Dear All:

Thank you for answering my previous questions.

Now I am trying to make solvation energy calculations for two proteins located at certain distance from each other in the solution. I also want to look at changes that might happen if I rotate one protein a certain angle. To do that I need to change coordinates of each atom inside the PQR file, but that is not efficient, because there are thousands of atoms and I need to perform several different runs. I was curious if there is a particular program or function in APBS that can do that for me: set one molecule certain distance away from another and if needed rotate one of the molecules?
Also in case of such calculculation do I have to specify each protein separately within the .in file, or should I include both in .pqr file? If I will specify them separately, what will be the best way to find appropriate grid length for my calculations? Thank you very much in advance. 

Best regards,
Vladimir Lankevich