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Ligand PDB files
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Author:  owenmcdougal [ Wed Apr 08, 2009 6:31 pm ]
Post subject:  Ligand PDB files

After conducting the run on C5-drawn and C6-drawn, I attempted to analyze the data. The pdb files for the individual results showed chlorine replaced with iodine atoms. This affects the additional calculations I needed to perform on the conformations which showed positive binding affinity. Also, I don't know when the elements were replaced and if that affected the outcome of the results. Any information on why this is happening and what I can do about it would be appreciated. Also, it appears the bond between the halogen and the aromatic ring does not show up in the PDB files either.

Thanks

Author:  bikadi [ Wed Apr 08, 2009 8:52 pm ]
Post subject:  Re: Ligand PDB files

The problem that causes the replacement of chloro atom to methyl group in your case is that the file format conversion program misinterprets "Cl" if the ligand was saved in a non-standard form and only read in the first "C" letter. This is the basis of a change from Cl to methyl. If you replace the "HETATM" lines to "ATOM " in the pdb file of your ligand structure, than it will not replace chlorine atoms. We are working on it right now to automatically do this replacement if necessary. We have never experienced a change from chlorine to iodine. Could you detail, where can we find those results?

Author:  owenmcdougal [ Wed Apr 08, 2009 9:20 pm ]
Post subject:  Re: Ligand PDB files

I found the replacement of Chloro with iodine when I input the result PDB files in any other viewer, they all came up with iodine instead of chlorine. So in either of the C5-drawn or C6-drawn dockings under Reed. This is the file which was manually drawn into the site. Both, Pymol and Viewer pro both read them as iodine instead of Chlorine. I don't know if there is a miscoding on my computer which would cause this, but I haven't ever run into this before.

Thanks

Author:  bikadi [ Wed Apr 08, 2009 10:54 pm ]
Post subject:  Re: Ligand PDB files

I have checked out the dockings. What you can see in Pymol is letter "l" (el), the second letter of Cl and not an uppercase i (Iodine). This is not a real problem, the docking calculations used chlorine, it is just an incompatibility in the position of the two letter atoms in the pdb files. So you do not have to worry about it. Anyway, you are right that it is confusing. Thank you for letting us know about this bug, we will solve it soon hopefully.

Author:  owenmcdougal [ Thu Apr 09, 2009 1:25 am ]
Post subject:  Re: Ligand PDB files

I'm pleased to know that the calculations are run with Chlorine. But this does not change the output file I need to continue my additional calculations through both Spartan and Gaussian. In each of these the bonds to the Chlorines don't show up, and Spartan shows a general "ligand" as the identity of the halogen atom. This will not work for me to do any reliable calculations on, not only is the charge of the atom different, the bond length is also affected.

Thanks for all the assistance, and except for this it is a wonderful service.

Author:  bikadi [ Thu Apr 09, 2009 4:17 pm ]
Post subject:  Re: Ligand PDB files

You can solve this problem by the following way, while we are working on the bug fixing:

1, Open your pdb file in Notepad or Wordpad

2, Find these lines:

...
ATOM 3 l1 <1> d 26.673 17.974 5.493 -1.42 +0.01
ATOM 4 C5 <1> d 28.175 18.991 3.637 -0.44 +0.03
ATOM 5 C6 <1> d 28.936 19.045 2.460 -0.34 -0.05
ATOM 6 l2 <1> d 29.699 20.481 1.989 -0.86 +0.02
ATOM 7 C7 <1> d 29.059 17.894 1.676 -0.33 +0.02
...

3, Write a letter C before letter l and delete one space between the atom number and symbol. It should look like this:

...
ATOM 3 Cl1 <1> d 26.673 17.974 5.493 -1.42 +0.01
ATOM 4 C5 <1> d 28.175 18.991 3.637 -0.44 +0.03
ATOM 5 C6 <1> d 28.936 19.045 2.460 -0.34 -0.05
ATOM 6 Cl2 <1> d 29.699 20.481 1.989 -0.86 +0.02
ATOM 7 C7 <1> d 29.059 17.894 1.676 -0.33 +0.02
...

4, Save the file, it should work now.

If you send these files by e-mail, we can also do it for you. Thank you for your nice words and hopefully this problem will be solved soon, too!

Author:  owenmcdougal [ Thu Apr 09, 2009 4:59 pm ]
Post subject:  Re: Ligand PDB files

Thank you for the assistance. That seems to work at the moment. It at least gives me Chlorine in the correct spot. Is there a way to have it recognize an aromatic ring in the PDB text. Or any of the bonds. Because when I put it into Spartan no bonds show up. If I use viewer pro and convert the file to mol it gives just single bonds instead of the bond variaties that exist. Neither of these will help with future calculations. What I'm asking is if there is a way to specify connectivity in the output PDB file.

Author:  bikadi [ Thu Apr 09, 2009 9:12 pm ]
Post subject:  Re: Ligand PDB files

Unfortunatelly, PDB format was originally invented for proteins and is not so perfect for ligands, e.g. you cannot indicate aromacity in it. The molecular viewer should recognise that based on atomic distances and angles. You should try to save molecules in mol2 format, which is able to handle small and large molecules and contains information about the bonds and atom types.

Author:  owenmcdougal [ Thu Apr 09, 2009 9:53 pm ]
Post subject:  Re: Ligand PDB files

Do you know what would be the best program to do that with? one, that could open the pdb and save it with all the bonds correctly? Thanks

Author:  bikadi [ Thu Apr 09, 2009 11:02 pm ]
Post subject:  Re: Ligand PDB files

I would recommend OpenBabel for format conversion tasks, you can get it from: http://openbabel.org/wiki/Get_Open_Babel

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