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
> <https://www.google.com/maps/search/Borowska+211A,+50-556+Wroclaw,+Poland?entry=gmail&source=g>
>
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Received on Sun Oct 20 2024 - 08:00:02 PDT
