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A nitrogen atom being wrongly protonated
https://www.dockingserver.com/forum/viewtopic.php?f=3&t=163
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Author:  chanataon [ Wed Apr 06, 2016 4:47 am ]
Post subject:  A nitrogen atom being wrongly protonated

Hi all,

After I draw a ligand, no matter which method I use for geometry optimization,
one of the nitrogen atoms in my aromatic ring is protonated incorrectly (picture attached),
making it have 4 bonds which I don't think I want it.

Could anyone please suggest how I could fix this problem?

Thanks,
Jay

Author:  bikadi [ Wed Apr 06, 2016 7:20 pm ]
Post subject:  Re: A nitrogen atom being wrongly protonated

Hi, try changing pH, it should help.

Author:  jaruwanchat [ Wed Apr 06, 2016 7:43 pm ]
Post subject:  Re: A nitrogen atom being wrongly protonated

Hi,

Thanks for the response; it does help! But I wonder if I should input the pH under physiological condition or the lowest pH that my compound is not protonated for docking calculation. Btw, my compound has an iso-cytosine ring contained in it.

Thanks in advance.

Jay

Author:  bikadi [ Sat Apr 09, 2016 9:51 am ]
Post subject:  Re: A nitrogen atom being wrongly protonated

You should try docking with different pHs if protonation is crucial in your system (docking will use the ligand in the form you prepared; protonated at low pH). Since local pH in the protein binding site can be very different from physiological condition, there is no golden rule which is the appropriate choice but you should consider your protein and known ligands.

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