Amber Archive Nov 2022: by subject

[AMBER] about mmgbsa method
- Dr. Anselm Horn via AMBER (Fri Nov 04 2022 - 01:41:29 PDT)
- laura zhang via AMBER (Wed Nov 02 2022 - 13:39:10 PDT)
- Dr. Anselm Horn via AMBER (Wed Nov 02 2022 - 08:41:06 PDT)
- laura zhang via AMBER (Wed Nov 02 2022 - 08:19:29 PDT)
[AMBER] Alchemical gti keyword questions
- accuratefreeenergy--- via AMBER (Tue Nov 08 2022 - 05:21:27 PST)
[AMBER] amber tools2016
- Dr. Anselm Horn via AMBER (Thu Nov 17 2022 - 06:22:03 PST)
- sxl18235290334--- via AMBER (Thu Nov 17 2022 - 05:50:31 PST)
[AMBER] AMBER-TI running error
- David A Case via AMBER (Mon Nov 07 2022 - 18:03:19 PST)
- Kevin Hauser via AMBER (Mon Nov 07 2022 - 17:47:07 PST)
- Hwang, Sunny via AMBER (Mon Nov 07 2022 - 17:06:48 PST)
[AMBER] AMBER20 GPU error
- Prithviraj Nandigrami via AMBER (Fri Nov 18 2022 - 11:44:16 PST)
- David A Case via AMBER (Sat Nov 12 2022 - 07:08:40 PST)
- Thomas Cheatham via AMBER (Fri Nov 11 2022 - 09:46:48 PST)
- Carlos Simmerling via AMBER (Fri Nov 11 2022 - 09:38:34 PST)
- Prithviraj Nandigrami via AMBER (Fri Nov 11 2022 - 08:55:11 PST)
- Thomas Cheatham via AMBER (Wed Nov 09 2022 - 20:24:20 PST)
- David A Case via AMBER (Wed Nov 09 2022 - 07:54:13 PST)
- Prithviraj Nandigrami via AMBER (Tue Nov 08 2022 - 15:01:18 PST)
- Prithviraj Nandigrami via AMBER (Sat Nov 05 2022 - 11:01:44 PDT)
- Thomas Cheatham via AMBER (Fri Nov 04 2022 - 16:30:42 PDT)
- Prithviraj Nandigrami via AMBER (Fri Nov 04 2022 - 16:22:31 PDT)
- Thomas Cheatham via AMBER (Thu Nov 03 2022 - 15:17:59 PDT)
- Prithviraj Nandigrami via AMBER (Thu Nov 03 2022 - 14:42:15 PDT)
- Thomas Cheatham via AMBER (Wed Nov 02 2022 - 19:15:44 PDT)
- Prithviraj Nandigrami via AMBER (Wed Nov 02 2022 - 18:50:55 PDT)
[AMBER] Amber22 GPU installation fails while building NVCC object `pmemd_xray_cuda_generated_BulkMaskGPU.cu.o`
- Nitin Kulhar via AMBER (Mon Oct 31 2022 - 22:50:18 PDT)
[AMBER] Announcement: Atomic Simulation Center Symposium 2022, Nov 28/29
- Dr. Anselm Horn via AMBER (Thu Nov 10 2022 - 05:36:25 PST)
[AMBER] Antechamber and py_resp qout format
- Shiji Zhao via AMBER (Mon Nov 28 2022 - 20:40:21 PST)
- Евгений Кадцын via AMBER (Thu Nov 24 2022 - 10:05:17 PST)
[AMBER] Applying position restraint on ligand
- Enrico Martinez via AMBER (Fri Nov 25 2022 - 01:55:22 PST)
- Enrico Martinez via AMBER (Fri Nov 25 2022 - 00:52:35 PST)
- Gustavo Seabra via AMBER (Thu Nov 24 2022 - 08:04:27 PST)
- Enrico Martinez via AMBER (Thu Nov 24 2022 - 07:51:11 PST)
[AMBER] Autoimage cannot find topology information
- Daniel Roe via AMBER (Tue Nov 08 2022 - 11:22:26 PST)
- Clorice Reinhardt via AMBER (Tue Nov 08 2022 - 10:51:23 PST)
- Hunter Wilson via AMBER (Tue Nov 08 2022 - 10:39:10 PST)
[AMBER] Changing CUDA toolkits - need recompile?
