Dear Paolo,
The new chemical chemical after alignment (UNK.pdb) file is in format of
RDKIT pdb file. Is it possible for the output in format of LIgParGen? I am
trying to run stimulation with the aligned chemical but it seems like it
can not read pdb file generated from RDKit.
Best,
Phuong Chau
On Wed, Aug 22, 2018 at 12:32 PM, Paolo Tosco <paolo.tosco.m...@gmail.com>
wrote:
> Dear Phuong,
>
> it works for me with the latest RDKit release. I am wondering if you are
> using an older RDKit version where maybe the PDB parser was not assigning
> formal charges based on connectivity? Then you would have to manually set
> the formal charge of the protonated nitrogen atom (# 2 N) to +1.
>
> Cheers,
> p.
>
> On 08/22/18 19:06, Phuong Chau wrote:
>
> Hi Paolo,
>
> I got this new error when I tried with different chemicals:
>
> python 3DAlignmentwith3OAwithGRO.py CCNC\(N\)N_afterMD.pdb
> CC\[NH2\+\]CCN_Ligpargen.pdb
> [12:02:45] Explicit valence for atom # 2 N, 4, is greater than permitted
> Traceback (most recent call last):
> File "3DAlignmentwith3OAwithGRO.py", line 12, in <module>
> rdDistGeom.EmbedMolecule(prbMolwithH)
> Boost.Python.ArgumentError: Python argument types in
> rdkit.Chem.rdDistGeom.EmbedMolecule(NoneType)
> did not match C++ signature:
> EmbedMolecule(RDKit::ROMol {lvalue} mol, unsigned int maxAttempts=0,
> int randomSeed=-1, bool clearConfs=True, bool useRandomCoords=False, double
> boxSizeMult=2.0, bool randNegEig=True, unsigned int numZeroFail=1,
> boost::python::dict {lvalue} coordMap={}, double forceTol=0.001, bool
> ignoreSmoothingFailures=False)
>
> The second argument I also downloaded it from Ligpargen but it gave me
> this error. I am not so sure why it happened.
>
> I also attached the two files :
>
> On Tue, Aug 21, 2018 at 3:19 PM, Paolo Tosco <paolo.tosco.m...@gmail.com>
> wrote:
>
>> 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 <paolo.tosco.m...@gmail.com>
>> 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
>>
>>
>>
>
>
> --
> Phuong Chau
> Smith College '20
> Engineering Major
>
>
>
--
Phuong Chau
Smith College '20
Engineering Major
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