I have a potential fix. I'm going to test it a bit more and should
hopefully have it implemented by tomorrow.
-Dan
On Mon, Oct 21, 2024 at 2:59 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> I think I see what's going on. The structures are different enough
> that the atoms aren't satisfying the tolerances in the chirality-based
> mapper. I may have to loosen them a bit.
>
> -Dan
>
> On Mon, Oct 21, 2024 at 2:30 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >
> > Seems like for some reason the atoms H10 and H11 in the target are not
> > being mapped to H2' and H2'' in the reference. Still checking why this
> > is happening.
> >
> > -Dan
> >
> > On Mon, Oct 21, 2024 at 2:17 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> > >
> > > Hi,
> > >
> > > Thanks for the files. Looking at your output, the relevant warning is here:
> > >
> > > > Warning: Not all atoms were mapped. Frames will not be modified.
> > >
> > > I'll look further into why this might be the case and get back to you.
> > >
> > > -Dan
> > >
> > > On Sun, Oct 20, 2024 at 10:35 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> > > >
> > > > Hi,
> > > >
> > > > Can you please post your exact cpptraj input as well as all the output you received? Thanks.
> > > >
> > > > -Dan
> > > >
> > > > On Sun, Oct 20, 2024 at 6:00 AM Maciej Spiegel via AMBER <amber.ambermd.org> wrote:
> > > >>
> > > >> Dear Amber Users,
> > > >>
> > > >> I followed the tutorial found at (https://amberhub.chpc.utah.edu/create-new-nucleotide-for-amber/ <https://amberhub.chpc.utah.edu/create-new-nucleotide-for-amber/>) to prepare a new nucleoside.
> > > >> At the stage of atommap, I provided the "*-with-charges.mol2" file, which includes the following data:
> > > >>
> > > >> 1 P1 -3.5100 -1.2500 -0.6450 P 1 XDA 1.100865
> > > >> 2 O1 -4.2060 -0.1880 -1.3550 O2 1 XDA -0.703738
> > > >> 3 O2 -2.3170 -0.8170 0.2900 OS 1 XDA -0.440370
> > > >> 4 C1 -2.4850 0.1250 1.3520 CT 1 XDA -0.211185
> > > >> 5 H1 -2.3730 -0.4150 2.2790 H1 1 XDA 0.172500
> > > >> 6 H2 -3.4730 0.5650 1.3120 H1 1 XDA 0.172500
> > > >> 7 C2 -1.4400 1.2140 1.2510 CT 1 XDA 0.336953
> > > >> 8 H3 -1.6380 1.9400 2.0310 H1 1 XDA 0.026244
> > > >> I used the "*-for-charges.pdb" file:
> > > >>
> > > >> ATOM 1 P XDA 1 2.314 1.777 -0.478
> > > >> ATOM 2 OP1 XDA 1 1.972 3.044 -1.215
> > > >> ATOM 3 O5' XDA 1 2.994 2.142 0.923
> > > >> ATOM 4 C5' XDA 1 2.156 2.552 2.020
> > > >> ATOM 5 H5' XDA 1 1.453 1.754 2.258
> > > >> ATOM 6 H5'' XDA 1 1.605 3.450 1.741
> > > >> ATOM 7 C4' XDA 1 3.008 2.848 3.243
> > > >> ATOM 8 H4' XDA 1 2.447 3.477 3.934
> > > >>
> > > >> However, in the output file "-with-charges-reordered.mol2," the atom names remain unchanged. They are the same as in the "-with-charges.mol2":
> > > >>
> > > >> 1 P1 -3.5100 -1.2500 -0.6450 P 1 1DA 1.100865
> > > >> 2 O1 -4.2060 -0.1880 -1.3550 O2 1 1DA -0.703738
> > > >> 3 O2 -2.3170 -0.8170 0.2900 OS 1 1DA -0.440370
> > > >> 4 C1 -2.4850 0.1250 1.3520 CT 1 1DA -0.211185
> > > >> 5 H1 -2.3730 -0.4150 2.2790 H1 1 1DA 0.172500
> > > >> 6 H2 -3.4730 0.5650 1.3120 H1 1 1DA 0.172500
> > > >> 7 C2 -1.4400 1.2140 1.2510 CT 1 1DA 0.336953
> > > >> 8 H3 -1.6380 1.9400 2.0310 H1 1 1DA 0.026244
> > > >>
> > > >> Shouldn’t the atom types shift to those in the original .pdb file? Actually, when looking at the atommap page (https://amberhub.chpc.utah.edu/atommap/ <https://amberhub.chpc.utah.edu/atommap/>), it states:
> > > >>
> > > >> ………."changenames If specified, change names of mapped atoms in to match those in .”
> > > >>
> > > >> Isn’t something missing here, which could explain the issue I mentioned?
> > > >>
> > > >> I am using the latest version of the program as available from GitHub (CPPTRAJ: Trajectory Analysis, V6.29.4).
> > > >> Thank you in advance.
> > > >> –
> > > >> Maciej Spiegel, MPharm PhD
> > > >> assistant professor
> > > >> .GitHub <https://farmaceut.github.io/>
> > > >>
> > > >> Department of Organic Chemistry and Pharmaceutical Technology,
> > > >> Faculty of Pharmacy, Wroclaw Medical University
> > > >> Borowska 211A, 50-556 Wroclaw, Poland
> > > >>
> > > >> _______________________________________________
> > > >> AMBER mailing list
> > > >> AMBER.ambermd.org
> > > >> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Oct 21 2024 - 13:00:02 PDT
