Amber2Gromos Example¶

[1]:

from pygromos.files.forcefield import _generic_force_field
from pygromos.files.gromos_system import gromos_system
from pygromos.files.forcefield.amber import amberff
from pygromos.gromos.gromosPP import _gromosPPbase

[2]:

# note: ambertools is required. you can install it eg with: conda install -c conda-forge ambertools
ff = amberff.AmberFF(name = "amberff_gaff")

[3]:

molecule = "example_files/amber2gromos/aniline.mol2"

[11]:

gromosPP_bin_dir = None #ADAPT HERE

create top + cnf for aniline¶

[12]:

ff.solvate = False
system = gromos_system.Gromos_System(work_folder = "example_files/amber2gromos",
                                     system_name = "aniline",
                                     forcefield = ff,
                                     auto_convert = True,
                                     in_mol2_file = molecule,
                                     in_gromosPP_bin_dir = gromosPP_bin_dir)

['/home/salome/pymol/envs/pygromosx/bin/antechamber', '-i', '/home/salome/PhD/pyg/PyGromosTools/examples/example_files/amber2gromos/aniline.mol2', '-fi', 'mol2', '-o', 'aniline.mol2', '-fo', 'mol2', '-s', '2', '-c', 'bcc', '-nc', '0']

Welcome to antechamber 21.0: molecular input file processor.

acdoctor mode is on: check and diagnose problems in the input file.
The atom type is set to gaff; the options available to the -at flag are
    gaff, gaff2, amber, bcc, and sybyl.
-- Check Format for mol2 File --
   Status: pass
Info: Ignoring Mol2 record type (@<TRIPOS>SUBSTRUCTURE).
Info: Finished reading file (/home/salome/PhD/pyg/PyGromosTools/examples/example_files/amber2gromos/aniline.mol2); atoms read (14), bonds read (14).
Info: Determining atomic numbers from atomic symbols which are case sensitive.
-- Check Unusual Elements --
   Status: pass
-- Check Open Valences --
   Status: pass
-- Check Geometry --
      for those bonded
      for those not bonded
   Status: pass
-- Check Weird Bonds --
   Status: pass
-- Check Number of Units --
   Status: pass
acdoctor mode has completed checking the input file.

Running: /home/salome/pymol/envs/pygromosx/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

Running: /home/salome/pymol/envs/pygromosx/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Info: Total number of electrons: 50; net charge: 0

Running: /home/salome/pymol/envs/pygromosx/bin/sqm -O -i sqm.in -o sqm.out

/bin/bash: /home/salome/pymol/envs/pygromosx/lib/libtinfo.so.6: no version information available (required by /bin/bash)
/bin/bash: /home/salome/pymol/envs/pygromosx/lib/libtinfo.so.6: no version information available (required by /bin/bash)


Running: /home/salome/pymol/envs/pygromosx/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /home/salome/pymol/envs/pygromosx/dat/antechamber/BCCPARM.DAT -s 2 -j 1

Running: /home/salome/pymol/envs/pygromosx/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC

['/home/salome/pymol/envs/pygromosx/bin/parmchk2', '-i', '/home/salome/PhD/pyg/PyGromosTools/examples/example_files/amber2gromos/antechamber_tmp/aniline.mol2', '-f', 'mol2', '-o', 'aniline.frcmod']
['/home/salome/pymol/envs/pygromosx/bin/tleap', '-f', 'aniline.cmd']
-I: Adding /home/salome/pymol/envs/pygromosx/dat/leap/prep to search path.
-I: Adding /home/salome/pymol/envs/pygromosx/dat/leap/lib to search path.
-I: Adding /home/salome/pymol/envs/pygromosx/dat/leap/parm to search path.
-I: Adding /home/salome/pymol/envs/pygromosx/dat/leap/cmd to search path.
-f: Source aniline.cmd.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./aniline.cmd
----- Source: /home/salome/pymol/envs/pygromosx/dat/leap/cmd/leaprc.gaff
----- Source of /home/salome/pymol/envs/pygromosx/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /home/salome/pymol/envs/pygromosx/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
----- Source: /home/salome/pymol/envs/pygromosx/dat/leap/cmd/leaprc.water.tip3p
----- Source of /home/salome/pymol/envs/pygromosx/dat/leap/cmd/leaprc.water.tip3p done
Loading library: /home/salome/pymol/envs/pygromosx/dat/leap/lib/atomic_ions.lib
Loading library: /home/salome/pymol/envs/pygromosx/dat/leap/lib/solvents.lib

