Body: <p>I did molecular dynamic simulations with DESMOND.</p>
  <p>Now, I want to obtain the interaction free energy using MM/PB(GB)SA.</p>
  <p>The free tools I found to perform such calculations are <a href="https://ambermd.org/AmberTools.php" rel="nofollow noreferrer">AmberTools</a> and <a href="http://rashmikumari.github.io/g_mmpbsa/" rel="nofollow noreferrer">g_mmpbsa</a>.
  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.</p>
  <p>I did that using VMD. In case of AMBER, I got the files <em>prmtop</em> and <em>mdcrd</em> whereas for GROMACS I got <em>gro</em> and <em>top</em> files. I also tried to use <a href="https://github.com/shirtsgroup/InterMol" rel="nofollow noreferrer">InterMol</a>, but I am getting an error on conversions.</p>
  <p>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.</p>
  <p>My question: <strong>Is there a way to accomplish this task?</strong> Any suggestion is welcome!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-07T02:56:16.457Z
Comments.Text: Try here: https://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.
Comments.UserDisplayName: user1271772
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-07T11:30:18.477Z
Comments.Text: Hi @user1271772 (or I must said @Nick? This is Camps, lol.
Comments.UserDisplayName: Camps
Tags: <software-recommendation><gromacs>
Title: MM/PB(GB)SA calculations for DESMOND trajectories
ThreadText: # MM/PB(GB)SA calculations for DESMOND trajectories
  
  (Asked by: username_0 on 2020-08-21)
  
  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](https://ambermd.org/AmberTools.php) and [g\_mmpbsa](http://rashmikumari.github.io/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](https://github.com/shirtsgroup/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!
  
  **Tags:** software-recommendation, gromacs
  
  > **Comments:**
  > **username_1**: Try here: https://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.  
  > **username_0**: Hi @username_1 (or I must said @Nick? This is username_0, lol.  
  
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  ## 0 answers
  
  