Amber Archive Jul 2023: by subject

[AMBER] [amber] ph constant simulation question
- SATYAJIT KHATUA via AMBER (Tue Jul 04 2023 - 12:07:05 PDT)
- Yang, Li-Yen via AMBER (Tue Jul 04 2023 - 11:19:53 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] [Sender Not Verified] Aligning MD snapshots excluding loops
- Steinbrecher, Thomas via AMBER (Wed Jul 26 2023 - 07:08:32 PDT)
[AMBER] [Sender Not Verified] Capping the N and C residues of protein
- Enrico Martinez via AMBER (Wed Jul 05 2023 - 08:43:44 PDT)
- Enrico Martinez via AMBER (Wed Jul 05 2023 - 02:56:26 PDT)
[AMBER] [Sender Not Verified] Crystal Simulation, protein broken across unit cell
- Steinbrecher, Thomas via AMBER (Fri Jul 14 2023 - 01:31:29 PDT)
[AMBER] [Sender Not Verified] Error about sander
- Steinbrecher, Thomas via AMBER (Tue Jul 11 2023 - 23:18:41 PDT)
[AMBER] [Sender Not Verified] How to build a protein simulation in gaseous environment?
- Steinbrecher, Thomas via AMBER (Tue Jul 18 2023 - 23:42:05 PDT)
[AMBER] [Sender Not Verified] Position restrains on the part of structure
- Enrico Martinez via AMBER (Mon Jul 24 2023 - 08:12:06 PDT)
- Enrico Martinez via AMBER (Fri Jul 21 2023 - 06:37:14 PDT)
- Enrico Martinez via AMBER (Fri Jul 21 2023 - 05:08:08 PDT)
- Enrico Martinez via AMBER (Fri Jul 21 2023 - 02:34:28 PDT)
[AMBER] [Sender Not Verified] Rmsf profile after removing periodicity
- Enrico Martinez via AMBER (Fri Jul 07 2023 - 05:46:32 PDT)
- Enrico Martinez via AMBER (Fri Jul 07 2023 - 01:42:41 PDT)
[AMBER] adQMMM multiple/shaped solvation regions
- Holden Paz via AMBER (Mon Jul 31 2023 - 16:18:54 PDT)
[AMBER] Aligning MD snapshots excluding loops
- Bhattacharjee, Sinjini via AMBER (Wed Jul 26 2023 - 06:37:27 PDT)
[AMBER] Amber 22 compilation
- FyD via AMBER (Fri Jul 14 2023 - 19:09:58 PDT)
- David A Case via AMBER (Fri Jul 14 2023 - 11:37:27 PDT)
- FyD via AMBER (Fri Jul 14 2023 - 07:41:50 PDT)
- FyD via AMBER (Thu Jul 13 2023 - 00:54:10 PDT)
[AMBER] AMBER aMD tutorial
- Prithviraj Nandigrami via AMBER (Mon Jul 10 2023 - 12:56:22 PDT)
[AMBER] Amber22 Installation
- David Case via AMBER (Tue Jul 04 2023 - 06:43:57 PDT)
- Waqqas Zia via AMBER (Tue Jul 04 2023 - 01:05:30 PDT)
[AMBER] AmberTools23 changes antechamber behavior for GAFF2
- brian.radak--- via AMBER (Thu Jul 06 2023 - 17:51:01 PDT)
- Junmei Wang via AMBER (Wed Jul 05 2023 - 07:20:35 PDT)
- Junmei Wang via AMBER (Tue Jul 04 2023 - 13:53:29 PDT)
- John Chodera via AMBER (Tue Jul 04 2023 - 08:37:04 PDT)
[AMBER] AMD hardware support
- Gerardo Zerbetto De Palma via AMBER (Mon Jul 24 2023 - 07:32:37 PDT)
[AMBER] Atom mask corresponded to first or last residues
