Hi, I'm up against a horrible deadline so I'm hoping for some help figuring out what I'm doing wrong.
I have a list of custom atom names in Gromacs of which I want to perform hydrogen bond analysis using MDAnalysis. As great as MDAnalysis is, I can't find enough documentation to help decipher how to fit in custom atom names.
Firstly, if you define a new class:
class HydrogenBondAnalysis_OtherFF(hbonds.HydrogenBondAnalysis):
DEFAULT_DONORS = {"OtherFF": tuple(set(["DH1","DH20","DH19","DH11","DH25","DH27","DH30"]))}
DEFAULT_ACCEPTORS = {"OtherFF": tuple(set(["DO1","DN2","DN6","DN5","DN4","DN3","DO2","DO3","DO4","DO5"]))}
Will this override everything? i.e., I can no longer use either protein or water in a selection.
Secondly, if the above is NOT true then I can't seem to get this working:
import MDAnalysis
import MDAnalysis.analysis.hbonds as hbonds
import pandas as pd
referenceFile = "/Users/anthonynash/Documents/AGES/DIC_CHEMRXIV/SIMULATIONS/DOGDIC/fixed_dihedrals.tpr"
trajectoryFile = "/Users/anthonynash/Documents/AGES/DIC_CHEMRXIV/SIMULATIONS/DOGDIC/fixed_dihedrals_nojump.xtc"
universe = MDAnalysis.Universe(referenceFile, trajectoryFile)
class HydrogenBondAnalysis_OtherFF(hbonds.HydrogenBondAnalysis):
DEFAULT_DONORS = {"OtherFF": tuple(set(["DH1","DH20","DH19","DH11","DH25","DH27","DH30"]))}
DEFAULT_ACCEPTORS = {"OtherFF": tuple(set(["DO1","DN2","DN6","DN5","DN4","DN3","DO2","DO3","DO4","DO5"]))}
hydrogenBondAnalysis = HydrogenBondAnalysis_OtherFF(universe, 'name DO1 DN2 DN6 DN5 DN4 DN3 DO2 DO3 DO4 DO5 DH20 DH19 DH11 DH25 DH27 DH30', 'resname SOL', distance=3.0, angle=120.0, forcefield=“OtherFF”)
hydrogenBondAnalysis.run()
I get the warnings:
/usr/local/lib/python3.7/site-packages/MDAnalysis/analysis/hbonds/hbond_analysis.py:650: SelectionWarning: No donors found in selection 1. You might have to specify a custom 'donors' keyword. Selection will update so continuing with fingers crossed.
warnings.warn(errmsg, category=SelectionWarning)
/usr/local/lib/python3.7/site-packages/MDAnalysis/analysis/hbonds/hbond_analysis.py:650: SelectionWarning: No acceptors found in selection 1. You might have to specify a custom 'acceptors' keyword. Selection will update so continuing with fingers crossed.
warnings.warn(errmsg, category=SelectionWarning)
/usr/local/lib/python3.7/site-packages/MDAnalysis/analysis/hbonds/hbond_analysis.py:650: SelectionWarning: No acceptors found in selection 2. You might have to specify a custom 'acceptors' keyword. Selection will update so continuing with fingers crossed.
warnings.warn(errmsg, category=SelectionWarning)
/usr/local/lib/python3.7/site-packages/MDAnalysis/analysis/hbonds/hbond_analysis.py:650: SelectionWarning: No donors found in selection 2. You might have to specify a custom 'donors' keyword. Selection will update so continuing with fingers crossed.
warnings.warn(errmsg, category=SelectionWarning)
Hi,
You can do that with gmx bond.
http://manual.gromacs.org/archive/5.0/programs/gmx-hbond.html
gmx hbond will not work with those atom names because they start with 'D' - gmx hbond makes assumptions about donors (only atom names starting with 'O' and 'N' and associated 'H' atoms) or acceptors (also only 'O' and 'N' allowed).
As Justin Lemkul said, these are new atom types I've added myself hence gmx bond won't work.
I managed to get it work using MDAnalysis. It required a bit of trial and error to fill in some of the blanks. Once I've finished with my analysis I'll put up a link to my code.
Anthony Nash Justin Lemkul I have a side question , in MDanalysis documentation , they say that Angle cutoff (degrees) is 120.0.
Do they mean H-D-A?
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