OpenFF Automatic ParametrizationΒΆ
[1]:
import os
import pygromos
from pygromos.files.forcefield.openff.openff import OpenFF
from pygromos.files.gromos_system.gromos_system import Gromos_System
Warning: Unable to load toolkit 'OpenEye Toolkit'. The Open Force Field Toolkit does not require the OpenEye Toolkits, and can use RDKit/AmberTools instead. However, if you have a valid license for the OpenEye Toolkits, consider installing them for faster performance and additional file format support: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html OpenEye offers free Toolkit licenses for academics: https://www.eyesopen.com/academic-licensing
[2]:
project_dir = os.path.abspath("example_files/off_files/")
[3]:
ff = OpenFF()
Found off: /home/mlehner/PyGromosTools/pygromos/data/ff/SMIRNOFF/openff_unconstrained-2.0.0.offxml
[4]:
gsys = Gromos_System(work_folder=project_dir,
system_name="testOFF",
forcefield=ff,
in_smiles="C1CCCCC1",
in_imd_path=project_dir+"/gas_sd.imd",
auto_convert=True,
adapt_imd_automatically=True)
Found off: /home/mlehner/PyGromosTools/pygromos/data/ff/SMIRNOFF/openff_unconstrained-2.0.0.offxml
[5]:
gsys.top.make_ordered()
[6]:
gsys.top.SOLUTEATOM
[6]:
SOLUTEATOM
# NRP: number of solute atoms
18
# ATNM: atom number
# MRES: residue number
# PANM: atom name of solute atom
# IAC: integer (van der Waals) atom type code
# MASS: mass of solute atom
# CG: charge of solute atom
# CGC: charge group code (0 or 1)
# INE: number of excluded atoms
# INE14: number of 1-4 interactions
# ATNM MRES PANM IAC MASS CG CGC INE
# INE14
1 1 C1 1 12.01078 -0.0764 0 10 2 3 5 6 7 8
9 10 17 18
5 4 11 12 15 16
2 1 C2 1 12.01078 -0.0764 0 9 3 4 6 7 8 9
10 11 12
5 5 13 14 17 18
3 1 C3 1 12.01078 -0.0764 0 8 4 5 9 10 11 12
13 14
5 6 7 8 15 16
4 1 C4 1 12.01078 -0.0764 0 8 5 6 11 12 13 14
15 16
4 9 10 17 18
5 1 C5 1 12.01078 -0.0764 0 7 6 13 14 15 16 17
18
4 7 8 11 12
6 1 C6 1 12.01078 -0.0764 0 6 7 8 15 16 17 18
4 9 10 13 14
7 1 H1 2 1.007947 0.0382 0 1 8
4 9 10 17 18
8 1 H2 2 1.007947 0.0382 0 0
4 9 10 17 18
9 1 H3 2 1.007947 0.0382 0 1 10
2 11 12
10 1 H4 2 1.007947 0.0382 0 0
2 11 12
11 1 H5 2 1.007947 0.0382 0 1 12
2 13 14
12 1 H6 2 1.007947 0.0382 0 0
2 13 14
13 1 H7 2 1.007947 0.0382 0 1 14
2 15 16
14 1 H8 2 1.007947 0.0382 0 0
2 15 16
15 1 H9 2 1.007947 0.0382 0 1 16
2 17 18
16 1 H10 2 1.007947 0.0382 0 0
2 17 18
17 1 H11 2 1.007947 0.0382 0 1 18
0
18 1 H12 2 1.007947 0.0382 1 0
0
END
[7]:
gsys.rebase_files()
[8]:
gsys.imd.AMBER
[8]:
AMBER
# AMBER AMBSCAL
1 1.200000
END
[9]:
gsys.imd.FORCE
[9]:
FORCE
# BONDS ANGLES IMPROPER DIHEDRAL ELECTROSTATIC VDW
0 1 1 1 1 1
# NEGR NRE
1 18
END
[10]:
atom = gsys.cnf.POSITION[7]
[11]:
atom.atomType
[11]:
'H'
[12]:
gsys.top.BONDANGLEBENDTYPE
[12]:
BONDANGLEBENDTYPE
# NBTY: number of angle types
2
# CT CHT T0
5.57203e+02 1.35622e-01 1.16548e+02
5.02731e+02 1.24333e-01 1.15603e+02
END
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