Amber Archive Oct 2022: by subject

[AMBER] "autoimage" function of cpptraj and holding molecule steady
- Carlos Simmerling via AMBER (Sat Oct 15 2022 - 13:25:45 PDT)
- SATYAJIT KHATUA via AMBER (Sat Oct 15 2022 - 12:36:27 PDT)
- Cenk Andac via AMBER (Sat Oct 15 2022 - 12:15:34 PDT)
[AMBER] Abrupt temperature rise carrying out Transition path sampling
- Adrian Roitberg via AMBER (Thu Oct 20 2022 - 11:37:34 PDT)
- Divya Rai via AMBER (Thu Oct 20 2022 - 11:14:03 PDT)
[AMBER] Amber 22 serial installation on ubuntu-18.04 without GPU support
- David A Case via AMBER (Thu Oct 27 2022 - 05:48:36 PDT)
- Dulal Mondal via AMBER (Tue Oct 25 2022 - 23:12:37 PDT)
[AMBER] amber Computational problem
- David A Case via AMBER (Thu Oct 27 2022 - 05:54:31 PDT)
- Ding Shuaiwei via AMBER (Wed Oct 26 2022 - 21:23:06 PDT)
[AMBER] AMBER GPU version: Segfault error with 12-6-4 parameters
- Jafari, Majid via AMBER (Thu Oct 20 2022 - 11:41:07 PDT)
[AMBER] amber-subscribe
- Aravind R via AMBER (Fri Oct 21 2022 - 04:28:28 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 - 00:53:35 PDT)
[AMBER] AMBER22 installation on Linux
- Scott Brozell via AMBER (Tue Oct 04 2022 - 11:42:40 PDT)
- SATYAJIT KHATUA via AMBER (Tue Oct 04 2022 - 07:11:24 PDT)
- Azurmendi, Hugo via AMBER (Mon Oct 03 2022 - 14:52:34 PDT)
[AMBER] Amber22 on Red Hat Enterprise Linux 8
- Carlos Navarro via AMBER (Thu Oct 13 2022 - 07:05:38 PDT)
[AMBER] Amber22, no DV/DL value with option gti_lam_sch
- Domenico Marson via AMBER (Sun Oct 16 2022 - 08:38:53 PDT)
[AMBER] Ambermd data erasure request - from Priya Dey - request: UFO3NP7F
- Jason Swails via AMBER (Sun Oct 16 2022 - 10:32:52 PDT)
- mmv.priya.dey--- via AMBER (Mon Oct 10 2022 - 11:17:00 PDT)
[AMBER] AmberTools installation issue MacOS
- Xavier Brazzolotto via AMBER (Tue Oct 18 2022 - 10:40:18 PDT)
- David A Case via AMBER (Tue Oct 18 2022 - 08:26:01 PDT)
- Xavier Brazzolotto via AMBER (Tue Oct 18 2022 - 04:22:30 PDT)
[AMBER] AmberTools22 installation compilation file comparisons failed
- David A Case via AMBER (Thu Oct 20 2022 - 08:32:02 PDT)
- Daniel Roe via AMBER (Wed Oct 19 2022 - 11:43:42 PDT)
- wy202210192022 via AMBER (Tue Oct 18 2022 - 23:45:52 PDT)
[AMBER] Antechamber with QM software other than Gaussian
- Shiji Zhao via AMBER (Sun Oct 30 2022 - 00:06:03 PDT)
- James Kress via AMBER (Sat Oct 29 2022 - 17:09:32 PDT)
- Alexander Izvorski via AMBER (Sat Oct 29 2022 - 14:41:31 PDT)
- Alexander Izvorski via AMBER (Sat Oct 29 2022 - 14:19:25 PDT)
- Barış KURT via AMBER (Sat Oct 29 2022 - 13:48:44 PDT)
- James Kress via AMBER (Sat Oct 29 2022 - 13:37:37 PDT)
- Alexander Izvorski via AMBER (Sat Oct 29 2022 - 13:06:31 PDT)
- Shiji Zhao via AMBER (Tue Oct 18 2022 - 00:34:17 PDT)
[AMBER] ANTECHAMBER: parametrization of charged ligand
- Enrico Martinez via AMBER (Fri Oct 07 2022 - 02:00:55 PDT)
- Enrico Martinez via AMBER (Thu Oct 06 2022 - 08:34:43 PDT)
- Dr. Anselm Horn via AMBER (Thu Oct 06 2022 - 08:33:03 PDT)
- Enrico Martinez via AMBER (Thu Oct 06 2022 - 07:38:44 PDT)
