Amber Archive Sep 2023: by subject

[AMBER] ?==?utf-8?q? ?==?utf-8?q? ?= Alternatives to NAB for building DN
- Fadaei Fatemeh Mgr. via AMBER (Sat Sep 30 2023 - 08:42:09 PDT)
[AMBER] [Sender Not Verified] Differences between the same dynamic
- Steinbrecher, Thomas via AMBER (Fri Sep 22 2023 - 02:28:20 PDT)
[AMBER] [Sender Not Verified] Query regarding unusual atom
- Steinbrecher, Thomas via AMBER (Tue Sep 19 2023 - 23:42:18 PDT)
[AMBER] Adding organic ligand in membrane system
- Enrico Martinez via AMBER (Tue Sep 26 2023 - 01:30:48 PDT)
[AMBER] Alternatives to NAB for building DNA
- aishen via AMBER (Thu Sep 21 2023 - 05:01:34 PDT)
- David A Case via AMBER (Wed Sep 20 2023 - 19:35:22 PDT)
- Claire Harmange Magnani via AMBER (Wed Sep 20 2023 - 16:14:24 PDT)
[AMBER] AMBER error slurmstepd
- Adrian Roitberg via AMBER (Mon Sep 18 2023 - 06:12:12 PDT)
- SATYAJIT KHATUA via AMBER (Mon Sep 18 2023 - 05:08:36 PDT)
- SATYAJIT KHATUA via AMBER (Mon Sep 18 2023 - 01:29:04 PDT)
- VERONICA MARTIN HERNANDEZ via AMBER (Mon Sep 18 2023 - 00:45:10 PDT)
[AMBER] amber unit
- Daniel Roe via AMBER (Mon Sep 25 2023 - 07:04:30 PDT)
- Dulal Mondal via AMBER (Sun Sep 24 2023 - 22:34:32 PDT)
[AMBER] Amber22 DDBoost Install Error
- Hantz, Eric via AMBER (Mon Sep 25 2023 - 12:42:29 PDT)
- Shi Zhang via AMBER (Mon Sep 25 2023 - 12:06:45 PDT)
- David A Case via AMBER (Mon Sep 25 2023 - 11:39:17 PDT)
- Hantz, Eric via AMBER (Mon Sep 25 2023 - 10:14:02 PDT)
[AMBER] AmberTools23 fails to build with python 3.11 - Reply
- Hai Nguyen via AMBER (Wed Sep 27 2023 - 20:43:40 PDT)
- Doležal Rafael via AMBER (Wed Sep 27 2023 - 07:32:44 PDT)
[AMBER] antechamber error: "This molecule may have more than one unit..."
- Yang, Li-Yen via AMBER (Tue Sep 19 2023 - 15:35:58 PDT)
- He, Amy via AMBER (Mon Sep 18 2023 - 16:01:31 PDT)
- Rodrigo Galindo-Murillo via AMBER (Mon Sep 18 2023 - 15:45:15 PDT)
- Yang, Li-Yen via AMBER (Mon Sep 18 2023 - 15:27:48 PDT)
[AMBER] attempting to run QUICK
- Andriy Kovalenko via AMBER (Thu Sep 21 2023 - 08:09:13 PDT)
- Goetz, Andreas via AMBER (Wed Sep 20 2023 - 21:24:51 PDT)
- Andriy Kovalenko via AMBER (Wed Sep 20 2023 - 10:11:34 PDT)
[AMBER] Autocorrelation function :
- Kankana Bhattacharjee via AMBER (Thu Sep 21 2023 - 12:14:54 PDT)
- Matthew Guberman-Pfeffer via AMBER (Thu Sep 21 2023 - 06:05:27 PDT)
- Kankana Bhattacharjee via AMBER (Thu Sep 21 2023 - 02:39:57 PDT)
[AMBER] Average RMSF calculation
- Hocine EL KHAOUDI ENYOURY via AMBER (Tue Sep 12 2023 - 11:56:55 PDT)
[AMBER] Calculation of RMSD
- Carlos Simmerling via AMBER (Thu Sep 14 2023 - 05:59:08 PDT)
- VERONICA MARTIN HERNANDEZ via AMBER (Thu Sep 14 2023 - 05:28:59 PDT)
[AMBER] charge extract from cpin file
- Dulal Mondal via AMBER (Tue Sep 19 2023 - 23:16:59 PDT)
[AMBER] Chirality flipped for 2 identical molecules
- Todd Minehardt via AMBER (Mon Sep 25 2023 - 07:23:45 PDT)
