Poledit polarization group assignment, add special case

[misterbrandonwalker]

Need to add special case for poledit polarization groups, with current code SP2 oxygen will be in group by itself if between an SP3 carbon and an SP2 carbon, this allows oxygen and SP3 carbon to be in same group.

[jayponder]

Hi Brandon, Do you have an example molecule with this situation? If you really mean sp2 oxygen, then it must be a positively charged oxygen? I can make this change, but I'd like to see and example and think about whether your change is "general". Thanks, Jay

[misterbrandonwalker]

Oh my so sorry that was a typo I meant SP3 oxygen! I will add an image of situation though.

[misterbrandonwalker]

Atom number 5 is the oxygen I was referring to, and atom 19 the neighboring SP3 carbon and 25 is the neighboring SP2 carbon. What will happen is the oxygen will wind up in its own polarization group, so I added a case to combine 19 and 25.

[jayponder]

But that's just an ether.. We have "always" made the oxygen atom a separate group in ethers. We've typically only included the attached sp3 carbon in the group with the oxygen when the other attachment on the oxygen is a hydrogen, as in alcohols. Same when the heteroatom is a nitrogen instead of an oxygen... You might ask Pengyu to see what he thinks about this. I know alkyl ethers work just fine with the oxygen in its own group.

[pren]

This molecule we are dealing with has issues when O is a group by itself. One side of the O is an aromatic benzyl ring which has very strong polarization. It may be ok for sp3 C on both sides. Also there is aCa2+ polarizing the Os.

If you try to minimize the molecule below using tinker.key.org (O 5 &6 are single groups), there is convergence issue. Once we put O in a group with Csp3 (aromatic C should be fine too), minimization has no issues. https://biomol.bme.utexas.edu/~pren/down/cryptand/

From: Jay Ponder @.> Sent: Monday, October 3, 2022 11:34 AM To: TinkerTools/tinker @.> Cc: Subscribed @.***> Subject: Re: [TinkerTools/tinker] Poledit polarization group assignment, add special case (PR #121)

But that's just an ether.. We have "always" made the oxygen atom a separate group in ethers. We've typically only included the attached sp3 carbon the group with the oxygen when the other attachment is a hydrogen, as in alcohols. Same when the heteroatom is a nitrogen instead of an oxygen... You might ask Pengyu to see what he thinks about this. I know alkyl ethers work just fine with the oxygen in its own group.

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[pren]

Actually, I think it is better to include O with the aromatic C or sp2 C, instead of sp3 C, as they are strongly coupled. It is more appropriate to think they belong to one group.

Anyway please test the molecule below.

From: Pengyu Ren @.> Sent: Monday, October 3, 2022 11:54 AM To: TinkerTools/tinker @.> Cc: Ren, Pengyu @.>; Your activity @.> Subject: Re: [TinkerTools/tinker] Poledit polarization group assignment, add special case (PR #121)

This molecule we are dealing with has issues when O is a group by itself. One side of the O is an aromatic benzyl ring which has very strong polarization. It may be ok for sp3 C on both sides. Also there is aCa2+ polarizing the Os.

If you try to minimize the molecule below using tinker.key.org (O 5 &6 are single groups), there is convergence issue. Once we put O in a group with Csp3 (aromatic C should be fine too), minimization has no issues. https://biomol.bme.utexas.edu/~pren/down/cryptand/

From: Jay Ponder @.<mailto:@.>> Sent: Monday, October 3, 2022 11:34 AM To: TinkerTools/tinker @.<mailto:@.>> Cc: Subscribed @.<mailto:@.>> Subject: Re: [TinkerTools/tinker] Poledit polarization group assignment, add special case (PR #121)

But that's just an ether.. We have "always" made the oxygen atom a separate group in ethers. We've typically only included the attached sp3 carbon the group with the oxygen when the other attachment is a hydrogen, as in alcohols. Same when the heteroatom is a nitrogen instead of an oxygen... You might ask Pengyu to see what he thinks about this. I know alkyl ethers work just fine with the oxygen in its own group.

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[jayponder]

Yes, what Pengyu suggests is better. It makes more sense to put the oxygen in the same group as the phenyl/aromatic carbon it is attached to (and therefore in the same group with the whole aromatic ring). For example, that is what we do for tyrosine, even though it is an "alcohol"/phenol and not an ether. Then the group should break between the oxygen and the sp3 carbon on the other side. That is more consistent with what we have done in the past. I'll make that change when I get a chance- probably later today. Best, Jay

[misterbrandonwalker]

Thank you!

[pren]

Jay, The benzene seems not in one group either, which it should.

Thanks Pengyu

From: Jay Ponder @.> Sent: Monday, October 3, 2022 12:27 PM To: TinkerTools/tinker @.> Cc: Ren, Pengyu @.>; Comment @.> Subject: Re: [TinkerTools/tinker] Poledit polarization group assignment, add special case (PR #121)

Yes, what Pengyu suggests is better. It makes more sense to put the oxygen in the same group as the phenyl/aromatic carbon it is attached to (and therefore in the same group with the whole aromatic ring). For example, that is what we do for tyrosine, even though it is an "alcohol"/phenol and not an ether. Then the group should break between the oxygen and the sp3 carbon on the other side. That is more consistent with what we have done in the past. I'll make that change when I get a chance- probably later today. Best, Jay

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[pren]

Probably false alarm about benzene ring as one group. Will check myself.

From: Ren, Pengyu Sent: Monday, October 3, 2022 12:32 PM To: TinkerTools/tinker @.>; TinkerTools/tinker @.> Cc: Comment @.***> Subject: RE: [TinkerTools/tinker] Poledit polarization group assignment, add special case (PR #121)

Jay, The benzene seems not in one group either, which it should.

Thanks Pengyu

From: Jay Ponder @.**@.>> Sent: Monday, October 3, 2022 12:27 PM To: TinkerTools/tinker @.**@.>> Cc: Ren, Pengyu @.**@.>>; Comment @.**@.>> Subject: Re: [TinkerTools/tinker] Poledit polarization group assignment, add special case (PR #121)

Yes, what Pengyu suggests is better. It makes more sense to put the oxygen in the same group as the phenyl/aromatic carbon it is attached to (and therefore in the same group with the whole aromatic ring). For example, that is what we do for tyrosine, even though it is an "alcohol"/phenol and not an ether. Then the group should break between the oxygen and the sp3 carbon on the other side. That is more consistent with what we have done in the past. I'll make that change when I get a chance- probably later today. Best, Jay

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[misterbrandonwalker]

The benzene group is a single group, I was interpreting the key wrong...

[jayponder]

Please send me by email the XYZ, DMA and/or key file for the molecule, and I will take a look. Obviously the whole phenyl ring should be in the same group.

[misterbrandonwalker]

22benzocryptand-peditin.txt 22benzocryptand.gdmaout.txt 22benzocryptand.key.txt 22benzocryptand.xyz.txt

Hi Jay,

Here are the files (have to add .txt extension since github is picky). The xyz/key generated will have the oxygen included in the group with the change I made, before that the oxygen is in its own group.

[jayponder]

Hi Brandon, I've made this change to the main Tinker repo on GitHub (separate from this pull request..). Sorry for the delay. Jay

[jayponder]

.

[misterbrandonwalker]

No worries, thanks!