Amber Archive Sep 2023: by thread

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