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 > > > ------------------------------------------------------------------------ > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >