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