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




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



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