Hi Phuong,
If you wish to retain Hs you just need to set removeHs = False when you
call MolFromPDBFile():
# align.py
import sys
from rdkit import Chem
from rdkit.Chem import rdDistGeom, rdMolAlign, rdForceFieldHelpers
from rdkit import Chem
refMolwithH = Chem.MolFromPDBFile(sys.argv[1], removeHs = False)
s = sys.argv[2]
prbMolwithH = Chem.MolFromPDBFile(s, removeHs = False)
idx=s.find('_')
chemB= s[:idx]
rdDistGeom.EmbedMolecule(prbMolwithH)
rdForceFieldHelpers.UFFOptimizeMolecule(prbMolwithH)
##Alignment
pyO3A = rdMolAlign.GetO3A(prbMolwithH, refMolwithH)
score = pyO3A.Align()
##3D coords of Chem B after alignmnet
Chem.MolToPDBFile(prbMolwithH,'{}.pdb'.format(chemB))
and then
./align.py drug.pdb UNK_A1C198.pdb
Cheers,
p.
On 08/20/18 19:02, Phuong Chau wrote:
Hello everyone,
I am trying to align two chemicals using their pdb files with the
following script:
*refMolwithH = Chem.MolFromPDBFile(sys.argv[1])*
*s = sys.argv[2]*
*prbMolwithH = Chem.MolFromPDBFile(s)*
*idx=s.find('_')*
*chemB= s[:idx]*
*
*
*rdDistGeom.EmbedMolecule(prbMolwithH)*
*AllChem.UFFOptimizeMolecule(prbMolwithH)*
*
*
*##Alignment*
*pyO3A = rdMolAlign.GetO3A(prbMolwithH, refMolwithH)*
*score = pyO3A.Align()*
*
*
*##3D coords of Chem B after alignmnet*
*Chem.MolToPDBFile(prbMolwithH,'{}.pdb'.format(chemB))*
The probe chemical pdb is generated from GRO file generated from
LigParGen browser by this script:
*gmx editconf -f input.gro -o output.pdb*
The problem is the new aligned chemical is not aligned with the refMol
but with probMol and the new chemical does not have H atoms on it.
Would you please help me with this problem? Are there other ways to
align the pdb files generated from LIgParGen?
Thank you so much for your help
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