- Carlos Simmerling via AMBER (Tue Sep 05 2023 - 16:29:56 PDT)
- Carlos Simmerling via AMBER (Tue Sep 05 2023 - 14:23:04 PDT)
- Todd Minehardt via AMBER (Tue Sep 05 2023 - 13:41:09 PDT)
[AMBER] Clarification on attempted TMD run
- Carlos Simmerling via AMBER (Tue Sep 05 2023 - 11:06:00 PDT)
- Carlos Simmerling via AMBER (Tue Sep 05 2023 - 11:01:27 PDT)
- Adrian Roitberg via AMBER (Tue Sep 05 2023 - 08:45:46 PDT)
- Carlos Simmerling via AMBER (Tue Sep 05 2023 - 08:07:50 PDT)
- Malcolm Lim via AMBER (Tue Sep 05 2023 - 07:34:35 PDT)
[AMBER] Coulomb energy in MMPBSA
- Ray Luo via AMBER (Fri Sep 01 2023 - 09:22:45 PDT)
- Richard Kullmann via AMBER (Fri Sep 01 2023 - 05:39:11 PDT)
[AMBER] CpHMD in amber18 using cuda
- Dulal Mondal via AMBER (Sat Sep 16 2023 - 11:36:13 PDT)
[AMBER] cpptraj nativecontacts
- Enrico Martinez via AMBER (Tue Sep 26 2023 - 06:54:46 PDT)
- Enrico Martinez via AMBER (Mon Sep 25 2023 - 02:20:43 PDT)
[AMBER] CPPTRAJ, protein width
- Matthew Guberman-Pfeffer via AMBER (Sat Sep 23 2023 - 08:18:24 PDT)
[AMBER] CUDA version of nabnmode?
- Cenk Andac via AMBER (Wed Sep 20 2023 - 00:28:54 PDT)
[AMBER] Differences between the same dynamic
- VERONICA MARTIN HERNANDEZ via AMBER (Fri Sep 22 2023 - 02:12:53 PDT)
[AMBER] error in amber22 installation
- Setyanto Md via AMBER (Thu Sep 21 2023 - 19:11:25 PDT)
[AMBER] Error in equillibrium step of MD
- Shreeramesh via AMBER (Tue Sep 26 2023 - 06:04:24 PDT)
[AMBER] Errors with .dcd files using MMPBSA
- Daniel Roe via AMBER (Thu Sep 07 2023 - 05:24:32 PDT)
- Ray Luo via AMBER (Wed Sep 06 2023 - 09:49:59 PDT)
- VERONICA MARTIN HERNANDEZ via AMBER (Wed Sep 06 2023 - 01:29:52 PDT)
[AMBER] extracting a frame from trajectory at a specific time
- SATYAJIT KHATUA via AMBER (Sun Sep 10 2023 - 21:11:00 PDT)
- James Kress via AMBER (Sun Sep 10 2023 - 18:39:26 PDT)
[AMBER] Failed test cases in $AMBERHOME/test/nfe/bbmd in Amber22/Amber23
- Vlad via AMBER (Wed Sep 20 2023 - 19:17:38 PDT)
[AMBER] high positive values for VDW interactions using LIE function
- Pirhadi, Somayeh via AMBER (Wed Sep 13 2023 - 11:09:58 PDT)
[AMBER] How can I resolve the issue of the 'NAB' command not being found in AmberTools23?
- David A Case via AMBER (Wed Sep 20 2023 - 09:45:24 PDT)
- Claire Harmange Magnani via AMBER (Tue Sep 19 2023 - 14:10:14 PDT)
- Fadaei Fatemeh Mgr. via AMBER (Tue Sep 19 2023 - 05:27:04 PDT)
[AMBER] How to designate the Bond type(Sodium) in amber 22
- Carlos Simmerling via AMBER (Fri Sep 22 2023 - 04:32:13 PDT)
- K A SIVASANKER via AMBER (Fri Sep 22 2023 - 04:17:42 PDT)
- Dr. Anselm Horn via AMBER (Fri Sep 22 2023 - 02:47:39 PDT)
- K A SIVASANKER via AMBER (Fri Sep 22 2023 - 01:51:44 PDT)
[AMBER] How to get Inherent structure (Minimization energy)
- David A Case via AMBER (Wed Sep 20 2023 - 09:51:23 PDT)
- Zafar,Muhammad Saqlain via AMBER (Tue Sep 19 2023 - 13:23:26 PDT)
[AMBER] How to get the Z component of ions from the trajectory file?
