I have a template 1ZK4 and query R-ADH of brevis. I was able to do modelling using modeller with cofactor NADP. But when i tried to add water I observe that the alignment between template and query is bad and not the same as it was without adding water. Due to this am getting irrelevant structure or structure is not completely getting fold to form 3D structure. Can anybody help me with this I am confused why the alignment is bad and structure is not proper?
I don't think there is any homology modeling software which incorporates water molecules in the modeling. Typically, water is not modeled because its position is often very transient.
Make with the model a MD simulation in a water grid (250 ps), then compare. The same with the template.
In Modeller folder you will find (C:\Program Files (x86)\Modeller9.13\examples\automodel) automodel folder. In this you will have align-ligand.ali and model-ligand.py files. use these files for giving input for modeller. if you get the problem send me ([email protected]) the template and query fasta. I will check.
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