I did molecular dynamic simulations with DESMOND.
Now, I want to obtain the interaction free energy using MM/PB(GB)SA.
The free tools I found to perform such calculations are AmberTools and g_mmpbsa. AmberTools work only on Amber-type files, whereas g_mmbbsa works with GROMACS-type. This imply that I have to convert the DESMOND trajectories to AMBER or GROMACS formats.
I did that using VMD. In case of AMBER, I got the files prmtop and mdcrd whereas for GROMACS I got gro and top files. I also tried to use InterMol, but I am getting an error on conversions.
For both tools, I need to prepare the input files. In case of AmberTools, there is a Python script (ante-MMPBSA) that extract the solvated complex, the complex, the ligand and the receptor from the trajectory files. This scrip is falling to do that from the converted trajectories. In case of g_mmpbsa, it also need the index.ndx file.
My question: Is there a way to accomplish this task? Any suggestion is welcome!