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