- Scott Brozell via AMBER (Thu Nov 10 2022 - 16:23:58 PST)
- James Kress via AMBER (Thu Nov 10 2022 - 11:14:56 PST)
[AMBER] compile AMBER 22 with non-default gcc
- Vlad Cojocaru via AMBER (Sat Nov 05 2022 - 12:23:50 PDT)
- David A Case via AMBER (Sat Nov 05 2022 - 07:48:27 PDT)
- Scott Brozell via AMBER (Fri Nov 04 2022 - 23:17:20 PDT)
- Vlad Cojocaru via AMBER (Fri Nov 04 2022 - 16:08:11 PDT)
[AMBER] Compiling Amber on Apple Silicon M2?
- David A Case via AMBER (Wed Nov 02 2022 - 06:13:18 PDT)
[AMBER] counting number of ions within cutoff region
- angad sharma via AMBER (Wed Nov 02 2022 - 07:27:43 PDT)
[AMBER] Cpptraj for loops and dataset operations
- Carlos Simmerling via AMBER (Wed Nov 30 2022 - 14:26:24 PST)
- James Kress via AMBER (Wed Nov 30 2022 - 14:25:04 PST)
- Daniel Roe via AMBER (Wed Nov 30 2022 - 09:30:54 PST)
- Daniel Roe via AMBER (Wed Nov 30 2022 - 05:07:59 PST)
- Pietro ARONICA via AMBER (Thu Nov 24 2022 - 22:13:00 PST)
[AMBER] Detect vacuum bubbles
- Carlos Simmerling via AMBER (Tue Nov 29 2022 - 05:53:00 PST)
- Hocine EL KHAOUDI ENYOURY via AMBER (Tue Nov 29 2022 - 05:12:35 PST)
[AMBER] Do RTX 3080Ti video cards supported by the amber20?
- Alessandro Contini via AMBER (Fri Nov 04 2022 - 07:48:56 PDT)
- David A Case via AMBER (Fri Nov 04 2022 - 07:44:09 PDT)
- Wei Jiao via AMBER (Wed Nov 02 2022 - 00:13:40 PDT)
[AMBER] Error - Amber 22 Installation with Cuda
- David A Case via AMBER (Mon Nov 28 2022 - 06:15:08 PST)
- Gert Kruger via AMBER (Thu Nov 24 2022 - 03:20:25 PST)
[AMBER] Extract all frame from a nc file using cpptraj
- Carlos Simmerling via AMBER (Fri Nov 18 2022 - 11:14:10 PST)
- Dulal Mondal via AMBER (Fri Nov 18 2022 - 11:04:14 PST)
[AMBER] Force filed for non-specific residue CAS
- Jelena Tosovic via AMBER (Tue Nov 15 2022 - 16:07:15 PST)
[AMBER] Free Energy Calculation using TI
- Suguna Sakkiah via AMBER (Tue Nov 01 2022 - 20:04:13 PDT)
[AMBER] Fwd: Aluminum parameters, URGENT
- Dr. Anselm Horn via AMBER (Thu Nov 10 2022 - 13:05:11 PST)
- Nour Alkhatib via AMBER (Thu Nov 10 2022 - 09:04:04 PST)
- David A Case via AMBER (Thu Nov 10 2022 - 06:20:48 PST)
- Nour Alkhatib via AMBER (Wed Nov 09 2022 - 09:06:51 PST)
[AMBER] Generating parameters for unnatural amino acids
- Suchetana Gupta via AMBER (Fri Nov 11 2022 - 09:15:14 PST)
- Dr. Anselm Horn via AMBER (Fri Nov 11 2022 - 02:12:10 PST)
- Suchetana Gupta via AMBER (Thu Nov 10 2022 - 18:03:58 PST)
- Suchetana Gupta via AMBER (Thu Nov 10 2022 - 17:44:18 PST)
[AMBER] Generation of CPIN in CpHMD simulations
- Divya Rai via AMBER (Tue Nov 22 2022 - 03:24:33 PST)
- Vinicius Wilian Cruzeiro via AMBER (Mon Nov 21 2022 - 07:55:44 PST)
- Divya Rai via AMBER (Mon Nov 21 2022 - 06:44:53 PST)
[AMBER] gmx_MMPBSA installation error
- İmren Bayıl via AMBER (Sat Nov 19 2022 - 02:26:33 PST)
[AMBER] gmx_MMPBSA installation error please help
- İmren Bayıl via AMBER (Sat Nov 19 2022 - 08:09:45 PST)
- David A Case via AMBER (Sat Nov 19 2022 - 06:16:34 PST)
- İmren Bayıl via AMBER (Fri Nov 18 2022 - 15:42:52 PST)
[AMBER] Gradual heating: Linear response pressure?