/bin/bash: /home/salome/pymol/envs/pygromosx/lib/libtinfo.so.6: no version information available (required by /bin/bash)
/bin/bash: /home/salome/pymol/envs/pygromosx/lib/libtinfo.so.6: no version information available (required by /bin/bash)

Loading parameters: /home/salome/pymol/envs/pygromosx/dat/leap/parm/frcmod.tip3p
Reading force field modification type file (frcmod)
Reading title:
This is the additional/replacement parameter set for TIP3P water
Loading parameters: /home/salome/pymol/envs/pygromosx/dat/leap/parm/frcmod.ions1lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set)
Loading parameters: /home/salome/pymol/envs/pygromosx/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008)
Loading parameters: /home/salome/pymol/envs/pygromosx/dat/leap/parm/frcmod.ions234lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set)
Loading parameters: /home/salome/pymol/envs/pygromosx/dat/leap/parm/frcmod.chcl3
Reading force field modification type file (frcmod)
Reading title:
 chloroform frcmod file
Using modified Bondi radii
Loading parameters: /home/salome/PhD/pyg/PyGromosTools/examples/example_files/amber2gromos/parmchk_tmp/aniline.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
Loading Mol2 file: /home/salome/PhD/pyg/PyGromosTools/examples/example_files/amber2gromos/antechamber_tmp/aniline.mol2
Reading MOLECULE named ligand_1
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 7 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:

        res     total affected

        LI1     1
  )
 (no restraints)
Writing pdb file: /home/salome/PhD/pyg/PyGromosTools/examples/example_files/amber2gromos/tleap_tmp/aniline.leap.pdb
        Quit

Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
converted topology saved to /home/salome/PhD/pyg/PyGromosTools/examples/example_files/amber2gromos/aniline.top
converted coordinates saved to /home/salome/PhD/pyg/PyGromosTools/examples/example_files/amber2gromos/aniline.cnf

create top + cnf for aniline, solvated in CHCl3¶

[6]:

ff.solvate = True
ff.solventbox = "CHCL3BOX"

[7]:

system = gromos_system.Gromos_System(work_folder = "example_files/amber2gromos",
                                     system_name = "aniline",
                                     forcefield = ff,
                                     auto_convert = True,
                                     in_mol2_file = molecule,
                                     in_gromosPP_bin_dir = gromosPP_bin_dir)

['/home/salome/pymol/envs/pygromosx/bin/antechamber', '-i', '/home/salome/PhD/pyg/PyGromosTools/examples/example_files/amber2gromos/aniline.mol2', '-fi', 'mol2', '-o', 'aniline.mol2', '-fo', 'mol2', '-s', '2', '-c', 'bcc', '-nc', '0']

Welcome to antechamber 21.0: molecular input file processor.

acdoctor mode is on: check and diagnose problems in the input file.
The atom type is set to gaff; the options available to the -at flag are
    gaff, gaff2, amber, bcc, and sybyl.
-- Check Format for mol2 File --
   Status: pass
Info: Ignoring Mol2 record type (@<TRIPOS>SUBSTRUCTURE).
Info: Finished reading file (/home/salome/PhD/pyg/PyGromosTools/examples/example_files/amber2gromos/aniline.mol2); atoms read (14), bonds read (14).
Info: Determining atomic numbers from atomic symbols which are case sensitive.
-- Check Unusual Elements --
   Status: pass
-- Check Open Valences --
   Status: pass
-- Check Geometry --
      for those bonded
      for those not bonded
   Status: pass
-- Check Weird Bonds --
   Status: pass
-- Check Number of Units --
   Status: pass
acdoctor mode has completed checking the input file.

