"No template found for residue..." Error
jaketanderson opened this issue · 4 comments
jaketanderson commented
Hi, I'm trying to use openmmforcefields to simulate a mixture of (GAFF-parameterized) TMAO and tip3p waters. I've tried following the steps on the README but I cannot get rid of "ValueError: No template found for residue 11 (TMA)" errors. I've tried keeping the TMAO residue as UNL (the default using openbabel), I've tried creating the openff molecule from an SDF file, and I've ensured that the CONECT information is in all my PDB files before using Packmol to create the mixture PDB. I'm at a loss here and would really appreciate some guidance!
Simulation:
from openmm.app import *
from openmm import *
from openmm.unit import *
from sys import stdout
from openff.toolkit.topology import Molecule
molecule = Molecule.from_pdb_and_smiles("../setup/TMAO.pdb", "C[N+](C)(C)[O-]")
from openmmforcefields.generators import GAFFTemplateGenerator
gaff = GAFFTemplateGenerator(molecules=molecule)
forcefield = ForceField('amber/tip3pfb_standard.xml', 'amber/tip3pfb_HFE_multivalent.xml')
forcefield.registerTemplateGenerator(gaff.generator)
gaff.generate_residue_template(molecule)
pdb = PDBFile('../setup/mixture.pdb')
sys = forcefield.createSystem(pdb.topology)Preparation:
packmol.input
#
# A mixture of water and TMAO
#
tolerance 2.0
filetype pdb
output mixture.pdb
connect yes
structure water.pdb
number 10
inside box 0. 0. 0. 80. 80. 80.
end structure
structure TMAO.pdb
number 1
inside box 0. 0. 0. 80. 80. 80.
end structure
water.pdb
COMPND HOH
AUTHOR GENERATED BY OPEN BABEL 3.1.0
HETATM 1 O HOH 1 0.994 0.071 0.066 1.00 0.00 O
HETATM 2 H1 HOH 1 1.962 0.040 0.101 1.00 0.00 H
HETATM 3 H2 HOH 1 0.716 -0.550 0.756 1.00 0.00 H
CONECT 1 2 3
CONECT 2 1
CONECT 3 1
MASTER 0 0 0 0 0 0 0 0 3 0 3 0
END
TMAO.pdb
HEADER
REMARK 99
REMARK 99 MOE v2020.09 (Chemical Computing Group ULC) Wed Aug 16 14:01:14 2023
HETATM 1 C TMA 0 2.778 -0.080 -0.540 1.00 0.00 C
HETATM 2 N TMA 0 1.459 0.049 0.265 1.00 0.00 N1+
HETATM 3 C TMA 0 1.461 1.584 0.218 1.00 0.00 C
HETATM 4 C TMA 0 0.261 -0.082 -0.710 1.00 0.00 C
HETATM 5 O TMA 0 1.452 -1.201 0.397 1.00 0.00 O1-
HETATM 6 H1 TMA 0 3.017 0.719 -1.229 1.00 0.00 H
HETATM 7 H2 TMA 0 2.869 -0.972 -1.153 1.00 0.00 H
HETATM 8 H3 TMA 0 3.635 -0.120 0.118 1.00 0.00 H
HETATM 9 H1 TMA 0 2.274 2.020 0.783 1.00 0.00 H
HETATM 10 H2 TMA 0 0.579 2.018 0.671 1.00 0.00 H
HETATM 11 H3 TMA 0 1.525 2.045 -0.761 1.00 0.00 H
HETATM 12 H1 TMA 0 0.119 0.713 -1.429 1.00 0.00 H
HETATM 13 H2 TMA 0 -0.678 -0.116 -0.174 1.00 0.00 H
HETATM 14 H3 TMA 0 0.250 -0.978 -1.325 1.00 0.00 H
CONECT 1 2 6 7 8
CONECT 2 1 3 4 5
CONECT 3 2 9 10 11
CONECT 4 2 12 13 14
CONECT 5 2
CONECT 6 1
CONECT 7 1
CONECT 8 1
CONECT 9 3
CONECT 10 3
CONECT 11 3
CONECT 12 4
CONECT 13 4
CONECT 14 4
END
mixture.pdb
HEADER
TITLE Built with Packmol
REMARK Packmol generated pdb file
REMARK Home-Page: http://m3g.iqm.unicamp.br/packmol
REMARK
HETATM 1 O HOH A 1 36.818 20.864 52.708 1.00 0.00 O
HETATM 2 H1 HOH A 1 36.688 19.906 52.638 1.00 0.00 H
HETATM 3 H2 HOH A 1 37.212 21.108 51.857 1.00 0.00 H
HETATM 4 O HOH A 2 52.649 14.294 57.800 1.00 0.00 O
HETATM 5 H1 HOH A 2 52.523 15.224 58.042 1.00 0.00 H
HETATM 6 H2 HOH A 2 53.310 13.977 58.434 1.00 0.00 H
HETATM 7 O HOH A 3 37.844 40.550 69.267 1.00 0.00 O
HETATM 8 H1 HOH A 3 37.368 41.347 69.545 1.00 0.00 H
HETATM 9 H2 HOH A 3 37.569 40.424 68.347 1.00 0.00 H
HETATM 10 O HOH A 4 56.705 24.553 15.266 1.00 0.00 O
HETATM 11 H1 HOH A 4 55.943 24.455 15.856 1.00 0.00 H
HETATM 12 H2 HOH A 4 56.659 23.771 14.695 1.00 0.00 H
HETATM 13 O HOH A 5 63.606 66.016 41.551 1.00 0.00 O
HETATM 14 H1 HOH A 5 62.881 66.292 40.970 1.00 0.00 H
HETATM 15 H2 HOH A 5 63.463 66.527 42.362 1.00 0.00 H
HETATM 16 O HOH A 6 40.477 44.772 30.262 1.00 0.00 O
HETATM 17 H1 HOH A 6 40.646 43.856 29.995 1.00 0.00 H