- David A Case via AMBER (Wed Nov 23 2022 - 09:06:35 PST)
- Carlos Simmerling via AMBER (Wed Nov 23 2022 - 06:55:20 PST)
- Carlos Simmerling via AMBER (Mon Nov 21 2022 - 08:14:16 PST)
- Hocine EL KHAOUDI ENYOURY via AMBER (Mon Nov 21 2022 - 02:16:50 PST)
- David A Case via AMBER (Fri Nov 18 2022 - 08:12:13 PST)
- Hocine EL KHAOUDI ENYOURY via AMBER (Thu Nov 17 2022 - 01:49:12 PST)
[AMBER] gti_cut vs. gti_cut_sc
- accuratefreeenergy--- via AMBER (Mon Nov 28 2022 - 06:53:31 PST)
[AMBER] How to use MCPB.py to deal with the oxygen atom Fe=O of CpdⅠ
- 张恒炜 via AMBER (Wed Nov 16 2022 - 00:02:49 PST)
[AMBER] Inconsistent GPU Results
- David A Case via AMBER (Mon Nov 28 2022 - 06:22:28 PST)
- Matthew Guberman-Pfeffer via AMBER (Sun Nov 27 2022 - 06:44:50 PST)
[AMBER] installation
- Nitin Kulhar via AMBER (Thu Nov 10 2022 - 11:50:45 PST)
- David A Case via AMBER (Wed Nov 09 2022 - 07:43:40 PST)
- Nitin Kulhar via AMBER (Tue Nov 08 2022 - 05:34:54 PST)
[AMBER] Installation of amber18 (MPI version) with CPU and intel mpi
- David A Case via AMBER (Thu Nov 17 2022 - 05:38:16 PST)
- Dulal Mondal via AMBER (Wed Nov 16 2022 - 06:46:57 PST)
- Dulal Mondal via AMBER (Mon Nov 14 2022 - 23:47:34 PST)
- David A Case via AMBER (Sat Nov 12 2022 - 07:13:30 PST)
- Dulal Mondal via AMBER (Fri Nov 11 2022 - 23:59:33 PST)
[AMBER] Installation of amber18 on on parallel CPU
- Dulal Mondal via AMBER (Fri Nov 11 2022 - 10:49:21 PST)
- David A Case via AMBER (Fri Nov 04 2022 - 07:42:20 PDT)
- Dulal Mondal via AMBER (Thu Nov 03 2022 - 22:04:28 PDT)
[AMBER] Installation of Amber19
- David A Case via AMBER (Tue Nov 15 2022 - 07:51:26 PST)
- SATYAJIT KHATUA via AMBER (Tue Nov 15 2022 - 02:23:36 PST)
[AMBER] Installation Problem
- David A Case via AMBER (Fri Nov 11 2022 - 08:13:03 PST)
- Matthew Guberman-Pfeffer via AMBER (Thu Nov 10 2022 - 06:06:36 PST)
- David A Case via AMBER (Thu Nov 10 2022 - 06:04:18 PST)
- Matthew Guberman-Pfeffer via AMBER (Thu Nov 10 2022 - 05:08:43 PST)
- Scott Brozell via AMBER (Wed Nov 09 2022 - 23:07:15 PST)
- Matthew Guberman-Pfeffer via AMBER (Wed Nov 09 2022 - 07:55:25 PST)
[AMBER] Installation problem on amber18 with parallel CPU in linux
- David A Case via AMBER (Sun Nov 06 2022 - 13:58:55 PST)
- Dulal Mondal via AMBER (Sat Nov 05 2022 - 23:40:32 PDT)
[AMBER] Lambda-Scheduling, what is TypeGen?
