Amber Archive May 2024: by subject

[AMBER-Developers] Release of Amber24 and AmberTools24
- David A Case via AMBER-Developers (Wed May 01 2024 - 09:16:14 PDT)
[AMBER] [EXTERNAL] Release of Amber24 and AmberTools24
- Chakrabarti, Mayukh \(NIH/NCI\) \[C\] via AMBER (Mon May 06 2024 - 09:47:55 PDT)
[AMBER] Absolute simulation box size
- Istvan Kolossvary via AMBER (Sat May 04 2024 - 10:29:57 PDT)
[AMBER] Alchemical membrane simulations with the AMBER TI code
- Dickson, Callum via AMBER (Tue May 07 2024 - 07:57:53 PDT)
- William Glass via AMBER (Tue May 07 2024 - 03:06:23 PDT)
[AMBER] Amber force fields for 5-Methylcytosine Nucleotide RNA
- SATYAJIT KHATUA via AMBER (Thu May 09 2024 - 09:01:51 PDT)
- SATYAJIT KHATUA via AMBER (Tue May 07 2024 - 07:38:02 PDT)
- Penumutchu, Srinivasa via AMBER (Tue May 07 2024 - 07:26:28 PDT)
[AMBER] amber19sb atom types doubts
- Carlos Simmerling via AMBER (Sat May 25 2024 - 05:04:45 PDT)
- Jones De Andrade via AMBER (Sat May 25 2024 - 05:00:34 PDT)
[AMBER] Amber22/AmberTools23: Enabling of libtorch & cudnn libraries breaks pbsa binaries
- Ray Luo via AMBER (Wed May 08 2024 - 10:03:54 PDT)
- Chakrabarti, Mayukh \(NIH/NCI\) \[C\] via AMBER (Tue May 07 2024 - 08:56:48 PDT)
[AMBER] Assistance with tleap
- Carlos Simmerling via AMBER (Fri May 10 2024 - 07:08:12 PDT)
- Carlos Simmerling via AMBER (Thu May 09 2024 - 13:41:40 PDT)
- Carlos Simmerling via AMBER (Thu May 09 2024 - 13:01:19 PDT)
- Xylia Peters via AMBER (Thu May 09 2024 - 10:07:00 PDT)
[AMBER] Atom type not found for RNA
- Carlos Simmerling via AMBER (Sat May 04 2024 - 08:04:04 PDT)
- Kavinda Kashi Juliyan Gunasinghe via AMBER (Fri May 03 2024 - 21:36:57 PDT)
[AMBER] Atom types more than 2 characters
- David A Case via AMBER (Fri May 03 2024 - 09:12:03 PDT)
[AMBER] Bond not formed in tleap for DNA phosphate
- Carlos Simmerling via AMBER (Tue May 21 2024 - 07:27:15 PDT)
- Vaibhav Bhatt via AMBER (Tue May 21 2024 - 02:14:10 PDT)
[AMBER] bug in cpptraj from amber tools 24 related to dcd trajectories ?
- Daniel Roe via AMBER (Sun May 19 2024 - 13:00:07 PDT)
- Daniel Roe via AMBER (Sat May 18 2024 - 16:21:13 PDT)
- Daniel Roe via AMBER (Sat May 18 2024 - 11:25:36 PDT)
- Daniel Roe via AMBER (Sat May 18 2024 - 03:47:59 PDT)
- Daniel Roe via AMBER (Fri May 17 2024 - 08:04:31 PDT)
- Vlad Cojocaru via AMBER (Fri May 17 2024 - 07:54:12 PDT)
[AMBER] Call for papers - 18th German Conference on Cheminformatics (GCC 2024)
- Guessregen, Stefan /DE via AMBER (Tue May 07 2024 - 15:10:46 PDT)
[AMBER] Changed atom name in NME cap residue library
- Jong Young Joung via AMBER (Thu May 16 2024 - 00:23:07 PDT)
[AMBER] Cpptraj distance for multiple copies of ligand vs protein
- Daniel Roe via AMBER (Mon May 06 2024 - 09:54:42 PDT)
- Martin Juhás via AMBER (Mon May 06 2024 - 07:10:23 PDT)
- Alexander Hung Lee via AMBER (Mon May 06 2024 - 06:46:44 PDT)
[AMBER] Cpptraj vs Leap residue number overflow
- David A Case via AMBER (Fri May 03 2024 - 08:55:42 PDT)
[AMBER] default lambda-sheduling in amber24
- Juraj Dobias via AMBER (Thu May 23 2024 - 00:23:59 PDT)
[AMBER] Does pdb4amber take care of protonation states?
