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Fix hydrides #52

Merged
merged 4 commits into from
May 7, 2024
Merged

Fix hydrides #52

merged 4 commits into from
May 7, 2024

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keitaroyam
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@keitaroyam keitaroyam commented Apr 9, 2024

XHn entries have not been updated (although some of them were wrong), since Acedrg could not handle them. Now it's possible, and they were regenerated using Acedrg 285. Some angles may need further corrections. Links should be updated also.

for the pep-NH2 link:

LINK: RES-NAME-1 ALA ATOM-NAME-1 C RES-NAME-2 NH2 ATOM-NAME-2 N DELETE ATOM OXT 1 DELETE ATOM H 2

@GaribMurshudov
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Should I approve it after we have done proper analysis for HOH? Why I am on it it would be good to have a list of such molecules so that I can try to do analysis using COD.

@keitaroyam
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I would like to wait for the proper analysis.

@GaribMurshudov
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Ok.

@keitaroyam
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keitaroyam commented Apr 26, 2024

Now the pep-NH2 link was updated and this PR is ready for review.
Although water's angle (107.4) is a bit different from the famous value (104.5), it follows the acedrg procedure and may be acceptable?

@keitaroyam keitaroyam marked this pull request as ready for review April 26, 2024 13:20
@keitaroyam
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Note that this PR also fixes the energy type of N of NH4. That was NT (hydrogen bond incapable) and lead to a wrong critical distance.

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@wojdyr wojdyr left a comment

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Looks good.

@keitaroyam keitaroyam merged commit 142c34c into master May 7, 2024
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@keitaroyam keitaroyam deleted the fix-hydrides branch May 7, 2024 13:59
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3 participants