- accuratefreeenergy--- via AMBER (Mon Nov 21 2022 - 20:06:37 PST)
[AMBER] LJ parameters for AL3+
- Nour Alkhatib via AMBER (Wed Nov 09 2022 - 12:01:22 PST)
[AMBER] MCPB.py (Error: the charges and atom numbers are mismatch)
- Saranya vasudevan via AMBER (Tue Nov 22 2022 - 07:27:45 PST)
[AMBER] Messages not getting through to the Amber Mailing List?
- Dr. Anselm Horn via AMBER (Wed Nov 23 2022 - 02:58:03 PST)
- David A Case via AMBER (Tue Nov 22 2022 - 10:28:02 PST)
- Suchetana Gupta via AMBER (Tue Nov 22 2022 - 08:28:13 PST)
- Gert Kruger via AMBER (Tue Nov 22 2022 - 08:25:48 PST)
[AMBER] Metal center created with MCPB.py collapses on MD start?
- Gustavo Seabra via AMBER (Tue Nov 08 2022 - 12:03:39 PST)
- Clorice Reinhardt via AMBER (Tue Nov 08 2022 - 06:38:44 PST)
- Gustavo Seabra via AMBER (Fri Nov 04 2022 - 19:06:39 PDT)
[AMBER] Missing GaMD restart file
- Matthew Guberman-Pfeffer via AMBER (Sat Nov 19 2022 - 21:50:21 PST)
[AMBER] Missing parameters while Simulating a Zn containing protein in Amber
- Suchetana Gupta via AMBER (Mon Nov 28 2022 - 10:14:58 PST)
[AMBER] MM/PBSA & MM/GBSA and three trajectories
- Ibrahim Said via AMBER (Sun Nov 20 2022 - 12:13:11 PST)
[AMBER] monovalent ions in methanol
- Antonija Tomić via AMBER (Wed Nov 30 2022 - 04:39:55 PST)
[AMBER] Only three atoms in water molecules instead of four
- Dmitry Suplatov via AMBER (Tue Nov 29 2022 - 08:43:26 PST)
- Dmitry Suplatov via AMBER (Tue Nov 29 2022 - 06:25:09 PST)
[AMBER] OPC3-pol
- Piia Bartos via AMBER (Tue Nov 29 2022 - 00:42:34 PST)
- Piia Bartos via AMBER (Sat Nov 26 2022 - 00:06:19 PST)
- Carlos Simmerling via AMBER (Mon Nov 21 2022 - 08:12:47 PST)
- Piia Bartos via AMBER (Mon Nov 21 2022 - 03:20:53 PST)
[AMBER] Position restraints in NPT
- Miroslav Suruzhon via AMBER (Thu Nov 24 2022 - 02:15:17 PST)
- Franz Waibl via AMBER (Wed Nov 23 2022 - 03:05:24 PST)
- Miroslav Suruzhon via AMBER (Tue Nov 22 2022 - 06:09:15 PST)
- Franz Waibl via AMBER (Thu Nov 17 2022 - 05:10:49 PST)
- Miroslav Suruzhon via AMBER (Wed Nov 16 2022 - 04:43:10 PST)
[AMBER] Postdoc and PhD position at IPB Halle (Germany)
- Mehdi D. Davari via AMBER (Mon Nov 14 2022 - 01:43:38 PST)
[AMBER] Problem with topology file generation
- Tanmoy Paul via AMBER (Sun Nov 06 2022 - 16:21:14 PST)
- David A Case via AMBER (Sun Nov 06 2022 - 14:00:46 PST)
- Tanmoy Paul via AMBER (Sun Nov 06 2022 - 02:43:48 PST)
- Tanmoy Paul via AMBER (Sat Nov 05 2022 - 17:26:47 PDT)
- Gustavo Seabra via AMBER (Sat Nov 05 2022 - 05:45:52 PDT)
- Tanmoy Paul via AMBER (Fri Nov 04 2022 - 20:19:16 PDT)
[AMBER] Query regarding AMBER tutorial
- Carlos Simmerling via AMBER (Thu Nov 17 2022 - 08:45:17 PST)
- Munazzah Fatima Ansari via AMBER (Wed Nov 09 2022 - 05:43:01 PST)
[AMBER] Query regarding AMBER tutorial Replica Exchange
- David A Case via AMBER (Wed Nov 02 2022 - 05:56:35 PDT)
- Munazzah Fatima Ansari via AMBER (Tue Nov 01 2022 - 22:47:12 PDT)