- Abdelrahman, Noureen via AMBER (Fri May 10 2024 - 12:02:50 PDT)
- David A Case via AMBER (Mon May 06 2024 - 20:12:11 PDT)
- He, Amy via AMBER (Mon May 06 2024 - 18:55:19 PDT)
- Abdelrahman, Noureen via AMBER (Mon May 06 2024 - 12:35:32 PDT)
[AMBER] easybuild for amber24
- David A Case via AMBER (Sat May 25 2024 - 14:38:35 PDT)
- Mooers, Blaine H.M. \(HSC\) via AMBER (Thu May 23 2024 - 20:54:02 PDT)
[AMBER] Error in production extension
- Daniel Roe via AMBER (Wed May 22 2024 - 06:56:50 PDT)
- Carlos Simmerling via AMBER (Wed May 22 2024 - 06:49:52 PDT)
- Priyasha Majee via AMBER (Wed May 22 2024 - 04:31:05 PDT)
[AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius!
- Timothy Giese via AMBER (Wed May 29 2024 - 06:29:08 PDT)
- AMANPREET KAUR via AMBER (Tue May 28 2024 - 23:12:51 PDT)
[AMBER] Errors using the ZAFF Modeling Tutorials with Center ID 4
- saverio lemme via AMBER (Fri May 10 2024 - 01:43:40 PDT)
[AMBER] Fwd: bug report and gmail filtering amber digest
- Ryan Snyder via AMBER (Fri May 17 2024 - 08:51:00 PDT)
- Ross Walker via AMBER (Fri May 17 2024 - 07:10:57 PDT)
[AMBER] Gaussian accelerated (GAMD) Question
- Ramdhan,Peter A via AMBER (Tue May 14 2024 - 08:18:55 PDT)
[AMBER] gnuplot of DCCM map
- Hector A. Baldoni via AMBER (Fri May 10 2024 - 11:49:34 PDT)
- Priyasha Majee via AMBER (Thu May 09 2024 - 23:11:48 PDT)
[AMBER] How to add new lipids into packmol-memgen for CHARMM
- Stephan Schott via AMBER (Tue May 07 2024 - 11:59:22 PDT)
- Evan Collins via AMBER (Tue May 07 2024 - 10:53:19 PDT)
[AMBER] Implicit solvent simulation of membrane system
- Enrico Martinez via AMBER (Fri May 17 2024 - 05:58:37 PDT)
- Enrico Martinez via AMBER (Fri May 17 2024 - 02:10:28 PDT)
- Enrico Martinez via AMBER (Thu May 16 2024 - 08:16:02 PDT)
- Enrico Martinez via AMBER (Thu May 16 2024 - 02:01:48 PDT)
[AMBER] Installation of AMBER-18
- David A Case via AMBER (Thu May 30 2024 - 20:09:50 PDT)
- Kriti Shukla via AMBER (Thu May 30 2024 - 00:19:22 PDT)
[AMBER] Installing Amber24 in M3 Mac
- KazuoOhta via AMBER (Fri May 24 2024 - 22:14:44 PDT)
- KazuoOhta via AMBER (Fri May 24 2024 - 19:28:26 PDT)
- Stephan Schott via AMBER (Fri May 24 2024 - 08:06:32 PDT)
- Marc Ciruela Jardí via AMBER (Wed May 22 2024 - 06:47:43 PDT)
[AMBER] Interpretation of Native contacts analysis output in cpptraj
- Shah, Tejas V. via AMBER (Wed May 01 2024 - 13:30:37 PDT)
[AMBER] License in Exxact workstation
- David A Case via AMBER (Sat May 25 2024 - 14:58:01 PDT)
- Carlos Simmerling via AMBER (Sat May 25 2024 - 14:40:30 PDT)
- Ali Saad via AMBER (Sat May 25 2024 - 12:08:43 PDT)
[AMBER] mcwat does not work in amber24
- Juraj Dobias via AMBER (Sat May 18 2024 - 11:52:37 PDT)
- Carlos Simmerling via AMBER (Sat May 18 2024 - 04:49:57 PDT)
- Juraj Dobias via AMBER (Fri May 17 2024 - 12:24:36 PDT)
[AMBER] Merge cpout files to analyze full simulation
- He, Amy via AMBER (Tue May 21 2024 - 07:09:29 PDT)
- Abdelrahman, Noureen via AMBER (Mon May 20 2024 - 23:18:57 PDT)
