Amber Archive Jul 2023 by thread
- Re: [AMBER] 回复: Keyerror about mmpbsa ZangRiran via AMBER (Sun Jul 02 2023 - 06:11:55 PDT)
- [AMBER] Kerror about mmpbsa ZangRiran via AMBER (Sun Jul 02 2023 - 06:22:06 PDT)
- Re: [AMBER] Kerror about MMPBSA Bill Miller III via AMBER (Sun Jul 02 2023 - 06:31:27 PDT)
- [AMBER] QM+Link final coordinates Hector A. Baldoni via AMBER (Sun Jul 02 2023 - 09:16:32 PDT)
- [AMBER] 回复: Kerror about MMPBSA Huang ZiJian via AMBER (Sun Jul 02 2023 - 21:02:25 PDT)
- Re: [AMBER] unsuscribe Sara Mahmoud via AMBER (Mon Jul 03 2023 - 06:30:32 PDT)
- [AMBER] output structure from tleap! Singh, Swapnil via AMBER (Mon Jul 03 2023 - 10:21:21 PDT)
- [AMBER] Original chain records in the prepared pdb Enrico Martinez via AMBER (Tue Jul 04 2023 - 00:52:40 PDT)
- [AMBER] Amber22 Installation Waqqas Zia via AMBER (Tue Jul 04 2023 - 01:05:30 PDT)
- [AMBER] Short hydrogen bonds Siddhique via AMBER (Tue Jul 04 2023 - 07:56:55 PDT)
- [AMBER] AmberTools23 changes antechamber behavior for GAFF2 John Chodera via AMBER (Tue Jul 04 2023 - 08:37:04 PDT)
- [AMBER] [amber] ph constant simulation question Yang, Li-Yen via AMBER (Tue Jul 04 2023 - 11:19:53 PDT)
- [AMBER] Error while running mmpbsa Riran via AMBER (Tue Jul 04 2023 - 18:07:21 PDT)
- [AMBER] Capping the N and C residues of protein Enrico Martinez via AMBER (Wed Jul 05 2023 - 02:34:00 PDT)
- [AMBER] Multiple thermostats within one simulation Dmitry Suplatov via AMBER (Wed Jul 05 2023 - 02:55:16 PDT)
- Re: [AMBER] [Sender Not Verified] Capping the N and C residues of protein Enrico Martinez via AMBER (Wed Jul 05 2023 - 02:56:26 PDT)
- [AMBER] Typo in amber manual German P. Barletta via AMBER (Thu Jul 06 2023 - 00:29:35 PDT)
- [AMBER] How to deal with the metal center contain a phosphorylated amino acid by MCPB.py 吕思凡 via AMBER (Thu Jul 06 2023 - 02:54:15 PDT)
- Re: [AMBER] cpptraj and nastruct Daniel Roe via AMBER (Thu Jul 06 2023 - 04:41:51 PDT)
- [AMBER] Rmsf profile after removing periodicity Enrico Martinez via AMBER (Thu Jul 06 2023 - 08:43:34 PDT)
- [AMBER] RESP fitting with constraints, qout output charges NaN Albert Gauss via AMBER (Fri Jul 07 2023 - 01:23:28 PDT)
- Re: [AMBER] [Sender Not Verified] Rmsf profile after removing periodicity Enrico Martinez via AMBER (Fri Jul 07 2023 - 01:42:41 PDT)
- [AMBER] Facing difficulty in performing Amber Crystal simulations KAJAL ABROL via AMBER (Fri Jul 07 2023 - 06:24:06 PDT)
- [AMBER] Atom mask corresponded to first or last residues Enrico Martinez via AMBER (Fri Jul 07 2023 - 07:10:54 PDT)
- [AMBER] Facing difficulty in performing Amber Crystal simulations KAJAL ABROL via AMBER (Mon Jul 10 2023 - 06:40:00 PDT)
- [AMBER] how to remove/delete bonds w/ cpptraj or parmed in pytraj ?? Thomas C. Bishop via AMBER (Mon Jul 10 2023 - 12:35:09 PDT)
- [AMBER] AMBER aMD tutorial Prithviraj Nandigrami via AMBER (Mon Jul 10 2023 - 12:56:22 PDT)
- [AMBER] NAMD TO AMBER Ramachandran, Balajee via AMBER (Mon Jul 10 2023 - 16:10:59 PDT)
- [AMBER] Error about sander Riran via AMBER (Tue Jul 11 2023 - 20:34:12 PDT)
- [AMBER] Facing problem with Ambertools topological files fateme haghighi via AMBER (Wed Jul 12 2023 - 00:04:17 PDT)
- [AMBER] Amber 22 compilation FyD via AMBER (Thu Jul 13 2023 - 00:54:10 PDT)
- [AMBER] Methylated DNA simulation Sneha Kandapal via AMBER (Thu Jul 13 2023 - 11:18:38 PDT)
- [AMBER] pressure control in constant ph simulation Yang, Li-Yen via AMBER (Thu Jul 13 2023 - 11:26:00 PDT)
- [AMBER] Crystal Simulation, protein broken across unit cell Matthew Guberman-Pfeffer via AMBER (Thu Jul 13 2023 - 20:32:16 PDT)