- Enrico Martinez via AMBER (Sun Jul 09 2023 - 06:05:53 PDT)
- Enrico Martinez via AMBER (Fri Jul 07 2023 - 07:10:54 PDT)
[AMBER] Capping the N and C residues of protein
- Enrico Martinez via AMBER (Wed Jul 05 2023 - 02:34:00 PDT)
[AMBER] Compare trajectories
- yunshi11 via AMBER (Mon Jul 24 2023 - 22:37:10 PDT)
- Dr. Anselm Horn via AMBER (Tue Jul 18 2023 - 05:10:32 PDT)
- yunshi11 via AMBER (Mon Jul 17 2023 - 23:06:15 PDT)
[AMBER] Conversion of NAMD to Amber
- Ramachandran, Balajee via AMBER (Fri Jul 14 2023 - 13:46:26 PDT)
- David A Case via AMBER (Fri Jul 14 2023 - 11:39:46 PDT)
- Ramachandran, Balajee via AMBER (Fri Jul 14 2023 - 07:01:51 PDT)
[AMBER] cpptraj and nastruct
- Daniel Roe via AMBER (Tue Jul 11 2023 - 11:05:36 PDT)
- Daniel Roe via AMBER (Mon Jul 10 2023 - 07:33:01 PDT)
- Daniel Roe via AMBER (Fri Jul 07 2023 - 11:00:24 PDT)
- David A Case via AMBER (Fri Jul 07 2023 - 08:49:24 PDT)
- Daniel Roe via AMBER (Fri Jul 07 2023 - 08:03:41 PDT)
- Daniel Roe via AMBER (Thu Jul 06 2023 - 04:41:51 PDT)
[AMBER] Crystal Simulation, protein broken across unit cell
- Matthew Guberman-Pfeffer via AMBER (Thu Jul 13 2023 - 20:32:16 PDT)
[AMBER] cutoff for pH constant simulation
- Carlos Simmerling via AMBER (Thu Jul 20 2023 - 11:11:47 PDT)
- Yang, Li-Yen via AMBER (Thu Jul 20 2023 - 10:06:58 PDT)
[AMBER] Default ensemble
- Carlos Simmerling via AMBER (Fri Jul 28 2023 - 11:45:40 PDT)
- Shuo-Lin Weng via AMBER (Fri Jul 28 2023 - 08:42:06 PDT)
[AMBER] DNA topology file error
- David A Case via AMBER (Tue Jul 18 2023 - 10:05:05 PDT)
- Sneha Kandapal via AMBER (Tue Jul 18 2023 - 08:02:40 PDT)
[AMBER] Error about sander
- David A Case via AMBER (Thu Jul 13 2023 - 08:19:30 PDT)
- Daniel Roe via AMBER (Wed Jul 12 2023 - 06:34:13 PDT)
- Riran via AMBER (Tue Jul 11 2023 - 20:34:12 PDT)
[AMBER] Error in generating prmtop and inpcrd file
- David A Case via AMBER (Mon Jul 17 2023 - 04:47:45 PDT)
- Priyasha Majee via AMBER (Mon Jul 17 2023 - 00:18:36 PDT)
[AMBER] Error running MCPB.py script step3
- Ritwika Chatterjee via AMBER (Sun Jul 16 2023 - 21:17:20 PDT)
[AMBER] Error while running mmpbsa
- Bill Miller III via AMBER (Wed Jul 12 2023 - 07:44:07 PDT)
- Riran via AMBER (Tue Jul 11 2023 - 20:20:01 PDT)
- David A Case via AMBER (Fri Jul 07 2023 - 08:57:59 PDT)
- SATYAJIT KHATUA via AMBER (Tue Jul 04 2023 - 21:18:28 PDT)
- Riran via AMBER (Tue Jul 04 2023 - 18:07:21 PDT)
[AMBER] Facing difficulty in performing Amber Crystal simulations
- KAJAL ABROL via AMBER (Mon Jul 10 2023 - 09:42:00 PDT)
- David A Case via AMBER (Mon Jul 10 2023 - 08:29:12 PDT)
- Carlos Simmerling via AMBER (Mon Jul 10 2023 - 06:50:31 PDT)
- KAJAL ABROL via AMBER (Mon Jul 10 2023 - 06:40:00 PDT)