[AMBER] bar-graph of the hydrogen bonds fraction using xm-grace
- Enrico Martinez via AMBER (Tue Oct 04 2022 - 06:16:46 PDT)
[AMBER] Best force field and water model for amyloid study
- maryam ghorbaninia via AMBER (Sun Oct 16 2022 - 15:46:30 PDT)
[AMBER] C4 terms in 12-6-4LJ model
- Sara Mahmoud via AMBER (Mon Oct 24 2022 - 03:37:10 PDT)
- David A Case via AMBER (Mon Oct 24 2022 - 05:38:58 PDT)
[AMBER] clustering trajectories based on RMSD cut-off
- Sorin Draga via AMBER (Mon Oct 17 2022 - 03:40:13 PDT)
- Carlos Simmerling via AMBER (Mon Oct 17 2022 - 03:37:09 PDT)
- Sorin Draga via AMBER (Mon Oct 17 2022 - 01:49:42 PDT)
[AMBER] co-alchemical ion
- accuratefreeenergy--- via AMBER (Mon Oct 24 2022 - 14:32:45 PDT)
- David A Case via AMBER (Mon Oct 24 2022 - 05:31:38 PDT)
- Pietro Vidossich via AMBER (Sun Oct 23 2022 - 01:24:12 PDT)
[AMBER] Computing electrostatic interaction
- David A Case via AMBER (Fri Oct 14 2022 - 09:07:24 PDT)
- FyD via AMBER (Wed Oct 12 2022 - 23:47:51 PDT)
[AMBER] CpHMD and Umbrella sampling
- Vinicius Wilian Cruzeiro via AMBER (Sat Oct 15 2022 - 11:33:47 PDT)
- Dulal Mondal via AMBER (Fri Oct 14 2022 - 22:55:49 PDT)
[AMBER] Dihedral PCA Cluster Plot
- Suchetana Gupta via AMBER (Mon Oct 17 2022 - 06:48:06 PDT)
[AMBER] Energy distribution check for REAF simulation
- kurisaki2013--- via AMBER (Mon Oct 24 2022 - 23:32:48 PDT)
- kurisaki2013--- via AMBER (Mon Oct 24 2022 - 00:13:53 PDT)
[AMBER] Error in generating parameters for BMT residue in Cyclosporin and Leap Error in Bond command
- Suchetana Gupta via AMBER (Wed Oct 05 2022 - 12:59:49 PDT)
[AMBER] ERROR while using receptor_mask in MMPBSA
- David A Case via AMBER (Wed Oct 26 2022 - 05:15:58 PDT)
- Amit Sharma \(Asstt. Prof., MCARS\) via AMBER (Tue Oct 25 2022 - 01:05:24 PDT)
[AMBER] Forcing a Peptide to be Helical
- Cianna Calia via AMBER (Thu Oct 20 2022 - 01:01:15 PDT)
- Cianna Calia via AMBER (Wed Oct 19 2022 - 20:49:40 PDT)
[AMBER] GaMD dihedral boosting Amber18
- Martin Juhás via AMBER (Tue Oct 18 2022 - 00:54:45 PDT)
[AMBER] glycam web server
- Moustafa, Ibrahim M. via AMBER (Fri Oct 14 2022 - 15:11:21 PDT)
[AMBER] Help in Standardizing NEB
- Aravind R via AMBER (Thu Oct 20 2022 - 00:12:13 PDT)
- Christina Bergonzo via AMBER (Wed Oct 26 2022 - 05:53:36 PDT)
- Aravind R via AMBER (Wed Oct 26 2022 - 03:41:22 PDT)
- Christina Bergonzo via AMBER (Fri Oct 21 2022 - 06:13:12 PDT)
- Aravind R via AMBER (Thu Oct 20 2022 - 23:18:40 PDT)
[AMBER] How to add gaff parameters to PARMCHK.DAT file
- David A Case via AMBER (Fri Oct 14 2022 - 09:03:18 PDT)
- Jiaan Zhu via AMBER (Sun Oct 09 2022 - 01:08:10 PDT)
- David A Case via AMBER (Sat Oct 08 2022 - 16:34:44 PDT)
- Jiaan Zhu via AMBER (Thu Oct 06 2022 - 09:35:49 PDT)
[AMBER] How to concatenate long trajs in a decent time
- Daniel Roe via AMBER (Tue Oct 04 2022 - 05:43:09 PDT)
- Giulia Sormani via AMBER (Tue Oct 04 2022 - 02:26:04 PDT)
[AMBER] How to restrain minimum distance between proteins?