- He, Amy via AMBER (Mon May 20 2024 - 15:33:45 PDT)
- Abdelrahman, Noureen via AMBER (Mon May 20 2024 - 15:16:37 PDT)
- He, Amy via AMBER (Mon May 20 2024 - 06:42:45 PDT)
- Abdelrahman, Noureen via AMBER (Mon May 20 2024 - 06:09:35 PDT)
[AMBER] Multiple types of water for SHAKE
- Tucker E. Burgin via AMBER (Fri May 10 2024 - 08:22:45 PDT)
[AMBER] NetCDF variable compression requires compiling with HDF5 support
- Martin Juhás via AMBER (Sun May 05 2024 - 13:41:46 PDT)
[AMBER] NMR restraints slowing down simulations
- Skanda Sastry via AMBER (Wed May 29 2024 - 17:04:03 PDT)
[AMBER] Parameters for HEM residues
- Enrico Martinez via AMBER (Wed May 15 2024 - 02:43:04 PDT)
[AMBER] pmemd.cuda does not reflect the PLUMED-contributed potential energy for replica exchange probabilities
- Miroslav Krepl via AMBER (Fri May 17 2024 - 09:25:37 PDT)
[AMBER] printcharges using Amber24 GFN2-xtB method
- Timothy Giese via AMBER (Mon May 20 2024 - 07:31:34 PDT)
- Niven Singh via AMBER (Fri May 17 2024 - 16:26:51 PDT)
- Timothy Giese via AMBER (Wed May 15 2024 - 08:51:59 PDT)
- Niven Singh via AMBER (Thu May 09 2024 - 14:34:40 PDT)
[AMBER] Problem with ZAFF Modeling Tutorial Center ID 4
- Erdem Yeler via AMBER (Wed May 29 2024 - 04:28:11 PDT)
- saverio lemme via AMBER (Wed May 29 2024 - 04:00:48 PDT)
[AMBER] Problems compiling with openHPC netcdf/-fortran
- Martin Juhás via AMBER (Tue May 07 2024 - 07:56:57 PDT)
- Martin Juhás via AMBER (Tue May 07 2024 - 07:32:52 PDT)
[AMBER] Problems with amber24 installation
- Elvis Martis via AMBER (Fri May 03 2024 - 03:28:29 PDT)
[AMBER] Proper way of using external OFF library files
- Danial Yousefi via AMBER (Fri May 24 2024 - 02:36:08 PDT)
[AMBER] Quantum mechanical calculation for charge
- Timothy Giese via AMBER (Fri May 31 2024 - 06:57:15 PDT)
- Kriti Shukla via AMBER (Fri May 31 2024 - 02:55:47 PDT)
[AMBER] Query on ASMD vs SMD
- Sruthi Sudhakar via AMBER (Thu May 23 2024 - 02:07:39 PDT)
[AMBER] Query Regarding AMBER Advanced Thermodynamic Integration calculation:
- Timothy Giese via AMBER (Tue May 28 2024 - 09:33:09 PDT)
- Kankana Bhattacharjee via AMBER (Mon May 27 2024 - 23:52:00 PDT)
[AMBER] Question regarding SMD simulation of ligand-receptor system
- Carlos Simmerling via AMBER (Mon May 27 2024 - 16:08:54 PDT)
- Frederico Henrique Ferreira via AMBER (Mon May 27 2024 - 14:22:29 PDT)
[AMBER] Regarding Advanced Thermodyanmic Integration Methods to mutate a ligand bound to a protein tutorial:
- David A Case via AMBER (Tue May 14 2024 - 14:38:35 PDT)
- Kankana Bhattacharjee via AMBER (Sat May 11 2024 - 00:16:25 PDT)
[AMBER] Regarding CG protein and Bilayer:
- David A Case via AMBER (Mon May 27 2024 - 20:51:55 PDT)
- Kankana Bhattacharjee via AMBER (Mon May 27 2024 - 04:56:16 PDT)
[AMBER] Regarding FE_Workflow tool :
- Timothy Giese via AMBER (Tue May 28 2024 - 09:42:50 PDT)
- Kankana Bhattacharjee via AMBER (Mon May 27 2024 - 22:26:10 PDT)
- Ryan Snyder via AMBER (Mon May 27 2024 - 07:17:03 PDT)
