Hello all, I have some doubt on modelling with ligand and need your help.
I have go over the tutorial on ligand but still I am not able to create my own.
I would like to include the ligand from the template pdb for the the models.
In my case, the substrate is cellotetraose (4 glucose units). Should one or four dots (....) to be added at the end of the alignment?
My other question in how do you build the alignment file (ali)? Do you simply add the dots to the alignment file or is there any tricks? (I am wondering do we need to modify the PDB file to include the BLK or HETATOM, and then create the ali?)
When I tried to simply add the dots to the ali file and ran the script to build the model, I got error with the structures not being recognized and it complained about the sequence length. Please kindly give us some advice or share with me your own precious experience if you've already done the same thing.
Thank you so much!