Leap (Amber): custom solvent box

This tutorial explains how to generate and use a custom solvent box to solvate a molecule for an MD simulation with Amber.

Note

Instead of creating a custom solvent box, it might be better to directly set up the whole system (solute + solvent) as described in this tutorial and that one. It is therefore not recommended to follow this tutorial!

1. Generate the box with packmol

   In this step we want to generate a .pdb file for the (non-optimized) solvent box.

   This can be done by following this tutorial and using only one species in packmol (e.g. solvent1).

2. Creating input files for Amber

   Now that we have a first structure of the solvent box, we need to equilibrate it. For that we will use the Amber package. We thus need to create input files for Amber.

   This can be done by following this tutorial with a single type of molecules (the solvent).

3. Equilibrate the custom box

   In this step we use the input files generated in the previous step to equilibrate the box.

   This can be done by following this tutorial.

4. Save custom box in library file

   Now that we have equilibrated our box. We will use leap to generate a library file for the box. This step requires to have a .pdb file of the equilibrated structure as well as a .mol2 file of the solvent molecule.

   Note

   The residue name of the solvent molecule must be the same in the two files and in the script below (SLV).

   leap.inp:

   # load parameters
   source leaprc.ff14SB
   source leaprc.gaff
   #
   # load solvent molecule parameters
   SLV = loadmol2 solvent.mol2
   loadamberparams solvent.frcmod
   check SLV
   #
   # load equilibrated pdb file
   MYBOX = loadpdb system.pdb
   #
   # set the dimensions of the box (check in pdb file)
   set MYBOX box {30,30,30}
   #
   # save box as library file
   saveoff MYBOX .my_box.lib
   quit
   

   Just load Amber and run leap:

   module load amber/14
   tleap -f leap.inp -s > leap.out &
   

5. Use a custom box

   Now that our box has been equilibrated, we can use it to solvate a molecule. Create an input file for leap (adapt it if needed). For this step you need to have a .mol2 and a .frcmod file for the solute (see this tutorial to generate those files).

   leap.inp:

   # load parameters
   source leaprc.ff14SB
   source leaprc.gaff
   #
   # load solute molecule
   SLU = loadmol2 solute.mol2
   loadamberparams solute.frcmod
   check SLU
   #
   # load the custom box library.
   # The box has been generated with the name MYBOX (see below)
   loadoff my_box.lib
   #
   # solvate solute in custom solvent
   # 14 is the minimal distance (in Angstroms) between
   # the solute and the edge of the box
   solvatebox SLU MYBOX 14
   #
   # save structure
   saveamberparm SLU solute_solv.top solute_solv.rst
   quit
   

   Just load Amber and run leap:

   module load amber/14
   tleap -f leap.inp -s > leap.out &
   

   Check that everything went fine and visualize:

   vmd -parm7 solute_solv.top -rst7 solute_solv.rst