fix PRO and all P-peptides #38
Conversation
N-terminal Pro lead to geometry target of NaN, because of MonomerLibrary/monomers#38
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did you also replace the link? |
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PRO has been updated again (Acedrg version number has not changed). Now N is protonated and DEL-HNP has also been updated. TODO: check other P-peptides to see if H2 is not used. Perhaps all P-peptides should also be updated.
Did not update the link using Acedrg. Just added H2 deletion to DEL-HNP. |
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New energy type for N should be N30, i.e. sp2 N with three bonds, none of them H |
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Shouldn't it be NR5? Acedrg 279 has actually put NR5 with: |
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NR5 is reserved for N on five membered aromatic rings with no H. It should be able to become an acceptor. N30 is neither acceptor nor donor. |
Chiral volume may become NaN in come cases. An example is the current PRO's chir_2, which will be fixed by MonomerLibrary/monomers#38
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What are the remaining problems related to this branch. I would like to fix it with the help of @flong-mrc |
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Now Pro has two hydrogen (H and H2; H2 is an extra hydrogen nonexistent in the CCD) bonded to N, so all P-peptide monomers should be updated accordingly. Then it's better to use H/H2 names consistently (otherwise we need an alias). The current Acedrg (279), however, adds an extra H3 to YPR, while in the CCD H2 is bonded to N (and there is no "H" in the monomer). Fei mentioned he would fix Acedrg to use "H" as an extra hydrogen in this case. Also, the aforementioned NR5/N30 problem should be fixed (we can do it manually, but it's better to fix Acedrg). |
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Thank you. it is clear now. I will talk to @flong-mrc tomorrow |
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All PRO-like peptides have been updated to have two hydrogen atoms using (pre-release) Acedrg 281. DEL-HNP was also fixed, now the type of N is NH0. Please test! |
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12L has been updated, which was missed due to an Acedrg installation issue. I was worried about the sigma values of omega, but a quick analysis of high res (1.5 A or better) PDB models told 5 degrees are reasonable for PTRANS/PCIS links, while Acedrg now gives 20 degrees. I think this branch can be merged. |
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Is not omega sp2-sp2 torsion angle? I thought acedrg sigma for these cases is 5. |
This is about P-peptides. In my understanding Acedrg has changed to give large sigmas for large substituents. |
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Is not omega a part of links? Within sungle peptides we will have sp2-sp3 links. I may be missing something |
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Yes it's part of links. All omegas (for peptides, P-peptides, and M-peptides) have sigma value of 5 degrees. I meant this seems ok as it is. And with Acedrg 284 gives |
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It needs to change. @flong-mrc could you please have a look this? We will change these when we have proper torsion angle statistics. |
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Yes, for the monomers considered as peptides (standard or variates),
sigma for sp2-sp2 torsion angles are set to 5.00. But for the links, it
is not considered as peptides anymore and therefore general rules apply.
But if we think we should keep the original 5.0 for link between
peptides. I can change. Maybe it is best to see what actual values are
from stats on COD molecules.
Thanks,
Fei
…On 2024-02-15 05:44, keitaroyam wrote:
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Yes it's part of links. All omegas (for peptides, P-peptides, and
M-peptides) have sigma value of 5 degrees. I meant this seems ok as it
is.
And with
LINK: RES-NAME-1 ALA ATOM-NAME-1 C RES-NAME-2 PRO ATOM-NAME-2 N DELETE
ATOM OXT 1
Acedrg 284 gives
ALA-PRO sp2_sp2_1 1 CA 1 C 2 N 2 CA 180.000 20 2
ALA-PRO sp2_sp3_1 1 C 2 N 2 CD 2 CG 180.000 10.0 6
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I think for now we should have: |
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Try the version of acedrg on hal/hex/max, it should be like that.
Fei
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I think for now we should have:
sp2-sp2 sigma 5
sp3-sp3 sigma 10
sp2-sp3 sigma 20 (we could make it five also, since period is 6 then
20 means that it can go from one minimum to another easily, distance
between minimum of the energy and maximum will be 30 degrees)
Obviously we should have better statistics for these things
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Dr. Fei Long
Structural Studies Division
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Cambridge Biomedical Campus,
Cambridge
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Thank you Fei, it now gave "right" sigma values. |
In #32 there was a mistake in PRO where N was considered sp2. This was fixed in Acedrg 279.
Edit: finally, all P-peptides have been updated