Amber Archive Apr 2023: by thread

[AMBER] Introducing ChatGPDB - The Ultimate Biomolecular Simulation Assistant Jason Swails via AMBER (Sat Apr 01 2023 - 07:59:31 PDT)
- Re: [AMBER] Introducing ChatGPDB - The Ultimate Biomolecular Simulation Assistant Francesca Mocci via AMBER (Sat Apr 01 2023 - 08:44:48 PDT)
- Re: [AMBER] Introducing ChatGPDB - The Ultimate Biomolecular Simulation Assistant Charo del Genio via AMBER (Sat Apr 01 2023 - 09:01:16 PDT)
[AMBER] compiling amber 22 with gcc 11 / cuda 11.6: cuda error with mdgx Vlad Cojocaru via AMBER (Sun Apr 02 2023 - 08:50:20 PDT)
Re: [AMBER] TI calculation regarding charge change in TI region. Michael T Kim via AMBER (Mon Apr 03 2023 - 10:30:00 PDT)
- Re: [AMBER] TI calculation regarding charge change in TI region. Michael T Kim via AMBER (Wed Apr 05 2023 - 15:29:25 PDT)
[AMBER] p5 to C.3 conversion in ATOMTYPE_CHECK.TAB Christopher Corbo via AMBER (Mon Apr 03 2023 - 10:42:17 PDT)
[AMBER] Repulsive restraints between two atoms or two groups of atoms Antonio Frances Monerris via AMBER (Tue Apr 04 2023 - 04:33:14 PDT)
- Re: [AMBER] Repulsive restraints between two atoms or two groups of atoms Carlos Simmerling via AMBER (Tue Apr 04 2023 - 04:53:36 PDT)
[AMBER] pmemd.cuda test possible failure Freddy Bernal via AMBER (Tue Apr 04 2023 - 05:12:11 PDT)
- Re: [AMBER] pmemd.cuda test possible failure David A Case via AMBER (Wed Apr 05 2023 - 14:13:42 PDT)
[AMBER] Internal pyrophosphates with Amber Harvey Dale via AMBER (Tue Apr 04 2023 - 15:38:51 PDT)
[AMBER] Wrong Coordination Number ! angad sharma via AMBER (Thu Apr 06 2023 - 02:44:25 PDT)
[AMBER] MMPBSA help - Sarah Abraham Abraham, Sarah via AMBER (Thu Apr 06 2023 - 06:24:05 PDT)
- Re: [AMBER] MMPBSA help - Sarah Abraham Bill Miller III via AMBER (Fri Apr 07 2023 - 16:56:25 PDT)
[AMBER] Thermodynamic property of the system Dulal Mondal via AMBER (Fri Apr 07 2023 - 06:36:52 PDT)
- Re: [AMBER] Thermodynamic property of the system David Case via AMBER (Fri Apr 07 2023 - 07:18:00 PDT)
[AMBER] Post-doc position open for one year in my lab in Nantes, France Téletchéa Stéphane via AMBER (Fri Apr 07 2023 - 10:02:11 PDT)
[AMBER] Question about implementing steered MD in Amber SONAL GAHLAWAT via AMBER (Fri Apr 07 2023 - 17:43:02 PDT)
[AMBER] Coordination Number angad sharma via AMBER (Sun Apr 09 2023 - 15:07:58 PDT)
Re: [AMBER] issue with pdb4amber Hai Nguyen via AMBER (Tue Apr 11 2023 - 11:22:07 PDT)
- Re: [AMBER] issue with pdb4amber Hai Nguyen via AMBER (Tue Apr 11 2023 - 12:52:44 PDT)
- Re: [AMBER] issue with pdb4amber David A Case via AMBER (Tue Apr 11 2023 - 13:22:32 PDT)
  - Re: [AMBER] issue with pdb4amber Andriy Kovalenko via AMBER (Tue Apr 11 2023 - 14:14:04 PDT)
- Re: [AMBER] issue with pdb4amber Hai Nguyen via AMBER (Wed Apr 12 2023 - 11:10:49 PDT)
[AMBER] Installing AmberTools18 CHAN LOK YUNG via AMBER (Wed Apr 12 2023 - 20:16:31 PDT)
- Re: [AMBER] Installing AmberTools18 SATYAJIT KHATUA via AMBER (Wed Apr 12 2023 - 20:48:58 PDT)
- Re: [AMBER] Installing AmberTools18 SATYAJIT KHATUA via AMBER (Wed Apr 12 2023 - 21:01:21 PDT)