[AMBER] Query regarding RMS in minimization of explicit solvent
- David A Case via AMBER (Tue Nov 15 2022 - 07:47:50 PST)
- Nitin Kulhar via AMBER (Tue Nov 15 2022 - 00:00:08 PST)
[AMBER] question on mmgbsa energy calculation
- Bill Miller III via AMBER (Thu Nov 03 2022 - 07:04:35 PDT)
- laura zhang via AMBER (Thu Nov 03 2022 - 06:53:37 PDT)
[AMBER] Questions about reading the right LJ_Acoef values in *.prmtop file
- Carlos Simmerling via AMBER (Sat Nov 26 2022 - 02:50:08 PST)
- ChenXin via AMBER (Fri Nov 25 2022 - 23:04:15 PST)
[AMBER] Questions about refinement of dihedral parameters by QM calculations
- Carlos Simmerling via AMBER (Mon Nov 21 2022 - 09:55:35 PST)
- He, Amy via AMBER (Mon Nov 21 2022 - 09:52:51 PST)
[AMBER] Reimaging issues
- Damiano Spadoni via AMBER (Mon Nov 28 2022 - 03:26:50 PST)
- Damiano Spadoni via AMBER (Tue Nov 08 2022 - 05:35:54 PST)
[AMBER] Restart and Topology Files Contain Different Numbers of Atoms
- Carlos Simmerling via AMBER (Fri Nov 18 2022 - 10:23:13 PST)
- Kerry Woolnough via AMBER (Fri Nov 18 2022 - 10:21:57 PST)
- David A Case via AMBER (Thu Nov 17 2022 - 12:47:03 PST)
- Kerry Woolnough via AMBER (Thu Nov 17 2022 - 12:16:21 PST)
- Kerry Woolnough via AMBER (Thu Nov 17 2022 - 09:29:31 PST)
- Carlos Simmerling via AMBER (Thu Nov 17 2022 - 09:32:08 PST)
[AMBER] Settings for CHAMM FF?
- Carlos Simmerling via AMBER (Thu Nov 03 2022 - 15:05:35 PDT)
- Matthew Guberman-Pfeffer via AMBER (Thu Nov 03 2022 - 14:57:18 PDT)
[AMBER] Simulating a Protein - cyclic peptide complex - question
- Dr. Anselm Horn via AMBER (Tue Nov 29 2022 - 02:21:50 PST)
- Suchetana Gupta via AMBER (Mon Nov 28 2022 - 13:21:06 PST)
- Suchetana Gupta via AMBER (Fri Nov 11 2022 - 09:12:09 PST)
- David A Case via AMBER (Fri Nov 11 2022 - 08:25:36 PST)
- Dr. Anselm Horn via AMBER (Fri Nov 11 2022 - 01:47:18 PST)
- Carol Pacheco via AMBER (Thu Nov 10 2022 - 17:36:40 PST)
- Suchetana Gupta via AMBER (Thu Nov 10 2022 - 17:02:52 PST)
[AMBER] Simulation of ssDNA folding
- Jiaan Zhu via AMBER (Sat Nov 12 2022 - 14:19:33 PST)
[AMBER] Temperature drop while switching from NVT to NPT during equilibration
- David A Case via AMBER (Thu Nov 17 2022 - 12:38:18 PST)
- Carlos Simmerling via AMBER (Thu Nov 17 2022 - 07:19:00 PST)
- Reim, Thorben via AMBER (Thu Nov 17 2022 - 03:46:21 PST)
[AMBER] test FAILURE in ired.vec.diff
- Daniel Roe via AMBER (Tue Nov 29 2022 - 09:08:45 PST)
- Martin Juhás via AMBER (Tue Nov 29 2022 - 08:05:49 PST)
[AMBER] Testing suite for openMP
- James Kress via AMBER (Tue Nov 15 2022 - 10:35:48 PST)
- David A Case via AMBER (Tue Nov 15 2022 - 07:55:57 PST)
- James Kress via AMBER (Sun Nov 13 2022 - 10:21:33 PST)
[AMBER] the mmgbsa output
- Bill Miller III via AMBER (Tue Nov 22 2022 - 09:59:27 PST)
- laura zhang via AMBER (Tue Nov 22 2022 - 06:52:10 PST)
[AMBER] TIP4P/Ice (2005) water model in AMBER?