- Maria Nagan via AMBER (Fri Jul 07 2023 - 07:03:34 PDT)
- KAJAL ABROL via AMBER (Fri Jul 07 2023 - 06:24:06 PDT)
[AMBER] Facing problem with Ambertools topological files
- Carlos Simmerling via AMBER (Wed Jul 12 2023 - 03:46:40 PDT)
- fateme haghighi via AMBER (Wed Jul 12 2023 - 00:04:17 PDT)
[AMBER] Force field parameters for Fructose-1,6-biphosphate
- ANANDITA MITRA via AMBER (Tue Jul 25 2023 - 00:31:58 PDT)
[AMBER] GPU choice for CUDA simulations
- Joanna Michelle Chua via AMBER (Sat Jul 29 2023 - 20:54:56 PDT)
[AMBER] How to build a protein simulation in gaseous environment?
- Sayan Poddar via AMBER (Tue Jul 18 2023 - 02:59:02 PDT)
[AMBER] How to deal with the metal center contain a phosphorylated amino acid by MCPB.py
- David A Case via AMBER (Fri Jul 07 2023 - 08:52:20 PDT)
- 吕思凡 via AMBER (Thu Jul 06 2023 - 02:54:15 PDT)
[AMBER] How to neutralize charge after replacing the charges calculated by antechamber
- Dr. Anselm Horn via AMBER (Thu Jul 27 2023 - 02:36:38 PDT)
- Amin Sagar via AMBER (Wed Jul 26 2023 - 09:54:59 PDT)
[AMBER] how to remove/delete bonds w/ cpptraj or parmed in pytraj ??
- Thomas C Bishop via AMBER (Wed Jul 12 2023 - 07:35:57 PDT)
- Daniel Roe via AMBER (Wed Jul 12 2023 - 06:40:45 PDT)
- Thomas C. Bishop via AMBER (Mon Jul 10 2023 - 12:35:09 PDT)
[AMBER] Kerror about MMPBSA
- Bill Miller III via AMBER (Sun Jul 02 2023 - 06:31:27 PDT)
- ZangRiran via AMBER (Sun Jul 02 2023 - 06:22:06 PDT)
[AMBER] Methylated DNA simulation
- Rodrigo Galindo-Murillo via AMBER (Thu Jul 13 2023 - 23:06:34 PDT)
- Rodrigo Galindo-Murillo via AMBER (Thu Jul 13 2023 - 11:45:33 PDT)
- Sneha Kandapal via AMBER (Thu Jul 13 2023 - 11:18:38 PDT)
[AMBER] MMPBSA error
- Bill Miller III via AMBER (Wed Jul 19 2023 - 13:52:45 PDT)
- Ramachandran, Balajee via AMBER (Wed Jul 19 2023 - 12:46:46 PDT)
[AMBER] mpi4py build fails in AmberTools23 installation
- accuratefreeenergy--- via AMBER (Sun Jul 30 2023 - 20:55:28 PDT)
- Kotaro TANAKA via AMBER (Sun Jul 30 2023 - 20:25:01 PDT)
- Kotaro TANAKA via AMBER (Thu Jul 27 2023 - 04:38:12 PDT)
[AMBER] Multiple thermostats within one simulation
- Dmitry Suplatov via AMBER (Wed Jul 05 2023 - 02:55:16 PDT)
[AMBER] NAMD TO AMBER
- Vlad Cojocaru via AMBER (Tue Jul 11 2023 - 00:30:50 PDT)
- Ramachandran, Balajee via AMBER (Mon Jul 10 2023 - 16:10:59 PDT)
[AMBER] Opening Job at UIUC VMD development team
- Md Fulbabu Sk via AMBER (Wed Jul 26 2023 - 12:28:10 PDT)
[AMBER] Original chain records in the prepared pdb
- Enrico Martinez via AMBER (Wed Jul 05 2023 - 02:37:05 PDT)
- Enrico Martinez via AMBER (Tue Jul 04 2023 - 00:52:40 PDT)
[AMBER] output structure from tleap!
