Setup FF from Amber’s Antechamber¶
This page shows an example of how to setup a FF model via Amber’s Antechamber program and it is assumed you have an Amber program pre-installed in your system.
The General Amber FF (GAFF) is a FF scheme specially designed for organic molecules including small drug molecules. The FF is implemented in DL_FIELD as amber16_gaff. However, what is missing is the partial charge values whcih can be obtained from Amber’s Antechamber program.
Example procedure
Let’s suppose you want to setup a GAFF model for ascorbic acid (Vitamin C) in water and the initial input file for the structure is in a PDB format. This file is located in the Examples/ folder in the DL_FIELD package (ascorbic_acid.pdb).
Step 1
The following command can be issued by calling antechamber as follows:
antechamber -if pdb -i ascorbic.pdb -fo mol2 -o ascorbic_acid.mol2 -c bcc
Which instructs the program to read in the pdb file and produce a mol2 output file. The bcc is the charge model being used, which is the abbreviation for AM1-BCC. The charge model was parameterised to reproduce HF/6-31G* RESP charges. These partial charge values are shown at the last column for each atom in the mol2 file (see below)
@<TRIPOS>MOLECULE
****
20 20 1 0 0
SMALL
bcc
@<TRIPOS>ATOM
1 C 0.5320 0.6960 0.5130 c3 1 *** 0.140400
2 C1 1.1130 -0.7070 0.4630 c3 1 *** 0.102100
3 H 1.1810 1.3910 1.0910 h1 1 *** 0.065200
4 O -0.7190 0.6670 1.1730 oh 1 *** -0.591800
5 H1 0.3760 1.1160 -0.5050 h1 1 *** 0.065200
6 H2 0.9650 -1.2210 1.4420 h1 1 *** 0.064700
7 O1 0.4260 -1.4590 -0.5120 oh 1 *** -0.599800
8 C2 2.5880 -0.7270 0.0980 c3 1 *** 0.148300
9 O2 3.3640 -0.0400 1.0670 os 1 *** -0.398900
10 H3 2.7690 -0.2680 -0.9010 h1 1 *** 0.112700
11 C3 3.1190 -2.1380 0.1410 c2 1 *** 0.041900
12 C4 4.2130 -0.9780 1.5850 c 1 *** 0.713800
13 O3 5.0310 -0.7710 2.4570 o 1 *** -0.549500
14 H4 -1.1250 1.5360 1.1300 ho 1 *** 0.414000
15 H5 0.8040 -2.3420 -0.5630 ho 1 *** 0.423000
16 O4 4.8120 -3.2890 1.4290 oh 1 *** -0.472100
17 C5 4.0860 -2.2150 1.0540 ce 1 *** -0.111100
18 O5 2.6680 -3.1720 -0.6010 oh 1 *** -0.467100
19 H6 3.1950 -3.9540 -0.3620 ho 1 *** 0.452000
20 H7 5.3850 -3.0020 2.1610 ho 1 *** 0.447000
@<TRIPOS>BOND
1 1 2 1
2 1 3 1
3 1 4 1
4 1 5 1
...
...
Step 2
Insert the mol2 as the input configuration and run the DL_FIELD control file with the following input options as follows:
Control file, for version 4.11
1 * Construct DL_POLY output files
none * Seconday output files (gromacs, chemshell, or none).
amber16_gaff * Type of force field require (see list below for choices).
kcal/mol * Energy unit: kcal/mol, kJ/mol, eV, or K.
normal * Conversion criteria (strict, normal, loose)
1 * Bond type (0=default, 1=harmonic , 2=Morse)
1 * Angle type (0=default, 1=harmonic, 2=harmonic cos)
none * Include user-defined information. Put 'none' or a .udff filename
1 * Verbosity mode: 1 = on, 0 = off
ascorbic_acid.mol2 * Configuration file.
none * Output file in PDB. Put 'none' if not needed.