- Gustavo Seabra via AMBER (Wed Oct 26 2022 - 11:39:23 PDT)
- Matthew Guberman-Pfeffer via AMBER (Mon Oct 24 2022 - 21:11:15 PDT)
[AMBER] How to restraint proteins to an axis
- Matthew Guberman-Pfeffer via AMBER (Sun Oct 23 2022 - 15:31:31 PDT)
- Matthew Guberman-Pfeffer via AMBER (Fri Oct 21 2022 - 13:53:21 PDT)
[AMBER] I implore you to fix the problem regarding MMPBSA analysis
- Carlos Simmerling via AMBER (Mon Oct 31 2022 - 08:33:41 PDT)
- Bill Miller III via AMBER (Mon Oct 31 2022 - 08:32:30 PDT)
- Subramanian Boopathi via AMBER (Mon Oct 31 2022 - 08:25:42 PDT)
[AMBER] Ion counting
- Daniel Roe via AMBER (Wed Oct 19 2022 - 11:53:19 PDT)
- George Madalin Giambasu via AMBER (Tue Oct 18 2022 - 15:34:56 PDT)
- angad sharma via AMBER (Tue Oct 18 2022 - 03:25:44 PDT)
[AMBER] Issues concerning keyboard on xleap interface
- David A Case via AMBER (Mon Oct 17 2022 - 06:41:08 PDT)
- Frederico Henrique Ferreira via AMBER (Sun Oct 16 2022 - 13:55:04 PDT)
[AMBER] MCPB, wrong bonding pair
- Matthew Guberman-Pfeffer via AMBER (Sat Oct 15 2022 - 08:42:31 PDT)
[AMBER] MCPB.py Failing with OPC water?
- Gustavo Seabra via AMBER (Thu Oct 13 2022 - 14:29:47 PDT)
[AMBER] MCPB: How to make a larger "small model"
- ışılay öztürk via AMBER (Tue Oct 25 2022 - 03:45:50 PDT)
- Vaibhav Dixit via AMBER (Mon Oct 24 2022 - 21:27:22 PDT)
- Matthew Guberman-Pfeffer via AMBER (Mon Oct 24 2022 - 08:05:32 PDT)
- Matthew Guberman-Pfeffer via AMBER (Sun Oct 23 2022 - 15:26:13 PDT)
[AMBER] mdl file for OPC water model
- David A Case via AMBER (Mon Oct 17 2022 - 06:25:22 PDT)
- Weronika Bagrowska via AMBER (Sat Oct 15 2022 - 16:29:13 PDT)
[AMBER] MMGBSA with Mn2+ ions
- David A Case via AMBER (Tue Oct 04 2022 - 11:48:27 PDT)
- Rafał Madaj via AMBER (Tue Oct 04 2022 - 03:21:15 PDT)
[AMBER] mmpbsa problem with OPC waters
- Antonija Tomić via AMBER (Mon Oct 24 2022 - 07:27:44 PDT)
- Carlos Simmerling via AMBER (Mon Oct 24 2022 - 04:51:20 PDT)
- Antonija Tomić via AMBER (Mon Oct 24 2022 - 04:15:42 PDT)
[AMBER] mmpbsa.py: error in the decomposition
- Bill Miller III via AMBER (Thu Oct 20 2022 - 08:50:59 PDT)
- Enrico Martinez via AMBER (Thu Oct 20 2022 - 05:03:19 PDT)
- Rafał Madaj via AMBER (Thu Oct 20 2022 - 03:27:57 PDT)
- Enrico Martinez via AMBER (Thu Oct 20 2022 - 02:19:48 PDT)
[AMBER] Multidihedral, average, lost residue numbers
- Rosellen, Martin via AMBER (Fri Oct 14 2022 - 07:05:07 PDT)
- Rosellen, Martin via AMBER (Thu Oct 13 2022 - 07:33:14 PDT)
[AMBER] New, sander based real life lmod examples
- Istvan Kolossvary via AMBER (Sun Oct 02 2022 - 19:42:18 PDT)
