Dear Noel.
I decided to correct this bug by adjusting valence angles "manually" for aromatic residues; it would force right conformation for the rings. (I do not want to use energy minimization at this step because this still would yeild non-identical conformations for ideal alpha-helix, what is ambigous.)
But I discovered that there's no function to adjust these angles. We can obtain their values (mol.GetAngle(...)), but not set them.
Do you have an idea, how do this? If I could set angle with something like mol.SetAngle('CB', 'CG', 'CD1', 120 deg), this would be a solution.
Anton.
17.09.2012, 21:35, "Noel O'Boyle" <baoille...@gmail.com>:
Looks like a Builder bug. The stochastic issue is due to the use of a
random vector in there. I don't think we should be using that.
Regarding gen3d versus Python code, gen3d does a forcefield
optimisation after calling the Builder. You should look at its code,
gen3d.cpp.
- Noel
On 16 September 2012 18:55, Чугунов Антон <batc...@yandex.ru> wrote:Hello All!
I encounter a very strange problem when I convert peptides from smiles to
3D. This problem persists for Phe and Tyr residues, but it's stochastic: it
appears approx. in one case in ten. The problem is that CB-CG-CD1 valence
angle is about 0 degrees, and the ring "folds back" to CB atom (see picture
and two PDB files). Here's the code:
#!/usr/bin/python
import pybel, openbabel
Smiles = {
'F': 'N[C@@H](CC1=CC=CC=C1)C(=O)',
'I': 'N[C@@H]([C@@H](C)CC)C(=O)',
'Y': 'N[C@@H](CC1=CC=C(C=C1)O)C(=O)'
}
seq = 'FIIFIIIYIIIIFIIY'
def make_3d(pep_seq):
pep_smiles = ''
for aa in pep_seq:
pep_smiles = pep_smiles + Smiles[aa]
pep = pybel.readstring("smi", pep_smiles)
openbabel.OBBuilder().Build(pep.OBMol)# Make 3D-coordinates
return pep
for i in range(20): # This makes 20 different peptides
print i
pep = make_3d(seq)
pep.write('pdb', 'pep{:d}.pdb'.format(i), overwrite = True)
This problem is still with me if I use a single Phe or Tyr residue; at the
same time, command line obabel tool does not seem to have this; at least
after 20 trials of obabel -:"N[C@@H](CC1=CC=CC=C1)C(=O)" -O pep${i}.pdb
--gen3d I didn't notice any problems.
Does anyone have idea, how to overcome this problem? Minimization corrects
this to some extent, but you'll still have different conformations of side
chains => there's no reproductivity in generated structures.
Chugunov Anton.
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