- Carlos Simmerling via AMBER (Mon Jul 03 2023 - 10:25:45 PDT)
- Singh, Swapnil via AMBER (Mon Jul 03 2023 - 10:21:21 PDT)
[AMBER] pGM force field files?
- Shiji Zhao via AMBER (Mon Jul 24 2023 - 09:14:00 PDT)
- Ray Luo via AMBER (Fri Jul 21 2023 - 08:27:38 PDT)
- Jones De Andrade via AMBER (Fri Jul 21 2023 - 06:15:09 PDT)
[AMBER] Position restrains on the part of structure
- Enrico Martinez via AMBER (Fri Jul 21 2023 - 01:46:06 PDT)
[AMBER] pressure control in constant ph simulation
- Yang, Li-Yen via AMBER (Thu Jul 13 2023 - 11:26:00 PDT)
[AMBER] pressure control question
- Vinicius Wilian Cruzeiro via AMBER (Wed Jul 19 2023 - 08:19:02 PDT)
- David A Case via AMBER (Tue Jul 18 2023 - 08:40:34 PDT)
- Adrian Roitberg via AMBER (Tue Jul 18 2023 - 05:36:40 PDT)
- Yang, Li-Yen via AMBER (Mon Jul 17 2023 - 12:52:34 PDT)
- Vinicius Wilian Cruzeiro via AMBER (Fri Jul 14 2023 - 13:30:16 PDT)
- Yang, Li-Yen via AMBER (Fri Jul 14 2023 - 12:33:42 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] Problems running a membrane-bound protein with ATP-Mg complex using CHARMM-GUI parameters
- Markowska (Mon Jul 31 2023 - 02:38:13 PDT)
- Markowska (Thu Jul 20 2023 - 05:04:26 PDT)
[AMBER] PyRESP tutorial available
- Shiji Zhao via AMBER (Mon Jul 24 2023 - 16:08:27 PDT)
[AMBER] QM+Link final coordinates
- Hector A. Baldoni via AMBER (Mon Jul 03 2023 - 06:24:00 PDT)
- Ross Walker via AMBER (Sun Jul 02 2023 - 14:08:26 PDT)
- Hector A. Baldoni via AMBER (Sun Jul 02 2023 - 09:16:32 PDT)
[AMBER] query
- SOMA ROY via AMBER (Fri Jul 28 2023 - 05:29:27 PDT)
- Dr. Anselm Horn via AMBER (Fri Jul 28 2023 - 02:57:43 PDT)
- SOMA ROY via AMBER (Thu Jul 27 2023 - 02:45:53 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] RESP fitting with constraints, qout output charges NaN
- Albert Gauss via AMBER (Fri Jul 07 2023 - 01:23:28 PDT)
[AMBER] RMS Fluctuation limit and difference in Temperature maximum Density (TMD)
- David A Case via AMBER (Wed Jul 19 2023 - 12:37:37 PDT)
- David A Case via AMBER (Tue Jul 18 2023 - 09:59:24 PDT)
- Zafar,Muhammad Saqlain via AMBER (Mon Jul 17 2023 - 21:09:36 PDT)
[AMBER] Rmsf profile after removing periodicity
- Enrico Martinez via AMBER (Thu Jul 06 2023 - 08:43:34 PDT)
[AMBER] Short hydrogen bonds
- Siddhique via AMBER (Wed Jul 12 2023 - 01:12:02 PDT)
- Siddhique via AMBER (Tue Jul 04 2023 - 07:56:55 PDT)
