Hi,
I'd like to use DiverseConfGen with added constraints to generate
conformers with two atoms frozen, but am unable to fix those two atoms. The
conformer generation tends to separate the fragments that I'm trying to
keep bonded through the AtomConstraints. I have also tried fixing the bond
distance, but had the same results.
Any help would be greatly appreciated. Thank you!
Here is the Python code I'm using:
atoms_to_freeze = [4, 28]
ff = ob.OBForceField_FindType('gaff')
constraints = ob.OBFFConstraints()
for atom in ob.OBMolAtomIter(obmol):
atom_id = atom.GetIndex() + 1
if atom_id in atoms_to_freeze:
constraints.AddAtomConstraint(atom_id)
ff.Setup(obmol, constraints)
ff.DiverseConfGen(0.5, 1000000, 50, True)
And here are the xyz coordinates of the input structure:
C 2.2306000000 -0.9007800000 1.3044400000
C 0.9975100000 -0.1842600000 -0.7416200000
C 0.9909800000 -0.7804100000 0.5670700000
C -0.2684600000 -1.1716300000 1.2148300000
C -0.3205400000 -1.2549200000 2.7273600000
C -1.3744100000 -2.3674600000 -0.7473100000
C -2.8847800000 -2.4011500000 -0.9849700000
C -4.9723800000 -1.3362400000 -0.4760500000
C -3.2768100000 -0.1100000000 -1.6197100000
H 0.1777200000 -0.4051500000 3.1898800000
H 0.1980500000 -2.1541000000 3.0601100000
H -1.3676900000 -1.2875200000 3.0486500000
H -3.0828600000 -2.6825500000 -2.0354700000
H -3.3195800000 -3.1930800000 -0.3598300000
H -0.8945500000 -1.6276100000 -1.3846600000
H -1.9184600000 -2.2787900000 1.2478300000
H -0.9569200000 -3.3524200000 -0.9913500000
H -5.1741700000 -2.0734400000 0.3068300000
H -5.4532700000 -1.6796700000 -1.4098300000
H -5.4374200000 -0.3898000000 -0.1849900000
H -3.6969200000 0.8401500000 -1.2724100000
H -2.2029700000 0.0239300000 -1.7681800000
H -3.7380800000 -0.3543200000 -2.5938200000
N -1.1272800000 -2.0573300000 0.6532200000
N -3.5374100000 -1.1460400000 -0.6248800000
O 2.3594800000 -1.3587500000 2.4375600000
O -0.0043100000 0.2179800000 -1.3504700000
N -1.3208400000 0.5652100000 1.0538200000
O 2.1693700000 0.0367900000 -1.3857900000
C 3.4700300000 -0.3809100000 0.5862800000
C 3.3869200000 -0.5740500000 -0.9186600000
C 3.3868900000 -2.0503100000 -1.3146400000
H 4.3325300000 -2.5185000000 -1.0250800000
H 2.5702700000 -2.5890700000 -0.8259900000
H 3.2679300000 -2.1403600000 -2.3980900000
C 4.4954400000 0.1770200000 -1.6413000000
H 4.4498000000 1.2420200000 -1.3969500000
H 5.4730000000 -0.2135400000 -1.3431500000
H 4.3849900000 0.0640100000 -2.7235600000
H 4.3408600000 -0.8894400000 1.0079000000
H 3.5661200000 0.6915900000 0.8051100000
H -1.1247100000 0.6742400000 0.0532300000
H -2.3137800000 0.3521100000 1.1583600000
C -0.8597800000 1.7182700000 1.8241600000
H 0.2282700000 1.6113700000 1.9266500000
H -1.2831000000 1.6511100000 2.8316100000
C -1.1984800000 3.0715100000 1.1947900000
H -2.2913000000 3.1760100000 1.1415300000
C -0.6005700000 3.2995100000 -0.2012300000
H -0.8404500000 3.8646900000 1.8668700000
H -0.9639700000 2.5150600000 -0.8785100000
C 0.9270100000 3.2285700000 -0.1908600000
C -1.0684000000 4.6483600000 -0.7490600000
H -0.6794300000 4.8188900000 -1.7576500000
H -0.7146500000 5.4668500000 -0.1102900000
H -2.1613500000 4.7055400000 -0.7925200000
H 1.2968000000 2.2621500000 0.1650100000
H 1.3422400000 4.0120200000 0.4562600000
H 1.3247600000 3.3699100000 -1.2001900000
Thanks again,
Alex
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