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
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
