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PostPosted: Mon Mar 21, 2011 4:41 pm 
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Dear all,
I had a further look into this matter. Based on the observations described below, I think that there is a problem in Vina and not in the specific files I was using.

1) Is the problem in my software installation?
I repeated on my system the covalent docking with your files and I DO GET 0

Answer: No

2)Is the problem due to my particular covalent ligand?
In my system, the flexible residue is not just a normal side chain, but a covalent adduct to a protein Tyr residue. I tried to repeat the docking with my protein, but having just the Tyr side chain as flexible residue. Again, the energy IS NOT 0.

Answer: No

3) Is the problem due to my protein file?
I took another pdb file (9PTI, for BPTI). Doing the docking again with a flexible Tyr side-chain (Tyr10) the energy IS NOT 0.

Answer: No

4) Is the problem connected with the specific side chain (Tyr)?
I tried with 9PTI with an arginine (Arg1), as in your example (you have 4 flexible residues, but all are arginines), and I DO GET 0.

Answer: YES!

5) Is the problem connected with all aromatic side chains?
I tried 9PTI Phe4, and I DO GET 0

Answer: No

6) Is the problem connected with OH groups (the only difference between Tyr and Phe)?
I tried 9PTI Ser47, Thr54 and Glu49 and in all cases the energy IS NOT 0

Answer: YES!

7) Are there problems with other side-chains?
I tried 9PTI Leu6, Lys15, and the energy was always 0

Answer: apparently not, but the analysis is not exhaustive.

If needed I can post all the files. However, I just used the pdb 9PTI file, and Oleg's ligand file. In all 9PTI calculations the grid was 20*20*20 and center on the CA of the flexible residue.

Oleg, could you have a look into this?

A very basic question: the program obviously takes into account the intramolecular energy, in order to choose the best orientation for the flexible side chain (this is shown also by the fact that the other poses have a worse energy compared to the best one). If this is so, why would you expect the best one to be always 0?

Thanks a lot,
Lorenzo


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PostPosted: Tue Mar 22, 2011 1:38 am 
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lorenzo.stella wrote:

A very basic question: the program obviously takes into account the intramolecular energy, in order to choose the best orientation for the flexible side chain (this is shown also by the fact that the other poses have a worse energy compared to the best one). If this is so, why would you expect the best one to be always 0?


By design. The first 5 paragraphs of the "Scoring function" section of the paper talk about this, specifically the paragraph preceding Eq. 4.

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PostPosted: Tue Mar 22, 2011 1:53 am 
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lorenzo.stella wrote:
Oleg, could you have a look into this?


If you think there might be a bug, please submit a full bug report as described in the manual.

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PostPosted: Mon Aug 26, 2013 2:25 pm 
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Hi
I was doing flexible docking with Vina. I got the output . Then I converted the output .pdb files using Babel and added it to the rigid coordinates file(rigid.pdb) of the protein and its called complex.pdb



Is the complex.pdb file look okay .
Also when I try to open the complex.pdb file in pymol is there a way to colur the ligand and the flexible residues and the rest of the protein atoms in 3 different colors.

Attached is the output.pdbqt, rigid.pdbqt ,flexresidues.pdbqt , output.pdb(only one output model) and rigid.pdb and flexresidues.pdb file and the complex.pdb file.


Will greatly appreciate the help.
Best
saharinku


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PostPosted: Sat Mar 07, 2015 12:29 am 
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How does one convert a free covalent ligand and free protein to the bound covalent state and call the bound ligand a flexible sidechain in such a manner that is recognized by Autodock?

I can make the covalent bond where i want in my ligand and active site of protein using Fuse command in pymol. However, this messes with the .pdb file such that it's not recognized by autodock properly. How do I fix this?

I then want to try the flexible sidechain method for docking the covalent ligand.

Any help or advice would be much appreciated!

-Tommy


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