[AMBER] NUMEXTRA Error
- Sally Pias via AMBER (Wed Oct 05 2022 - 16:06:43 PDT)
- Sally Pias via AMBER (Mon Oct 03 2022 - 12:12:19 PDT)
[AMBER] Occupancy calculation
- angad sharma via AMBER (Sun Oct 30 2022 - 14:45:15 PDT)
[AMBER] parameterization for non-standard nucleotide
- Moustafa, Ibrahim M. via AMBER (Tue Oct 11 2022 - 06:18:05 PDT)
- Dr. Anselm Horn via AMBER (Mon Oct 10 2022 - 04:54:43 PDT)
- Moustafa, Ibrahim M. via AMBER (Sat Oct 08 2022 - 21:25:50 PDT)
- Moustafa, Ibrahim M. via AMBER (Sat Oct 08 2022 - 21:18:25 PDT)
- David A Case via AMBER (Sat Oct 08 2022 - 18:35:13 PDT)
- Maria Nagan via AMBER (Sat Oct 08 2022 - 13:44:49 PDT)
- Moustafa, Ibrahim M. via AMBER (Sat Oct 08 2022 - 13:09:01 PDT)
[AMBER] Parameterization of magnesium ions binding site using MCPB.py
- David A Case via AMBER (Thu Oct 20 2022 - 08:30:50 PDT)
- Huang ZiJian via AMBER (Wed Oct 19 2022 - 21:24:43 PDT)
[AMBER] Phase space overlap questions in alchemical free energy calculations
- David A Case via AMBER (Tue Oct 11 2022 - 08:29:43 PDT)
- Liao via AMBER (Fri Oct 07 2022 - 12:17:40 PDT)
- Liao via AMBER (Thu Oct 06 2022 - 21:30:05 PDT)
[AMBER] PLUMED misformatted output file
- Tucker Burgin via AMBER (Wed Oct 12 2022 - 09:42:50 PDT)
[AMBER] problem regarding "change" command
- Daniel Roe via AMBER (Fri Oct 14 2022 - 07:28:00 PDT)
- Saikat Pal via AMBER (Wed Oct 12 2022 - 16:35:15 PDT)
[AMBER] problem with MMPBSA.py (and/or ante-MMPBSA.py)
- Artur Hermano via AMBER (Tue Oct 04 2022 - 05:55:34 PDT)
[AMBER] Problem: Minimization and TI
- Matthew Guberman-Pfeffer via AMBER (Mon Oct 31 2022 - 18:19:56 PDT)
[AMBER] Question about h-bond analysis via cpptraj
- Enrico Martinez via AMBER (Wed Oct 12 2022 - 08:54:12 PDT)
[AMBER] Question about sasa values
- SATYAJIT KHATUA via AMBER (Thu Oct 13 2022 - 03:23:36 PDT)
- Sayan Poddar via AMBER (Thu Oct 13 2022 - 01:45:58 PDT)
[AMBER] RESTRAINT versus NMR restraint in output?
- David A Case via AMBER (Wed Oct 26 2022 - 05:08:06 PDT)
- Matthew Guberman-Pfeffer via AMBER (Mon Oct 24 2022 - 05:51:51 PDT)
[AMBER] RTX4090 Benchmarks
- filip fratev via AMBER (Sat Oct 22 2022 - 15:59:43 PDT)
- Ross Walker via AMBER (Fri Oct 14 2022 - 08:48:47 PDT)
[AMBER] Running the TI code on a single residue results in NaN electrostatics
- Miroslav Suruzhon via AMBER (Mon Oct 10 2022 - 03:26:52 PDT)
- David A Case via AMBER (Wed Oct 05 2022 - 06:39:23 PDT)
- Miroslav Suruzhon via AMBER (Tue Oct 04 2022 - 07:00:02 PDT)
[AMBER] Separation of protein and ligand during TI simulation.