- Markowska (Mon Sep 18 2023 - 03:01:19 PDT)
[AMBER] Incomplete installation: "Fixing Miniconda script shebangs"
- Claire Harmange Magnani via AMBER (Mon Sep 18 2023 - 15:57:19 PDT)
[AMBER] Installing on Ubuntu 22.04/CUDA 12.2
- David A Case via AMBER (Sat Sep 09 2023 - 12:07:12 PDT)
- John McDonnell via AMBER (Fri Sep 08 2023 - 09:35:45 PDT)
[AMBER] Installing on Ubuntu Question
- David A Case via AMBER (Wed Sep 20 2023 - 09:55:56 PDT)
- Matthew Guberman-Pfeffer via AMBER (Wed Sep 20 2023 - 06:31:06 PDT)
[AMBER] Issue with bond and angle parameters
- Koirala, Kushal via AMBER (Mon Sep 18 2023 - 16:03:33 PDT)
[AMBER] Issue with MMPBSA calculation
- Enrico Martinez via AMBER (Thu Sep 07 2023 - 00:41:30 PDT)
- Enrico Martinez via AMBER (Wed Sep 06 2023 - 09:20:22 PDT)
- Enrico Martinez via AMBER (Wed Sep 06 2023 - 09:03:48 PDT)
[AMBER] Maestro PDB to Amber PDB
- Vinicius Cruzeiro $Vinny$ via AMBER (Mon Sep 18 2023 - 15:53:57 PDT)
- He, Amy via AMBER (Fri Sep 15 2023 - 15:19:17 PDT)
- Matthew Guberman-Pfeffer via AMBER (Fri Sep 15 2023 - 15:09:39 PDT)
- Vinicius Cruzeiro $Vinny$ via AMBER (Fri Sep 15 2023 - 14:30:54 PDT)
[AMBER] MMPBSA calculation of multiple complex simulations:
- Bill Miller III via AMBER (Tue Sep 12 2023 - 06:49:56 PDT)
- Kankana Bhattacharjee via AMBER (Tue Sep 12 2023 - 02:48:04 PDT)
[AMBER] MMPBSA issue:
- VERONICA MARTIN HERNANDEZ via AMBER (Mon Sep 11 2023 - 00:40:43 PDT)
- Bill Miller III via AMBER (Thu Sep 07 2023 - 11:32:08 PDT)
- Kankana Bhattacharjee via AMBER (Thu Sep 07 2023 - 01:38:52 PDT)
[AMBER] MMPBSA PBRadii:
- Bill Miller III via AMBER (Mon Sep 11 2023 - 14:12:03 PDT)
- Kankana Bhattacharjee via AMBER (Sun Sep 10 2023 - 23:33:17 PDT)
[AMBER] Optimization and balancing steps for a membrane protein, small molecule and POPC bilayer membrane complex system
- 李美玲 via AMBER (Wed Sep 20 2023 - 19:14:57 PDT)
[AMBER] PhD position at University Complutense of Madrid in biocondensate modelling
- Andres Tejedor Reyes via AMBER (Mon Sep 18 2023 - 09:13:26 PDT)
[AMBER] Pressure controlling keyword:
- Carlos Simmerling via AMBER (Mon Sep 04 2023 - 04:37:43 PDT)
- Kankana Bhattacharjee via AMBER (Mon Sep 04 2023 - 04:35:42 PDT)
- Dr. Anselm Horn via AMBER (Mon Sep 04 2023 - 03:39:07 PDT)
- Nikolay N. Kuzmich via AMBER (Sat Sep 02 2023 - 04:42:29 PDT)
[AMBER] Problem preparing structures
- Dr. Anselm Horn via AMBER (Fri Sep 29 2023 - 02:50:07 PDT)
- VERONICA MARTIN HERNANDEZ via AMBER (Fri Sep 29 2023 - 01:18:05 PDT)
[AMBER] Problem with adding new atoms in prep file
- Barbara Lech via AMBER (Thu Sep 28 2023 - 02:37:19 PDT)
[AMBER] Problem with water molecules angle in MD simulation
- Carlos Simmerling via AMBER (Wed Sep 06 2023 - 02:07:30 PDT)
- Zafar,Muhammad Saqlain via AMBER (Mon Sep 04 2023 - 22:50:16 PDT)
[AMBER] Query Regarding PDB2GMX Error with Amber Force Field
- Fadaei Fatemeh Mgr. via AMBER (Sat Sep 30 2023 - 02:15:15 PDT)
