Generate .mol2 file for leap and Amber¶
This tutorial explains how to generate a .mol2 file and eventually a
.frcmod file that can be used by leap to create input files for
molecular dynamics with Amber.
Note
When setting up files for Amber calculations, the residue names can be
of great importance. Try to be as consistent as possible during those
steps with the name of the residues (in the original .pdb file also
use the -rn option of antechamber).
Method 1: directly from a .pdb file¶
You can use the antechamber program to generate a .mol2 file from a
molecule.pdb file. Just run antechamber as follows:
module load amber/14
antechamber -i molecule.pdb -fi pdb -o molecule.mol2 -fo mol2 -c bcc -nc 0 -m 1
Method 2: Use RESP charges from Gaussian¶
It might be better to use RESP charges obtained from a Gaussian calculations to
generate the .mol2 file (see this tutorial for the
generation of RESP charges).
In this case the .mol2 file is obtained by calling antechamber
in the following way:
antechamber -i electrostatic_grid.log -fi gout -o solute.mol2 -fo mol2 -c resp -nc 0 -m 1 -rn MOL
Extra parameters¶
Some extra parameters might be required. They can be obtained in a .frcmod file
with parmchk as:
parmchk -i solute.mol2 -f mol2 -o solute.frcmod