Leap (Amber): solvate molecule in TIP3P water

This tutorial explains how to generate input files for Amber (topology and structure) for a molecule solvated in water. It assumes that a complete .mol2 file is available for the solute (solute.mol2). An additional solute.frcmod file might be required.

Check this tutorial to see how to get the .mol2 and .frcmod files.

From here, everything can be done in one step, by generating an input for the leap program.

leap.inp:

# load parameters
source leaprc.ff14SB
source leaprc.gaff
#
# load solute molecule
SLU = loadmol2 solute.mol2
list
loadamberparams solute.frcmod
check SLU
#
# solvate solute in water (TIP3P)
# 14 is the minimal distance (in Angstroms) between
# the solute and the edge of the box
solvatebox SLU TIP3PBOX 14
#
# save structure
saveamberparm SLU solute_solv.top solute_solv.rst
quit

Be sure to adapt the name of the input (and output) files in the script, as well as the size of the box (here we have a minimal distance of 14 Angstroms between the solute and the edge of the box). You can also chose another standard solvent (displayed after the list command in tleap). Check this tutorial to use a custom solvent box.

Finally, we just need to load Amber and run leap:

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

Check that everything went fine in the leap.out file and visualize the result in vmd:

module load vmd
vmd -parm7 solute_solv.top -rst7 solute_solv.rst