Running: /home/salome/pymol/envs/pygromosx/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

Running: /home/salome/pymol/envs/pygromosx/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Info: Total number of electrons: 50; net charge: 0

Running: /home/salome/pymol/envs/pygromosx/bin/sqm -O -i sqm.in -o sqm.out

/bin/bash: /home/salome/pymol/envs/pygromosx/lib/libtinfo.so.6: no version information available (required by /bin/bash)
/bin/bash: /home/salome/pymol/envs/pygromosx/lib/libtinfo.so.6: no version information available (required by /bin/bash)


Running: /home/salome/pymol/envs/pygromosx/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /home/salome/pymol/envs/pygromosx/dat/antechamber/BCCPARM.DAT -s 2 -j 1

Running: /home/salome/pymol/envs/pygromosx/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC

['/home/salome/pymol/envs/pygromosx/bin/parmchk2', '-i', '/home/salome/PhD/pyg/PyGromosTools/examples/example_files/ambertools_pipeline/antechamber_tmp/aniline.mol2', '-f', 'mol2', '-o', 'aniline.frcmod']
['/home/salome/pymol/envs/pygromosx/bin/tleap', '-f', 'aniline.cmd']
-I: Adding /home/salome/pymol/envs/pygromosx/dat/leap/prep to search path.
-I: Adding /home/salome/pymol/envs/pygromosx/dat/leap/lib to search path.
-I: Adding /home/salome/pymol/envs/pygromosx/dat/leap/parm to search path.
-I: Adding /home/salome/pymol/envs/pygromosx/dat/leap/cmd to search path.
-f: Source aniline.cmd.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./aniline.cmd
----- Source: /home/salome/pymol/envs/pygromosx/dat/leap/cmd/leaprc.gaff
----- Source of /home/salome/pymol/envs/pygromosx/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /home/salome/pymol/envs/pygromosx/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
----- Source: /home/salome/pymol/envs/pygromosx/dat/leap/cmd/leaprc.water.tip3p
----- Source of /home/salome/pymol/envs/pygromosx/dat/leap/cmd/leaprc.water.tip3p done
Loading library: /home/salome/pymol/envs/pygromosx/dat/leap/lib/atomic_ions.lib
Loading library: /home/salome/pymol/envs/pygromosx/dat/leap/lib/solvents.lib
Loading parameters: /home/salome/pymol/envs/pygromosx/dat/leap/parm/frcmod.tip3p
Reading force field modification type file (frcmod)
Reading title:
This is the additional/replacement parameter set for TIP3P water
Loading parameters: /home/salome/pymol/envs/pygromosx/dat/leap/parm/frcmod.ions1lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set)
Loading parameters: /home/salome/pymol/envs/pygromosx/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008)
Loading parameters: /home/salome/pymol/envs/pygromosx/dat/leap/parm/frcmod.ions234lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set)
Loading parameters: /home/salome/pymol/envs/pygromosx/dat/leap/parm/frcmod.chcl3
Reading force field modification type file (frcmod)
Reading title:
 chloroform frcmod file
Using modified Bondi radii
Loading parameters: /home/salome/PhD/pyg/PyGromosTools/examples/example_files/ambertools_pipeline/parmchk_tmp/aniline.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
Loading Mol2 file: /home/salome/PhD/pyg/PyGromosTools/examples/example_files/ambertools_pipeline/antechamber_tmp/aniline.mol2
Reading MOLECULE named ligand_1
  Solute vdw bounding box:              8.593 7.203 3.895
  Total bounding box for atom centers:  36.593 35.203 31.895
  Solvent unit box:                     56.496 56.496 56.496
  Total vdw box size:                   40.347 38.887 35.650 angstroms.
  Volume: 55933.916 A^3
  Total mass 28741.446 amu,  Density 0.853 g/cc
  Added 240 residues.
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 7 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:

        res     total affected

        LI1     1
  )
 (no restraints)