- Surajit Kalita via AMBER (Thu Nov 24 2022 - 00:40:58 PST)
[AMBER] Trouble reproducing solvateOct output from Tutorial 1.4
- Kerry Woolnough via AMBER (Thu Nov 10 2022 - 08:28:00 PST)
[AMBER] Unable to access xleap software!
- Suchetana Gupta via AMBER (Tue Nov 15 2022 - 14:18:04 PST)
- Swapnil Singh via AMBER (Tue Nov 15 2022 - 13:06:23 PST)
- David A Case via AMBER (Tue Nov 15 2022 - 10:30:13 PST)
- Swapnil Singh via AMBER (Tue Nov 15 2022 - 09:09:18 PST)
[AMBER] unbalanced usage of GPU cards in Replica Exchange MD
- kurisaki2013--- via AMBER (Mon Nov 07 2022 - 23:54:03 PST)
[AMBER] Updates to mdinfo with amber 22
- Greenberg, Jerry via AMBER (Wed Nov 30 2022 - 13:46:26 PST)
[AMBER] Vacuum simulation problem
- David A Case via AMBER (Mon Nov 21 2022 - 06:33:11 PST)
- James Kress via AMBER (Sun Nov 20 2022 - 13:29:27 PST)
- Matthew Guberman-Pfeffer via AMBER (Sun Nov 20 2022 - 11:37:34 PST)
[AMBER] What is the "right" number of unit cells for simulating protein crystals?
- David A Case via AMBER (Wed Nov 09 2022 - 07:50:09 PST)
- Reim, Thorben via AMBER (Tue Nov 08 2022 - 06:14:18 PST)
[AMBER] {SPAM?} AMBER-TI running error
- Matthew Guberman-Pfeffer via AMBER (Mon Nov 07 2022 - 17:39:46 PST)
[AMBER] {SPAM?} Force filed for non-specific residue CAS
- Carlos Simmerling via AMBER (Wed Nov 16 2022 - 07:24:49 PST)
- Matthew Guberman-Pfeffer via AMBER (Tue Nov 15 2022 - 18:53:03 PST)
[AMBER] {SPAM?} Inconsistent GPU Results
- Matthew Guberman-Pfeffer via AMBER (Sun Nov 27 2022 - 07:58:35 PST)
[AMBER] {SPAM?} scbeta, wrong default?
- accuratefreeenergy--- via AMBER (Tue Nov 29 2022 - 05:34:55 PST)
- accuratefreeenergy--- via AMBER (Mon Nov 28 2022 - 06:54:12 PST)
[AMBER] 你好amber@ambermd.org
- 3163490855--- via AMBER (Tue Nov 15 2022 - 18:46:52 PST)
Alchemical gti keyword questions
- accuratefreeenergy--- via AMBER (Sat Nov 12 2022 - 05:06:23 PST)
Inconsistent GPU Results
- Matthew Guberman-Pfeffer via AMBER (Mon Nov 28 2022 - 07:57:58 PST)
Installation Problem
- Matthew Guberman-Pfeffer via AMBER (Fri Nov 11 2022 - 08:15:19 PST)
Vacuum simulation problem
- Matthew Guberman-Pfeffer via AMBER (Mon Nov 21 2022 - 06:44:54 PST)
- Matthew Guberman-Pfeffer via AMBER (Sun Nov 20 2022 - 14:15:09 PST)

Amber Archive Nov 2022 by subject