I am having problem with adding heteroatoms to my model. My template is a dimer with each having one inhibitor and one cofactor. I use '.' for HETATM and 'w' for water molecule in my alignment file. But each time I run, the .log file told me there are " too many non-bonded pairs. Increase MPAIRS". What does it mean? What should I do?
By the way, what should the comment line be with 2 chains and 4 HETATM and one H2O all together? The last several letters of the alignment file is: DHYRY/....w* Is it right?