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Optional automatic protonation feature of Nitrogen in DW using EL [message #1824] Mon, 30 January 2023 13:59 Go to next message
Jo W
Messages: 34
Registered: July 2021
Member
When creating docking scores in DW, you can select whether to protonate the ligand or not.
At the moment I am using this feature with nitrogen heterocyclic ligands.

However, when you use this feature with an EL based on docking scores, the program seems to automatically protonate the nitrogen in nitrogen-containing resulting ligands.

Is there any way to underdo this feature or at least have it as an option?
Many thanks in advance
Jon
Re: Optional automatic protonation feature of Nitrogen in DW using EL [message #1828 is a reply to message #1824] Wed, 01 February 2023 01:04 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 679
Registered: June 2014
Senior Member
An option to skip (de-)protonation for docking fitness in evolutionary libraries will be in the next dev version...
Re: Optional automatic protonation feature of Nitrogen in DW using EL [message #1829 is a reply to message #1828] Wed, 01 February 2023 16:23 Go to previous messageGo to next message
Jo W
Messages: 34
Registered: July 2021
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Thanks. Do you know approximately when the next development version will be?
Re: Optional automatic protonation feature of Nitrogen in DW using EL [message #1830 is a reply to message #1829] Thu, 02 February 2023 12:03 Go to previous messageGo to next message
thomas is currently offline  thomas
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Registered: June 2014
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I assume it is a matter of days, but I need to finish a few changes regarding conformation generation
Re: Optional automatic protonation feature of Nitrogen in DW using EL [message #1841 is a reply to message #1830] Tue, 07 February 2023 16:09 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 679
Registered: June 2014
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I just deployed an update with this thing solved, but realized that the conformation generation has a fundamental dewsign flaw, which I need to tackle. Thus, another update will follow later...
Re: Optional automatic protonation feature of Nitrogen in DW using EL [message #1842 is a reply to message #1841] Thu, 09 February 2023 00:14 Go to previous messageGo to next message
Jo W
Messages: 34
Registered: July 2021
Member
OK Many Thanks, Thomas. Approximately - are we talking days or weeks for the further update?

[Updated on: Thu, 09 February 2023 00:17]

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Re: Optional automatic protonation feature of Nitrogen in DW using EL [message #1847 is a reply to message #1842] Thu, 09 February 2023 22:00 Go to previous message
thomas is currently offline  thomas
Messages: 679
Registered: June 2014
Senior Member
hopefully before the end of next week...
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