Dear Suchetana,

MMGBSA is a metod to estimate the free energy of binding/interaction, thus, you don't need to use it if the only what you need is an interaction map. Furthermore, as I don't use amber I'm not even sure how amber's outputs represent this kind of calculations.

To find interacting residues you don't need any sophisticated methods. All you probably need is i.e. VMD with a standard plugin library.

Dear Rafal

I am looking for doing an analysis over the entire trajectory. Which plug-in in VMD do you suggest?

You have AMBERTOOLS14, which contains AMBER14 free use on CPU. Why don't you use AMBER14 to do MMPBSA?

To analyze the interaction among resides, you can use CPPTRAJ in AMBERTOOLS to find hydrogen bonds or mask around the residues you are interested in. Also, you may calculate the VdW and Elec interaction energy with keyword LIE. Do not use VMD plug-in to analyze AMBER trajectory. CPPTRAJ is the much more efficient. If you want to visualize it, I suggest you convert trajectory to DCD format and use VMD. 

Thanks. Since I wanted to do an interaction energy calculation between the substrate and the enzyme alone, I stripped the metal ion and managed to do MMPBSA with Amber12 itself. Earlier the problem was with the metal ion not being stripped from the trajectory.

Hi Stephane

I did recompile, yet was getting the error. Then later I realised that I wasn't stripping the Cobalt ion correctly while preparing the stripped trajectory. Doing that correctly (precisely by using the correct atom type) I got my solution.

Thanks

Suchetana