[AMBER] Widom insertion method, calculate chemical potential Alexej Jerschow via AMBER (Thu Apr 13 2023 - 06:31:56 PDT)
[AMBER] Why uinsg a cutoff or 8.0 for proteins and 10.0 for proteins embeded in a membrane? Téletchéa Stéphane via AMBER (Mon Apr 17 2023 - 09:29:16 PDT)
- Re: [AMBER] Why uinsg a cutoff or 8.0 for proteins and 10.0 for proteins embeded in a membrane? Téletchéa Stéphane via AMBER (Mon Apr 17 2023 - 09:32:42 PDT)
  - Re: [AMBER] [Sender Not Verified] Re: Why uinsg a cutoff or 8.0 for proteins and 10.0 for proteins embeded in a membrane? Steinbrecher, Thomas via AMBER (Mon Apr 17 2023 - 23:21:11 PDT)
[AMBER] Why using a cutoff or 8.0 for proteins and 10.0 for proteins embeded in a membrane? Téletchéa Stéphane via AMBER (Mon Apr 17 2023 - 09:35:38 PDT)
[AMBER] correlation matrix Dulal Mondal via AMBER (Tue Apr 18 2023 - 05:44:34 PDT)
- Re: [AMBER] [Sender Not Verified] correlation matrix Steinbrecher, Thomas via AMBER (Tue Apr 18 2023 - 05:58:42 PDT)
[AMBER] constant ph calculations Hoang, Oanh Tu via AMBER (Wed Apr 19 2023 - 04:32:27 PDT)
- Re: [AMBER] constant ph calculations Vinicius Wilian Cruzeiro via AMBER (Wed Apr 19 2023 - 09:35:45 PDT)
- [AMBER] Question about "nfft1 must be in the range of 6 to 512!" Dr. Anselm Horn via AMBER (Thu Apr 20 2023 - 07:17:29 PDT)
  - Re: [AMBER] Question about "nfft1 must be in the range of 6 to 512!" Dr. Anselm Horn via AMBER (Fri Apr 21 2023 - 08:30:26 PDT)
[AMBER] Restraints not read by Sander for QM/MM Abdullah Bin Faheem via AMBER (Wed Apr 19 2023 - 12:09:50 PDT)
- Re: [AMBER] Restraints not read by Sander for QM/MM Carlos Simmerling via AMBER (Wed Apr 19 2023 - 12:13:21 PDT)
  - Re: [AMBER] Restraints not read by Sander for QM/MM Abdullah Bin Faheem via AMBER (Wed Apr 19 2023 - 12:31:54 PDT)
    - Re: [AMBER] Restraints not read by Sander for QM/MM Carlos Simmerling via AMBER (Wed Apr 19 2023 - 12:49:16 PDT)
- Re: [AMBER] Restraints not read by Sander for QM/MM David A Case via AMBER (Wed Apr 19 2023 - 17:05:51 PDT)
  - Re: [AMBER] Restraints not read by Sander for QM/MM Abdullah Bin Faheem via AMBER (Thu Apr 20 2023 - 00:28:10 PDT)
[AMBER] Help in determining no. of molecules for ionic liquid Delwakkada Liyanage, Senal Dinuka via AMBER (Fri Apr 21 2023 - 19:40:50 PDT)
- Re: [AMBER] [Sender Not Verified] Help in determining no. of molecules for ionic liquid Steinbrecher, Thomas via AMBER (Sun Apr 23 2023 - 23:53:47 PDT)
[AMBER] Separating a trajectory by output from clusterdihedral Osman, Roman via AMBER (Sun Apr 23 2023 - 10:38:14 PDT)
- Re: [AMBER] {SPAM?} Separating a trajectory by output from clusterdihedral Matthew Guberman-Pfeffer via AMBER (Sun Apr 23 2023 - 11:15:28 PDT)
  - Re: [AMBER] {SPAM?} Separating a trajectory by output from clusterdihedral Osman, Roman via AMBER (Sun Apr 23 2023 - 11:36:27 PDT)
- Re: [AMBER] Separating a trajectory by output from clusterdihedral Daniel Roe via AMBER (Sun Apr 23 2023 - 12:11:10 PDT)
[AMBER] Not able to reproduce MMPBSA values using data from the tutorial devendra.prajapat.cys19--- via AMBER (Mon Apr 24 2023 - 04:01:17 PDT)