HETATM 18 H2 HOH A 6 41.346 45.099 30.537 1.00 0.00 H
HETATM 19 O HOH A 7 41.809 54.797 8.137 1.00 0.00 O
HETATM 20 H1 HOH A 7 42.722 54.475 8.151 1.00 0.00 H
HETATM 21 H2 HOH A 7 41.805 55.457 7.427 1.00 0.00 H
HETATM 22 O HOH A 8 60.341 67.903 22.677 1.00 0.00 O
HETATM 23 H1 HOH A 8 59.998 67.030 22.922 1.00 0.00 H
HETATM 24 H2 HOH A 8 61.231 67.719 22.343 1.00 0.00 H
HETATM 25 O HOH A 9 52.652 63.762 26.810 1.00 0.00 O
HETATM 26 H1 HOH A 9 52.362 62.842 26.905 1.00 0.00 H
HETATM 27 H2 HOH A 9 52.753 63.877 25.853 1.00 0.00 H
HETATM 28 O HOH A 10 41.346 16.006 16.906 1.00 0.00 O
HETATM 29 H1 HOH A 10 42.065 16.436 16.418 1.00 0.00 H
HETATM 30 H2 HOH A 10 40.582 16.581 16.748 1.00 0.00 H
HETATM 31 C TMA B 1 0.815 2.645 77.501 1.00 0.00 C
HETATM 32 N TMA B 1 2.307 2.451 77.878 1.00 0.00 N1+
HETATM 33 C TMA B 1 2.071 1.077 78.521 1.00 0.00 C
HETATM 34 C TMA B 1 3.061 1.866 76.657 1.00 0.00 C
HETATM 35 O TMA B 1 2.538 3.604 77.433 1.00 0.00 O1-
HETATM 36 H1 TMA B 1 0.227 1.752 77.336 1.00 0.00 H
HETATM 37 H2 TMA B 1 0.629 3.234 76.608 1.00 0.00 H
HETATM 38 H3 TMA B 1 0.280 3.168 78.282 1.00 0.00 H
HETATM 39 H1 TMA B 1 1.475 1.132 79.422 1.00 0.00 H
HETATM 40 H2 TMA B 1 2.988 0.608 78.855 1.00 0.00 H
HETATM 41 H3 TMA B 1 1.583 0.326 77.910 1.00 0.00 H
HETATM 42 H1 TMA B 1 2.812 0.857 76.359 1.00 0.00 H
HETATM 43 H2 TMA B 1 4.127 1.825 76.838 1.00 0.00 H
HETATM 44 H3 TMA B 1 2.968 2.428 75.732 1.00 0.00 H
CONECT 1 2 3
CONECT 2 1
CONECT 3 1
CONECT 4 5 6
CONECT 5 4
CONECT 6 4
CONECT 7 8 9
CONECT 8 7
CONECT 9 7
CONECT 10 11 12
CONECT 11 10
CONECT 12 10
CONECT 13 14 15
CONECT 14 13
CONECT 15 13
CONECT 16 17 18
CONECT 17 16
CONECT 18 16
CONECT 19 20 21
CONECT 20 19
CONECT 21 19
CONECT 22 23 24
CONECT 23 22
CONECT 24 22
CONECT 25 26 27
CONECT 26 25
CONECT 27 25
CONECT 28 29 30
CONECT 29 28
CONECT 30 28
CONECT 31 32 36 37 38
CONECT 32 31 33 34 35
CONECT 33 32 39 40 41
CONECT 34 32 42 43 44
CONECT 35 32
CONECT 36 31
CONECT 37 31
CONECT 38 31
CONECT 39 33
CONECT 40 33
CONECT 41 33
CONECT 42 34
CONECT 43 34
CONECT 44 34
END
mattwthompson commented
Does the order here matter?
forcefield.registerTemplateGenerator(gaff.generator)
gaff.generate_residue_template(molecule)jaketanderson commented
Does the order here matter?
forcefield.registerTemplateGenerator(gaff.generator) gaff.generate_residue_template(molecule)
Unfortunately swapping these two lines does not fix the issue. The README example for GAFF actually does not use the first line at all, but I added it to see if it works as a fix. It does not seem to.
mattwthompson commented
You probably don't need the PDB file for system generation at all; you can create the (OpenMM)` topology just with OpenFF objects, and then later on set the positions on the context.
This code runs without error, I figure it can be extended to run a simulation. I forget if the system needs residue information or the topology, in which case that might still need to be set.
In [3]: from openmm.app import ForceField
...: from openff.toolkit import Molecule, Topology
...:
...: molecule = Molecule.from_smiles("C[N+](C)(C)[O-]")
...: water = Molecule.from_smiles("O")
...:
...: from openmmforcefields.generators import GAFFTemplateGenerator
...:
...: gaff = GAFFTemplateGenerator(molecules=molecule)
...:
...: forcefield = ForceField(
...: "amber/tip3pfb_standard.xml", "amber/tip3pfb_HFE_multivalent.xml"
...: )
...: forcefield.registerTemplateGenerator(gaff.generator)
...: gaff.generate_residue_template(molecule)
...:
...: topology = Topology.from_molecules([water, water, molecule]) # add more waters as you wish
...: sys = forcefield.createSystem(topology.to_openmm())jaketanderson commented
Thanks very much @mattwthompson! I've got it up and running with your suggestion of making the topology in OpenFF and combining it with the PDB's positions.