Molecular Docking Server

PDB vs. MOL2
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Author:  owenmcdougal [ Thu Feb 19, 2009 12:18 am ]
Post subject:  PDB vs. MOL2

I have a particular ligand I am submitting, but when I submit it as a pdb file the Cl atoms are automatically replaced with CH3 atoms. As well as one of the Nitrogen atoms being protonated. i thought to correct this problem by submitting it as a mol2 file. But when I did this there was an error in the calculations, even though it did not remove or change any atom. So how can I fix the error and yet maintain the correct ligand structure. The two ligands are C5(mol2) and C5-1A(pdb).

Author:  hazaie [ Thu Feb 19, 2009 2:31 pm ]
Post subject:  Re: PDB vs. MOL2

We have checked the problem and right now I think the best solution -before we find a general solution to fix this problem-is to draw in the ligand (and do not upload it)- in that case the ligand processing works fine. Your ligand looks fine, so we have to further check what has caused the problem.

Author:  owenmcdougal [ Mon Apr 06, 2009 7:23 pm ]
Post subject:  Re: PDB vs. MOL2

Do you have any idea about what is wrong and how long. Now when I upload the same ligand PDB file, it replaces the chlorines with methyl groups. I don't know why it does that. The current file is C5, under the directory Reed. It should have Cl instead of CH3. Also, when I did draw it in, it ran fine, but the result files did not have the final bond in the OH so when I put it into other programs to analyze the results the molecule was incomplete and couldn't have further calculations done on it.


Author:  bikadi [ Mon Apr 06, 2009 11:22 pm ]
Post subject:  Re: PDB vs. MOL2

The drawn ligand has been corrected in your account - it seems that it was not geometry optimized using the geometry optimization checkbox, which caused the error. Uploading ligand files is always a more difficult case because of the incompatibility of the different molecular modelling softwares. We will try to figure out some solution for your special problem.

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