Leap (Amber): set up a non-standard system from a .pdb file

This tutorial explains how to obtain input files for Amber, from a .pdb file containing residues not automatically recognized by Amber force fields.

An example of this might be when you generate a .pdb file from packmol as described in this tutorial.

We will therefore assume that we have a system.pdb which contains three types of molecules, with the structure described into solute.pdb, solvent1.pdb, and solvent2.pdb, and residue names SLU, SV1, and SV2, respectively.

In addition, we will need the .mol2 and .frcmod files for all three species. These can be obtained as described in this tutorial.

Once all the required files have been produced, a simple input file for leap can be written and executed to generate inputs for Amber.

leap.inp:

source leaprc.ff14SB
source leaprc.gaff
#
# load solute
SLU = loadmol2 solute.mol2
loadamberparams solute.frcmod
check SLU
#
# load solvent1
SV1 = loadmol2 solvent1.mol2
loadamberparams solvent1.frcmod
check SV1
#
# load solvent2
SV1 = loadmol2 solvent2.mol2
loadamberparams solvent2.frcmod
check SV2
#
# load system
SYS = loadpdb system.pdb
# The dimension of the box should match those used to create system.pdb with packmol
set SYS box {30,30,30}
saveamberparm SYS system.top system.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 (it should match the box size used in packmol).

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 system.top -rst7 system.rst