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 <joel.tyndall AT otago.ac.nz>
To: deepti <s_pinkbutterfly AT rediffmail.com>, modeller_usage@listsrv.ucsf.edu
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
> 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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>
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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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Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti 9054
Aotearoa

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