Hi Phuong,
it does have hydrogens after the alignment:
$ ls
UNK_A1C198.pdb align.py drug.pdb
$ python align.py drug.pdb UNK_A1C198.pdb
$ ls
UNK.pdb UNK_A1C198.pdb align.py drug.pdb
$ cat UNK.pdb
ATOM 1 C00 UNK 1 37.884 56.016 51.678 1.00
0.00 C
ATOM 2 C01 UNK 1 37.501 54.554 51.968 1.00
0.00 C
ATOM 3 C02 UNK 1 36.085 54.316 52.531 1.00
0.00 C
ATOM 4 C03 UNK 1 35.697 55.221 53.715 1.00
0.00 C
ATOM 5 C04 UNK 1 34.907 56.485 53.304 1.00
0.00 C
ATOM 6 C05 UNK 1 35.788 57.733 53.108 1.00
0.00 C
ATOM 7 C06 UNK 1 36.227 57.998 51.654 1.00
0.00 C
ATOM 8 C07 UNK 1 36.813 56.799 50.889 1.00
0.00 C
ATOM 9 H08 UNK 1 38.821 56.001 51.080 1.00
0.00 H
ATOM 10 H09 UNK 1 38.160 56.522 52.625 1.00
0.00 H
ATOM 11 H0A UNK 1 37.598 53.969 51.027 1.00
0.00 H
ATOM 12 H0B UNK 1 38.243 54.138 52.684 1.00
0.00 H
ATOM 13 H0C UNK 1 35.325 54.368 51.723 1.00
0.00 H
ATOM 14 H0D UNK 1 36.057 53.262 52.884 1.00
0.00 H
ATOM 15 H0E UNK 1 35.031 54.622 54.375 1.00
0.00 H
ATOM 16 H0F UNK 1 36.586 55.471 54.333 1.00
0.00 H
ATOM 17 H0G UNK 1 34.203 56.712 54.134 1.00
0.00 H
ATOM 18 H0H UNK 1 34.270 56.304 52.411 1.00
0.00 H
ATOM 19 H0I UNK 1 35.198 58.620 53.428 1.00
0.00 H
ATOM 20 H0J UNK 1 36.665 57.714 53.788 1.00
0.00 H
ATOM 21 H0K UNK 1 36.982 58.814 51.667 1.00
0.00 H
ATOM 22 H0M UNK 1 35.352 58.378 51.082 1.00
0.00 H
ATOM 23 H0N UNK 1 35.991 56.144 50.537 1.00
0.00 H
ATOM 24 H0O UNK 1 37.280 57.194 49.960 1.00
0.00 H
CONECT 1 2 8 9 10
CONECT 2 3 11 12
CONECT 3 4 13 14
CONECT 4 5 15 16
CONECT 5 6 17 18
CONECT 6 7 19 20
CONECT 7 8 21 22
CONECT 8 23 24
END
p.
On 08/21/18 20:46, Phuong Chau wrote:
Hi Paolo,
I tried the code, it worked with the alignment but the new chemical
after alignment still does not have any H atoms. If I add H after
alignment, it has weird structure with H atoms. Would you please show
me how to fix this problem?
Best,
Phuong Chau
On Tue, Aug 21, 2018 at 8:01 AM, Paolo Tosco
<[email protected] <mailto:[email protected]>> wrote:
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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--
Phuong Chau
Smith College '20
Engineering Major
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