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
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Received on Sun Oct 20 2024 - 03:30:02 PDT