- [AMBER] Conversion of NAMD to Amber Ramachandran, Balajee via AMBER (Fri Jul 14 2023 - 07:01:51 PDT)
- [AMBER] pressure control question Yang, Li-Yen via AMBER (Fri Jul 14 2023 - 12:33:42 PDT)
- [AMBER] Error running MCPB.py script step3 Ritwika Chatterjee via AMBER (Sun Jul 16 2023 - 21:17:20 PDT)
- [AMBER] Error in generating prmtop and inpcrd file Priyasha Majee via AMBER (Mon Jul 17 2023 - 00:18:36 PDT)
- [AMBER] [fglaser.technion.ac.il: Fwd: MaxNumberTIAtom on PPI-GaMD - BUG?] David A Case via AMBER (Mon Jul 17 2023 - 04:41:30 PDT)
- [AMBER] RMS Fluctuation limit and difference in Temperature maximum Density (TMD) Zafar,Muhammad Saqlain via AMBER (Mon Jul 17 2023 - 21:09:36 PDT)
- [AMBER] Compare trajectories yunshi11 via AMBER (Mon Jul 17 2023 - 23:06:15 PDT)
- [AMBER] How to build a protein simulation in gaseous environment? Sayan Poddar via AMBER (Tue Jul 18 2023 - 02:59:02 PDT)
- [AMBER] DNA topology file error Sneha Kandapal via AMBER (Tue Jul 18 2023 - 08:02:40 PDT)
- [AMBER] Zn protease Hector A. Baldoni via AMBER (Tue Jul 18 2023 - 14:29:59 PDT)
- Re: [AMBER] [Sender Not Verified] Re: Capping the N and C residues of protein Enrico Martinez via AMBER (Wed Jul 19 2023 - 01:29:36 PDT)
- [AMBER] Problem with time records in cpout- files in REMD CpHMD simulation Elvira Tarasova via AMBER (Wed Jul 19 2023 - 10:31:30 PDT)
- [AMBER] MMPBSA error Ramachandran, Balajee via AMBER (Wed Jul 19 2023 - 12:46:46 PDT)
- [AMBER] Problems running a membrane-bound protein with ATP-Mg complex using CHARMM-GUI parameters Markowska (Thu Jul 20 2023 - 05:04:26 PDT)
- [AMBER] cutoff for pH constant simulation Yang, Li-Yen via AMBER (Thu Jul 20 2023 - 10:06:58 PDT)
- [AMBER] Position restrains on the part of structure Enrico Martinez via AMBER (Fri Jul 21 2023 - 01:46:06 PDT)
- Re: [AMBER] [Sender Not Verified] Position restrains on the part of structure Enrico Martinez via AMBER (Fri Jul 21 2023 - 02:34:28 PDT)
- [AMBER] TIP5P water model parameter files issue Zafar,Muhammad Saqlain via AMBER (Sun Jul 23 2023 - 22:52:35 PDT)
- [AMBER] AMD hardware support Gerardo Zerbetto De Palma via AMBER (Mon Jul 24 2023 - 07:32:37 PDT)
- [AMBER] Thermodynamic Integration problems Prokopios Andrikopoulos via AMBER (Mon Jul 24 2023 - 09:27:17 PDT)
- [AMBER] PyRESP tutorial available Shiji Zhao via AMBER (Mon Jul 24 2023 - 16:08:27 PDT)
- [AMBER] Force field parameters for Fructose-1,6-biphosphate ANANDITA MITRA via AMBER (Tue Jul 25 2023 - 00:31:58 PDT)
- [AMBER] smaller cutoff resulting in NaNs Yang, Li-Yen via AMBER (Tue Jul 25 2023 - 13:05:30 PDT)
- [AMBER] Query regarding Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Munazzah Fatima Ansari via AMBER (Wed Jul 26 2023 - 04:17:50 PDT)
- [AMBER] Aligning MD snapshots excluding loops Bhattacharjee, Sinjini via AMBER (Wed Jul 26 2023 - 06:37:27 PDT)
- [AMBER] How to neutralize charge after replacing the charges calculated by antechamber Amin Sagar via AMBER (Wed Jul 26 2023 - 09:54:59 PDT)
- [AMBER] Opening Job at UIUC VMD development team Md Fulbabu Sk via AMBER (Wed Jul 26 2023 - 12:28:10 PDT)
- [AMBER] query SOMA ROY via AMBER (Thu Jul 27 2023 - 02:45:53 PDT)
- [AMBER] mpi4py build fails in AmberTools23 installation Kotaro TANAKA via AMBER (Thu Jul 27 2023 - 04:38:12 PDT)
- [AMBER] Default ensemble Shuo-Lin Weng via AMBER (Fri Jul 28 2023 - 08:42:06 PDT)
- [AMBER] GPU choice for CUDA simulations Joanna Michelle Chua via AMBER (Sat Jul 29 2023 - 20:54:56 PDT)
- [AMBER] adQMMM multiple/shaped solvation regions Holden Paz via AMBER (Mon Jul 31 2023 - 16:18:54 PDT)
- Last message date: Mon Jul 31 2023 - 16:30:02 PDT
- Archived on: Fri Apr 26 2024 - 05:56:20 PDT