[AMBER] Query regarding unusual atom
- Carlos Simmerling via AMBER (Wed Sep 20 2023 - 08:24:03 PDT)
- Sourav Bhowmik via AMBER (Tue Sep 19 2023 - 22:28:31 PDT)
[AMBER] Reagarding AMBER ff14SB-ildn
- Carlos Simmerling via AMBER (Sat Sep 16 2023 - 16:12:46 PDT)
- Midhun K Madhu 1620103 via AMBER (Sat Sep 16 2023 - 14:02:19 PDT)
[AMBER] Regarding atom types while using antechamber for modified DNA bases
- Sruthi Sudhakar via AMBER (Tue Sep 05 2023 - 04:58:32 PDT)
[AMBER] Regarding issue in the minimization output
- David A Case via AMBER (Sat Sep 09 2023 - 12:04:37 PDT)
- David A Case via AMBER (Sat Sep 09 2023 - 12:03:06 PDT)
- Daniel Roe via AMBER (Thu Sep 07 2023 - 05:26:53 PDT)
- KAJAL ABROL via AMBER (Thu Sep 07 2023 - 00:39:48 PDT)
[AMBER] Regarding periodic box dimentions
- Cianna Calia via AMBER (Fri Sep 22 2023 - 11:24:46 PDT)
- Carlos Simmerling via AMBER (Fri Sep 22 2023 - 06:30:22 PDT)
- Midhun K Madhu 1620103 via AMBER (Fri Sep 22 2023 - 06:15:30 PDT)
[AMBER] RNA simulation basics
- Carlos Simmerling via AMBER (Fri Sep 15 2023 - 11:10:33 PDT)
- Debarati DasGupta via AMBER (Fri Sep 15 2023 - 11:06:36 PDT)
[AMBER] SASA calculation:
- Kankana Bhattacharjee via AMBER (Tue Sep 26 2023 - 02:11:57 PDT)
- Dr. Anselm Horn via AMBER (Tue Sep 26 2023 - 02:04:31 PDT)
- Kankana Bhattacharjee via AMBER (Mon Sep 25 2023 - 23:57:29 PDT)
[AMBER] Strategies to run MMPBSA.py for multimeric systems
- yunshi11 via AMBER (Wed Sep 06 2023 - 18:29:26 PDT)
[AMBER] Support or H100s
- Goetz, Andreas via AMBER (Fri Sep 22 2023 - 12:02:42 PDT)
- Pieri, Elisa via AMBER (Fri Sep 22 2023 - 09:15:26 PDT)
[AMBER] test message
- David A Case via AMBER (Fri Sep 08 2023 - 06:46:06 PDT)
[AMBER] the parameter mctrdz in mmpbsa.in
- Ray Luo via AMBER (Wed Sep 13 2023 - 17:06:53 PDT)
- shiyu wang via AMBER (Tue Sep 12 2023 - 20:28:39 PDT)
[AMBER] Umbrella Sampling
- Carlos Simmerling via AMBER (Fri Sep 15 2023 - 11:09:21 PDT)
- Jing Qu via AMBER (Fri Sep 15 2023 - 10:58:51 PDT)
- Carlos Simmerling via AMBER (Fri Sep 08 2023 - 15:08:54 PDT)
- Carlos Simmerling via AMBER (Fri Sep 08 2023 - 13:58:44 PDT)
- Jing Qu via AMBER (Fri Sep 08 2023 - 13:52:18 PDT)
[AMBER] Visualizing amber MD trajectory in vmd:
- SATYAJIT KHATUA via AMBER (Tue Sep 05 2023 - 23:43:06 PDT)
- SATYAJIT KHATUA via AMBER (Tue Sep 05 2023 - 23:37:47 PDT)
- SATYAJIT KHATUA via AMBER (Tue Sep 05 2023 - 23:19:08 PDT)
- Kankana Bhattacharjee via AMBER (Tue Sep 05 2023 - 23:08:53 PDT)
[AMBER] watershell cpptraj:
- Kankana Bhattacharjee via AMBER (Tue Sep 26 2023 - 05:53:21 PDT)
[AMBER] What is the best way to do triplicate runs
- Carlos Simmerling via AMBER (Fri Sep 08 2023 - 13:55:49 PDT)
- Romero, Maria via AMBER (Fri Sep 08 2023 - 12:32:51 PDT)
[AMBER] 回复: extracting a frame from trajectory at a specific time
- Huang ZiJian via AMBER (Sun Sep 10 2023 - 18:54:27 PDT)

Amber Archive Sep 2023 by subject