1 80 molecules 12.0 * Solution Maker: on/off, density, unit, cutoff)
0 * Optimise FIELD output size, if possible? 1=yes 0=no
2 * Atom display: 1 = DL_FIELD format. 2 = Standard format
2 * Vdw display format: 1 = 12-6 format 2 = LJ format
default * Epsilon mixing rule (organic FF only) : default, or 1 = geometric, 2 = arithmatic
...
...
0 * Tether atoms? 1 = Yes (see below) 0 = No
1 * Constrain bonds? 1 = Yes (see below) 0 = No
0 * Apply rigid body? 1 = Yes (see below) 0 = No
1 * Periodic condition ? 0=no, other number = type of box (see below)
80.0 0.0 0.0 * Cell vector a (x, y, z)
0.0 80.0 0.0 * Cell vector b (x, y, z)
0.0 0.0 80.0 * Cell vector c (x, y, z)
default * 1-4 scaling for coulombic (put default or x for scaling=x)
default * 1-4 scaling for vdw (put default or x for scaling=x)
0 300.0 * Include velocity? 1=yes, 0=no and scaling temperature.
1 * Position solute at origin? 1 = yes, 0=no
spc 2.0 default * Solvate model? none or specify solvent (see below) and distance criteria.
0 5.0 * Add counter ions? 1=yes, 0=no, minimum distance from solute
...
...
...
########################################################
Atom state specification: type Molecular_Group filter [value]
CONSTRAIN not_define h-bond
#########################################################
...
...
The highlighted options instructs DL_FIELD to produce FF files for Amber GAFF force field by duplicating 80 ascorbic acid molecules in a cubic system of size 80 Å, and each molecule is separated by at least 12 Å from one another. After that, the system is solvated with the SPC water model. All H-containing bonds are also constrained.
Note
The Molecular Group is called ‘not_define’ because it is not clearly defined in the .mol2 file and DL_FIELD will automatically label the system with a default Molecular Group name as ‘not_define’.
Step 3
Run DL_FIELD to produce a dl_poly.FIELD file. The top portion of the file is shown as follows:
Generated by DL_FIELD v4.11
Units kcal/mol
Molecular types 2
Molecule name not_define
nummols 80
atoms 20
c3 12.01150 0.14040 1 0
c3 12.01150 0.10210 1 0
h1 1.00797 0.06520 1 0
oh 15.99940 -0.59180 1 0
h1 1.00797 0.06520 1 0
h1 1.00797 0.06470 1 0
oh 15.99940 -0.59980 1 0
c3 12.01150 0.14830 1 0
os 15.99940 -0.39890 1 0
h1 1.00797 0.11270 1 0
c2 12.01150 0.04190 1 0
c 12.01150 0.71380 1 0
o 15.99940 -0.54950 1 0
ho 1.00797 0.41400 1 0
ho 1.00797 0.42300 1 0
...
...
Notice the ATOM_KEYs and charge values are extracted, as is, from the input mol2 file.
If a force field scheme other than amber16_gaff is used, then the ATOM_KEYs and charge values from the mol2 file will be ignored and a new FF data will be produced. For example, consider CVFF FF scheme is used, then the dl_poly.FIELD produced is shown below:
Generated by DL_FIELD v4.11
Units kcal/mol
Molecular types 2
Molecule name not_define
nummols 80
atoms 20
c2 12.01150 -0.17000 1 0
c1 12.01150 -0.07000 1 0
h 1.00797 0.10000 1 0
oh 15.99940 -0.38000 1 0
h 1.00797 0.10000 1 0
h 1.00797 0.10000 1 0
oh 15.99940 -0.38000 1 0
c1 12.01150 0.15000 1 0
o 15.99940 -0.18000 1 0
h 1.00797 0.10000 1 0
c= 12.01150 -0.07030 1 0
c' 12.01150 0.41000 1 0
o' 15.99940 -0.38000 1 0
ho 1.00797 0.35000 1 0
ho 1.00797 0.35000 1 0
oh 15.99940 -0.37970 1 0
...
...
Can you see the difference?