ligand protein interactions for trajectory with united atoms
See original GitHub issueThank you for creating this repository!
I am working with a united atom trajectory which causes issues at the the fp.run
method:
lig = u.select_atoms("resname LIG")
prot = u.select_atoms("resnum 3-200")
fp = plf.Fingerprint()
fp.run(u.trajectory[::10], lig, prot)
Which gives the assertion error:
No hydrogen atom could be found in the topology, but the converter requires all hydrogens to be explicit. You can use the parameter ''NoImplicit=False'' when using the converter to allow implicit hydrogens and disable inferring bond orders and charges. You can also use ''force=True'' to ignore this error.
I have confirmed that the plf.Molecule.from_mda
method works with the NoImplicit=False
and gives the correct topology when viewed in Jupyter notebook:
pmol = plf.Molecule.from_mda(prot, NoImplicit=False)
lmol = plf.Molecule.from_mda(lig, NoImplicit=False)
I hope I didn’t missed something obvious! but how do I use the converted molecules with fp.run
?, it seems to expect an MDAanalysis atom group does not seem to have kwargs during plf.Fingerprint()
or fp.run
Thanks in advance,
Ali
Issue Analytics
- State:
- Created 2 years ago
- Comments:9 (5 by maintainers)
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Hi Cedric,
Happy to report that I’ve now solved this issue using PyMOL, I did it by adding missing hydrogen atoms to all simulation frames.
How to:
(lig sel)
and set thevalence
of their bonds using thevalence guess, lig_sel
command. (see notes for some tips on this)load_traj
h_add
(see notes)save_trj
or as individual pdb files - much slower and larger files. Thesave_trj
function must be installed from hereuni.atoms.guess_bonds()
whereuni
is the universe object. More on this in #25Notes:
valence
command may not work for complex ligands, in this case a combination of thevalence
andbond
with the appropriate options may be neededalter atom_sel, element="BR"
. This can also be done in MDAnalysis by iterating over the atoms and setting their elementsh_add
otherwise hydrogens will be added incorrectly i.e. for aromatic systemsThanks for your help Cedric! Feel free to close the ticket or provide any comments on this.
Hi Ali,
Good to know that you’ve managed to solve the issue! Thanks for posting the procedure that you’ve used, I’m sure that it will be helpful to someone.
Take care, Cédric