- Re: [AMBER] Not able to reproduce MMPBSA values using data from the tutorial Ray Luo via AMBER (Mon Apr 24 2023 - 10:14:17 PDT)
[AMBER] Using atom OD with parmchk and ff15ipq amin sagar via AMBER (Mon Apr 24 2023 - 06:25:25 PDT)
[AMBER] Query regarding atomicfluct command Roy, Rajarshi via AMBER (Mon Apr 24 2023 - 09:41:57 PDT)
- Re: [AMBER] Query regarding atomicfluct command SATYAJIT KHATUA via AMBER (Mon Apr 24 2023 - 09:51:20 PDT)
- Re: [AMBER] Query regarding atomicfluct command SATYAJIT KHATUA via AMBER (Mon Apr 24 2023 - 10:28:20 PDT)
- Re: [AMBER] Query regarding atomicfluct command SATYAJIT KHATUA via AMBER (Mon Apr 24 2023 - 11:06:54 PDT)
- Re: [AMBER] Query regarding atomicfluct command SATYAJIT KHATUA via AMBER (Mon Apr 24 2023 - 11:25:00 PDT)
- Re: [AMBER] Query regarding atomicfluct command Thomas Cheatham via AMBER (Mon Apr 24 2023 - 11:25:10 PDT)
  - Re: [AMBER] Query regarding atomicfluct command Roy, Rajarshi via AMBER (Mon Apr 24 2023 - 12:38:24 PDT)
    - Re: [AMBER] Query regarding atomicfluct command Faezeh Salehi via AMBER (Mon Apr 24 2023 - 12:40:13 PDT)
- Re: [AMBER] Query regarding atomicfluct command Faezeh Salehi via AMBER (Tue Apr 25 2023 - 22:39:01 PDT)
[AMBER] density input Andriy Kovalenko via AMBER (Mon Apr 24 2023 - 18:52:46 PDT)
- Re: [AMBER] density input David Case via AMBER (Mon Apr 24 2023 - 19:03:00 PDT)
[AMBER] Restraining Counterions in Regular MD Simulations Rory Crean via AMBER (Tue Apr 25 2023 - 03:17:46 PDT)
- Re: [AMBER] Restraining Counterions in Regular MD Simulations Christina Bergonzo via AMBER (Tue Apr 25 2023 - 08:13:20 PDT)
- Re: [AMBER] Restraining Counterions in Regular MD Simulations David A Case via AMBER (Tue Apr 25 2023 - 13:49:51 PDT)
  - Re: [AMBER] Restraining Counterions in Regular MD Simulations Rory Crean via AMBER (Wed Apr 26 2023 - 01:23:38 PDT)
[AMBER] Using atom OD with parmchk and ff15ipq aamin.sagar--- via AMBER (Tue Apr 25 2023 - 06:28:10 PDT)
- Re: [AMBER] Using atom OD with parmchk and ff15ipq Carlos Simmerling via AMBER (Tue Apr 25 2023 - 06:34:10 PDT)
[AMBER] cphstats in CpHMD analysis Dulal Mondal via AMBER (Wed Apr 26 2023 - 00:15:37 PDT)
- Re: [AMBER] cphstats in CpHMD analysis Jason Swails via AMBER (Fri Apr 28 2023 - 06:10:07 PDT)
[AMBER] Fwd: Query regarding restarting the replica exchange molecular dynamics simulation Munazzah Fatima Ansari via AMBER (Wed Apr 26 2023 - 06:00:28 PDT)
[AMBER] Multisander, Vilhelm Ekberg via AMBER (Wed Apr 26 2023 - 07:35:55 PDT)
[AMBER] amber19 compilation Dulal Mondal via AMBER (Wed Apr 26 2023 - 09:43:42 PDT)
- Re: [AMBER] amber19 compilation David A Case via AMBER (Wed Apr 26 2023 - 13:10:50 PDT)
[AMBER] taking Center of mass of 2 atoms in umbrella sampling angad sharma via AMBER (Fri Apr 28 2023 - 10:28:23 PDT)
[AMBER] protonation state of a residue e.g. Histidine Dulal Mondal via AMBER (Sat Apr 29 2023 - 09:47:48 PDT)
[AMBER] Release of AmberTools23 David A Case via AMBER (Sun Apr 30 2023 - 04:57:46 PDT)

Amber Archive Apr 2023 by thread