- Dr. Anselm Horn via AMBER (Mon Oct 17 2022 - 07:35:45 PDT)
- Fanyu Zhao via AMBER (Mon Oct 17 2022 - 06:41:11 PDT)
- Fanyu Zhao via AMBER (Sat Oct 15 2022 - 20:47:32 PDT)
- David A Case via AMBER (Fri Oct 14 2022 - 09:09:29 PDT)
- Fanyu Zhao via AMBER (Thu Oct 13 2022 - 06:20:35 PDT)
[AMBER] Simulation of ssDNA folding
- Thomas Cheatham via AMBER (Sun Oct 30 2022 - 14:41:43 PDT)
- zhujiaan16.mails.ucas.ac.cn via AMBER (Sun Oct 30 2022 - 09:51:14 PDT)
- Carlos Simmerling via AMBER (Sun Oct 30 2022 - 08:27:12 PDT)
- Jiaan Zhu via AMBER (Sun Oct 30 2022 - 07:54:12 PDT)
[AMBER] Some questiones about Gaussian/Amber QM/MM simulation
- David A Case via AMBER (Mon Oct 24 2022 - 05:36:46 PDT)
- 张兴赫 via AMBER (Sun Oct 23 2022 - 21:09:37 PDT)
[AMBER] survival or residence time
- angad sharma via AMBER (Mon Oct 03 2022 - 23:44:57 PDT)
[AMBER] Thermostat Question
- Carlos Simmerling via AMBER (Mon Oct 31 2022 - 11:07:18 PDT)
- Matthew Guberman-Pfeffer via AMBER (Mon Oct 31 2022 - 10:54:10 PDT)
[AMBER] tiMerge error with ff19SB
- jinfeng liu via AMBER (Sat Oct 22 2022 - 00:43:48 PDT)
[AMBER] Umbrella Sampling at constant pH using amber 22
- Adrian Roitberg via AMBER (Thu Oct 27 2022 - 11:07:39 PDT)
- Dulal Mondal via AMBER (Thu Oct 27 2022 - 10:19:56 PDT)
[AMBER] Unsubsrcibe
- Jason Swails via AMBER (Sun Oct 16 2022 - 10:33:08 PDT)
- Matthew Noto via AMBER (Sat Oct 15 2022 - 13:02:48 PDT)
[AMBER] using MCPB.py
- ışılay öztürk via AMBER (Thu Oct 27 2022 - 07:11:05 PDT)
- ışılay öztürk via AMBER (Thu Oct 27 2022 - 05:03:30 PDT)
- Barış KURT via AMBER (Thu Oct 27 2022 - 04:59:04 PDT)
- ışılay öztürk via AMBER (Thu Oct 27 2022 - 04:32:33 PDT)
- Erdem Yeler via AMBER (Thu Oct 27 2022 - 02:30:18 PDT)
- ışılay öztürk via AMBER (Wed Oct 12 2022 - 15:13:04 PDT)
- ışılay öztürk via AMBER (Wed Oct 12 2022 - 14:12:58 PDT)
[AMBER] ValueError in MCPB.py at step 3
- Dr. Vaibhav Anil Dixit via AMBER (Sat Oct 01 2022 - 22:56:29 PDT)
[AMBER] {SPAM?} MCPB, wrong bonding pair
- Matthew Guberman-Pfeffer via AMBER (Mon Oct 17 2022 - 04:03:59 PDT)
[AMBER] 你好amber@ambermd.org你好
- 3163490855--- via AMBER (Fri Oct 28 2022 - 01:28:19 PDT)
RESTRAINT versus NMR restraint in output?
- Matthew Guberman-Pfeffer via AMBER (Wed Oct 26 2022 - 08:50:42 PDT)

Amber Archive Oct 2022 by subject