Amber Archive Jan 2025 by messages with attachments

114 messages: Starting Wed Jan 01 2025 - 03:00:02 PST, Ending Fri Jan 31 2025 - 00:30:02 PST
This period: Most recent messages
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Re: [AMBER] Regarding QMMM simulation run error: Kankana Bhattacharjee via AMBER (Sat Jan 04 2025 - 19:11:02 PST)
1. qmmm.in (366 bytes)
[AMBER] Is this the place to ask about CPPTRAJ issues? James Kress via AMBER (Sat Jan 04 2025 - 21:01:28 PST)
1. cpptraj_configure_and_install_output.txt (42664 bytes)
[AMBER] aMD run Dulal Mondal via AMBER (Sun Jan 05 2025 - 04:39:03 PST)
1. 01-05_18-07-05.png (249134 bytes)
[AMBER] Regarding QM-MM error: Kankana Bhattacharjee via AMBER (Sun Jan 05 2025 - 23:13:39 PST)
1. qmmm.in (393 bytes)
[AMBER] Unphysical temperature spikes Kiriko Terai via AMBER (Mon Jan 06 2025 - 09:13:17 PST)
1. image001.png (87895 bytes)
Re: [AMBER] Unphysical temperature spikes David A Case via AMBER (Mon Jan 06 2025 - 12:25:35 PST)
1. npt32.temp.pdf (4916 bytes)
2. npt32.bond.spike.pdf (6039 bytes)
[AMBER] Problem in stapled peptides Airy Sanjeev via AMBER (Wed Jan 08 2025 - 06:03:14 PST)
1. recal.pdb (24363 bytes)
2. link.frcmod (1290 bytes)
3. leap.in (314 bytes)
4. rec_rest.pdb (216143 bytes)
5. link.mol2 (6737 bytes)
Re: [AMBER] prmtop and inpcrd file generation error: Kankana Bhattacharjee via AMBER (Thu Jan 09 2025 - 20:37:34 PST)
1. solv-qmmm.inpcrd (376 bytes)
2. solv-qmmm.prmtop (11903 bytes)
Re: [AMBER] prmtop and inpcrd file generation error: Kankana Bhattacharjee via AMBER (Thu Jan 09 2025 - 20:52:20 PST)
1. leap.log (84628 bytes)
2. mm-leap.jpeg (93393 bytes)
[AMBER] sander.quick.cuda error: Kankana Bhattacharjee via AMBER (Fri Jan 10 2025 - 09:16:40 PST)
1. myjob.sh (442 bytes)
[AMBER] reporting ΔG? or ΔΔG? vs experimental ΔG using FEP+ and TI King Wang via AMBER (Mon Jan 13 2025 - 15:52:54 PST)
1. 01-13_at_1.26.30___PM.png (220608 bytes)
2. 01-13_at_1.29.15___PM.png (447371 bytes)
Re: [AMBER] MMPBSA Error (Topology I think) Vishwaa Kannan via AMBER (Sun Jan 19 2025 - 18:48:34 PST)
1. _MMPBSA_complex_pb.mdout.17 (328431 bytes)
[AMBER] protonated imidazole but post antechamber two N+ in ring.... Debarati DasGupta via AMBER (Sun Jan 26 2025 - 08:21:36 PST)
1. image.png (39438 bytes)
2. image.png (45197 bytes)