- Kankana Bhattacharjee via AMBER (Mon May 27 2024 - 02:49:50 PDT)
[AMBER] Regarding GIST analysis
- Jenny 148 via AMBER (Fri May 24 2024 - 05:34:07 PDT)
[AMBER] Regarding Packmol-Memgen:
- Kankana Bhattacharjee via AMBER (Tue May 28 2024 - 06:10:12 PDT)
- Stephan Schott via AMBER (Tue May 28 2024 - 05:58:43 PDT)
[AMBER] Regarding using two basis sets in QUICK
- Goetz, Andreas via AMBER (Mon May 20 2024 - 13:32:16 PDT)
- Kriti Shukla via AMBER (Mon May 20 2024 - 04:57:17 PDT)
[AMBER] Register Now! Amber Free Energy Workshop 2024 at SDSC/UCSD, Aug. 12-16
- King Wang via AMBER (Mon May 13 2024 - 18:46:17 PDT)
- Darrin York via AMBER (Mon May 13 2024 - 17:18:48 PDT)
[AMBER] Release of Amber24 and AmberTools24
- Dr. Anselm Horn via AMBER (Fri May 03 2024 - 00:47:22 PDT)
[AMBER] Restarting constant pH replica exchange MD
- He, Amy via AMBER (Sat May 11 2024 - 06:52:44 PDT)
- Dulal Mondal via AMBER (Sat May 11 2024 - 01:36:14 PDT)
- Dulal Mondal via AMBER (Sat May 11 2024 - 01:33:48 PDT)
- He, Amy via AMBER (Fri May 10 2024 - 16:11:39 PDT)
- Dulal Mondal via AMBER (Fri May 10 2024 - 01:39:06 PDT)
[AMBER] Runtime errors when using nmropt restraints
- David A Case via AMBER (Thu May 09 2024 - 08:34:16 PDT)
- Pye, Aaron Wesley via AMBER (Thu May 09 2024 - 04:56:32 PDT)
[AMBER] Specifying a mask with scale in PARMED
- Carlos Simmerling via AMBER (Mon May 13 2024 - 09:40:27 PDT)
- Ford, Baily Wayne via AMBER (Mon May 13 2024 - 09:29:20 PDT)
[AMBER] Suspicion pKa shift in Constant pH Molecular Dynamics simulation
- David A Case via AMBER (Tue May 28 2024 - 15:15:28 PDT)
- David A Case via AMBER (Sat May 25 2024 - 14:56:12 PDT)
- Abuhasan, Osama via AMBER (Fri May 24 2024 - 02:56:33 PDT)
[AMBER] Thermodynamic Integration calculation:
- David A Case via AMBER (Fri May 03 2024 - 09:23:16 PDT)
[AMBER] TIP 3P IONS
- David A Case via AMBER (Fri May 17 2024 - 11:40:50 PDT)
- Ramírez, Gustavo via AMBER (Fri May 17 2024 - 09:13:14 PDT)
[AMBER] tleap can't distinguish two protein chains even though I used TER
- David A Case via AMBER (Fri May 10 2024 - 15:21:05 PDT)
- Abdelrahman, Noureen via AMBER (Fri May 10 2024 - 14:59:32 PDT)
[AMBER] Using TCPB with Terachem in Amber
- Carlos Simmerling via AMBER (Fri May 31 2024 - 13:37:08 PDT)
- Carlos Simmerling via AMBER (Fri May 31 2024 - 13:23:46 PDT)
- Abdelrahman, Noureen via AMBER (Fri May 31 2024 - 12:34:25 PDT)
Amber22/AmberTools23: Enabling of libtorch & cudnn libraries breaks pbsa binaries
- Ray Luo via AMBER (Thu May 16 2024 - 14:37:41 PDT)
- Chakrabarti, Mayukh \(NIH/NCI\) \[C\] via AMBER (Tue May 14 2024 - 15:34:07 PDT)
- Chakrabarti, Mayukh \(NIH/NCI\) \[C\] via AMBER (Mon May 13 2024 - 14:36:01 PDT)
- Yongxian Wu via AMBER (Sat May 11 2024 - 19:47:19 PDT)
- Chakrabarti, Mayukh \(NIH/NCI\) \[C\] via AMBER (Fri May 10 2024 - 07:07:10 PDT)
- Yongxian Wu via AMBER (Thu May 09 2024 - 22:55:41 PDT)
- Chakrabarti, Mayukh \(NIH/NCI\) \[C\] via AMBER (Wed May 08 2024 - 14:25:55 PDT)

Amber Archive May 2024 by subject