[AMBER] smaller cutoff resulting in NaNs
- Carlos Simmerling via AMBER (Tue Jul 25 2023 - 14:14:00 PDT)
- Yang, Li-Yen via AMBER (Tue Jul 25 2023 - 13:05:30 PDT)
[AMBER] Thermodynamic Integration problems
- accuratefreeenergy--- via AMBER (Wed Jul 26 2023 - 08:16:11 PDT)
- Prokopios Andrikopoulos via AMBER (Tue Jul 25 2023 - 04:50:49 PDT)
- Shi Zhang via AMBER (Mon Jul 24 2023 - 15:37:03 PDT)
- accuratefreeenergy--- via AMBER (Mon Jul 24 2023 - 11:52:00 PDT)
- Maria Nagan via AMBER (Mon Jul 24 2023 - 10:12:17 PDT)
- Maria Nagan via AMBER (Mon Jul 24 2023 - 09:51:59 PDT)
- Carlos Simmerling via AMBER (Mon Jul 24 2023 - 09:45:11 PDT)
- Prokopios Andrikopoulos via AMBER (Mon Jul 24 2023 - 09:27:17 PDT)
- Carlos Simmerling via AMBER (Mon Jul 24 2023 - 09:32:41 PDT)
[AMBER] TIP5P water model parameter files issue
- Brent Krueger via AMBER (Thu Jul 27 2023 - 05:35:58 PDT)
- SATYAJIT KHATUA via AMBER (Wed Jul 26 2023 - 08:25:20 PDT)
- Zafar,Muhammad Saqlain via AMBER (Wed Jul 26 2023 - 07:29:04 PDT)
- David A Case via AMBER (Wed Jul 26 2023 - 07:11:41 PDT)
- Zafar,Muhammad Saqlain via AMBER (Mon Jul 24 2023 - 22:32:59 PDT)
- David A Case via AMBER (Mon Jul 24 2023 - 09:30:21 PDT)
- Zafar,Muhammad Saqlain via AMBER (Sun Jul 23 2023 - 22:52:35 PDT)
[AMBER] Typo in amber manual
- German P. Barletta via AMBER (Thu Jul 06 2023 - 00:29:35 PDT)
[AMBER] unsuscribe
- Giulia Sormani via AMBER (Thu Jul 06 2023 - 01:50:42 PDT)
- Sara Mahmoud via AMBER (Mon Jul 03 2023 - 07:40:39 PDT)
- Ryan Novosielski via AMBER (Mon Jul 03 2023 - 06:34:35 PDT)
- Sara Mahmoud via AMBER (Mon Jul 03 2023 - 06:30:32 PDT)
[AMBER] Zn protease
- Hector A. Baldoni via AMBER (Tue Jul 18 2023 - 14:29:59 PDT)
[AMBER] 回复: Kerror about MMPBSA
- SATYAJIT KHATUA via AMBER (Mon Jul 03 2023 - 03:13:37 PDT)
- ZangRiran via AMBER (Mon Jul 03 2023 - 02:56:04 PDT)
- Huang ZiJian via AMBER (Sun Jul 02 2023 - 21:02:25 PDT)
[AMBER] 回复: Keyerror about mmpbsa
- ZangRiran via AMBER (Sun Jul 02 2023 - 06:11:55 PDT)
Capping the N and C residues of protein
- Enrico Martinez via AMBER (Wed Jul 19 2023 - 05:16:30 PDT)
- Enrico Martinez via AMBER (Wed Jul 19 2023 - 01:29:36 PDT)
How to neutralize charge after replacing the charges calculated by antechamber
- Amin Sagar via AMBER (Thu Jul 27 2023 - 05:59:48 PDT)

Amber Archive Jul 2023 by subject