/bin/bash: /home/salome/pymol/envs/pygromosx/lib/libtinfo.so.6: no version information available (required by /bin/bash)
/bin/bash: /home/salome/pymol/envs/pygromosx/lib/libtinfo.so.6: no version information available (required by /bin/bash)

Writing pdb file: /home/salome/PhD/pyg/PyGromosTools/examples/example_files/ambertools_pipeline/tleap_tmp/anilineleap_CHCL3BOX.pdb
   printing CRYST1 record to PDB file with box info
        Quit

Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
converted topology saved to /home/salome/PhD/pyg/PyGromosTools/examples/example_files/ambertools_pipeline/aniline_CHCL3BOX.top
  40.3470000  38.8870000  35.6500000  90.0000000  90.0000000  90.0000000

converted coordinates saved to /home/salome/PhD/pyg/PyGromosTools/examples/example_files/ambertools_pipeline/aniline_CHCL3BOX.cnf

[8]:

ff.amber.solvate

[8]:

True

create top + cnf for aniline, solvated in TIP3P water¶

[9]:

ff.solventbox = "TIP3PBOX"

[10]:

system = gromos_system.Gromos_System(work_folder = "example_files/amber2gromos",
                                     system_name = "aniline",
                                     forcefield = ff,
                                     auto_convert = True,
                                     in_mol2_file = molecule,
                                     in_gromosPP_bin_dir = gromosPP_bin_dir)

['/home/salome/pymol/envs/pygromosx/bin/antechamber', '-i', '/home/salome/PhD/pyg/PyGromosTools/examples/example_files/amber2gromos/aniline.mol2', '-fi', 'mol2', '-o', 'aniline.mol2', '-fo', 'mol2', '-s', '2', '-c', 'bcc', '-nc', '0']

Welcome to antechamber 21.0: molecular input file processor.

acdoctor mode is on: check and diagnose problems in the input file.
The atom type is set to gaff; the options available to the -at flag are
    gaff, gaff2, amber, bcc, and sybyl.
-- Check Format for mol2 File --
   Status: pass
Info: Ignoring Mol2 record type (@<TRIPOS>SUBSTRUCTURE).
Info: Finished reading file (/home/salome/PhD/pyg/PyGromosTools/examples/example_files/amber2gromos/aniline.mol2); atoms read (14), bonds read (14).
Info: Determining atomic numbers from atomic symbols which are case sensitive.
-- Check Unusual Elements --
   Status: pass
-- Check Open Valences --
   Status: pass
-- Check Geometry --
      for those bonded
      for those not bonded
   Status: pass
-- Check Weird Bonds --
   Status: pass
-- Check Number of Units --
   Status: pass
acdoctor mode has completed checking the input file.

Running: /home/salome/pymol/envs/pygromosx/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

Running: /home/salome/pymol/envs/pygromosx/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Info: Total number of electrons: 50; net charge: 0

Running: /home/salome/pymol/envs/pygromosx/bin/sqm -O -i sqm.in -o sqm.out

/bin/bash: /home/salome/pymol/envs/pygromosx/lib/libtinfo.so.6: no version information available (required by /bin/bash)
/bin/bash: /home/salome/pymol/envs/pygromosx/lib/libtinfo.so.6: no version information available (required by /bin/bash)


Running: /home/salome/pymol/envs/pygromosx/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /home/salome/pymol/envs/pygromosx/dat/antechamber/BCCPARM.DAT -s 2 -j 1

Running: /home/salome/pymol/envs/pygromosx/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC

