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!

  • $\begingroup$ Try here: mattermodeling.stackexchange.com. There's way more VMD questions there, plus there's an entire tag just for GROMACS, and AMBER is on topic there too. $\endgroup$ – user1271772 Dec 7 '20 at 2:56
  • $\begingroup$ Hi @user1271772 (or I must said @Nick? This is Camps, lol. $\endgroup$ – user9085 Dec 7 '20 at 11:30

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