['/home/salome/pymol/envs/pygromosx/bin/parmchk2', '-i', '/home/salome/PhD/pyg/PyGromosTools/examples/example_files/ambertools_pipeline/antechamber_tmp/aniline.mol2', '-f', 'mol2', '-o', 'aniline.frcmod']
['/home/salome/pymol/envs/pygromosx/bin/tleap', '-f', 'aniline.cmd']
-I: Adding /home/salome/pymol/envs/pygromosx/dat/leap/prep to search path.
-I: Adding /home/salome/pymol/envs/pygromosx/dat/leap/lib to search path.
-I: Adding /home/salome/pymol/envs/pygromosx/dat/leap/parm to search path.
-I: Adding /home/salome/pymol/envs/pygromosx/dat/leap/cmd to search path.
-f: Source aniline.cmd.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./aniline.cmd
----- Source: /home/salome/pymol/envs/pygromosx/dat/leap/cmd/leaprc.gaff
----- Source of /home/salome/pymol/envs/pygromosx/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /home/salome/pymol/envs/pygromosx/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
----- Source: /home/salome/pymol/envs/pygromosx/dat/leap/cmd/leaprc.water.tip3p
----- Source of /home/salome/pymol/envs/pygromosx/dat/leap/cmd/leaprc.water.tip3p done
Loading library: /home/salome/pymol/envs/pygromosx/dat/leap/lib/atomic_ions.lib
Loading library: /home/salome/pymol/envs/pygromosx/dat/leap/lib/solvents.lib
Loading parameters: /home/salome/pymol/envs/pygromosx/dat/leap/parm/frcmod.tip3p
Reading force field modification type file (frcmod)
Reading title:
This is the additional/replacement parameter set for TIP3P water
Loading parameters: /home/salome/pymol/envs/pygromosx/dat/leap/parm/frcmod.ions1lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set)
Loading parameters: /home/salome/pymol/envs/pygromosx/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008)
Loading parameters: /home/salome/pymol/envs/pygromosx/dat/leap/parm/frcmod.ions234lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set)
Loading parameters: /home/salome/pymol/envs/pygromosx/dat/leap/parm/frcmod.chcl3
Reading force field modification type file (frcmod)
Reading title:
 chloroform frcmod file
Using modified Bondi radii
Loading parameters: /home/salome/PhD/pyg/PyGromosTools/examples/example_files/ambertools_pipeline/parmchk_tmp/aniline.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
Loading Mol2 file: /home/salome/PhD/pyg/PyGromosTools/examples/example_files/ambertools_pipeline/antechamber_tmp/aniline.mol2
Reading MOLECULE named ligand_1
  Solute vdw bounding box:              8.593 7.203 3.895
  Total bounding box for atom centers:  36.593 35.203 31.895
  Solvent unit box:                     18.774 18.774 18.774
  Total vdw box size:                   39.546 38.307 34.954 angstroms.

/bin/bash: /home/salome/pymol/envs/pygromosx/lib/libtinfo.so.6: no version information available (required by /bin/bash)
/bin/bash: /home/salome/pymol/envs/pygromosx/lib/libtinfo.so.6: no version information available (required by /bin/bash)

  Volume: 52950.481 A^3
  Total mass 21982.566 amu,  Density 0.689 g/cc
  Added 1215 residues.
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 7 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:

        res     total affected

        LI1     1
        WAT     1215
  )
 (no restraints)
Writing pdb file: /home/salome/PhD/pyg/PyGromosTools/examples/example_files/ambertools_pipeline/tleap_tmp/anilineleap_TIP3PBOX.pdb
   printing CRYST1 record to PDB file with box info
        Quit

Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
converted topology saved to /home/salome/PhD/pyg/PyGromosTools/examples/example_files/ambertools_pipeline/aniline_TIP3PBOX.top
  39.5462090  38.3065070  34.9536470  90.0000000  90.0000000  90.0000000

converted coordinates saved to /home/salome/PhD/pyg/PyGromosTools/examples/example_files/ambertools_pipeline/aniline_TIP3PBOX.cnf

[ ]:

[ ]: