Amber Archive Jun 2022: by thread

[AMBER] cpptraj autoimage Neha Gandhi (Wed Jun 08 2022 - 16:43:26 PDT)
Re: [AMBER] Extract trajectories REMD Juliette Newell via AMBER (Wed Jun 15 2022 - 02:40:59 PDT)
- Re: [AMBER] Extract trajectories REMD Daniel Roe via AMBER (Wed Jun 15 2022 - 11:27:52 PDT)
- Re: [AMBER] Extract trajectories REMD Daniel Roe via AMBER (Thu Jun 16 2022 - 05:47:58 PDT)
- Re: [AMBER] Extract trajectories REMD Daniel Roe via AMBER (Fri Jun 17 2022 - 05:49:50 PDT)
[AMBER] Antechamber error in creating FF for charged organic molecule Giulia Sormani via AMBER (Wed Jun 15 2022 - 03:40:03 PDT)
- Re: [AMBER] Antechamber error in creating FF for charged organic molecule David A Case via AMBER (Wed Jun 15 2022 - 06:53:35 PDT)
  - Re: [AMBER] Antechamber error in creating FF for charged organic molecule Erdem Yeler via AMBER (Wed Jun 15 2022 - 07:58:18 PDT)
Re: [AMBER] Twist and roll angles in base stack Cenk Andac via AMBER (Wed Jun 15 2022 - 05:55:11 PDT)
[AMBER] Any help for TI calculation with pmemd.cuda Suguna Sakkiah via AMBER (Wed Jun 15 2022 - 10:15:18 PDT)
- Re: [AMBER] Any help for TI calculation with pmemd.cuda Maria Nagan via AMBER (Thu Jun 16 2022 - 08:54:06 PDT)
[AMBER] Force field interfaces Piia Bartos via AMBER (Fri Jun 17 2022 - 00:44:40 PDT)
- Re: [AMBER] Force field interfaces Carlos Simmerling via AMBER (Fri Jun 17 2022 - 04:40:12 PDT)
  - Re: [AMBER] Force field interfaces Piia Bartos via AMBER (Fri Jun 17 2022 - 05:26:24 PDT)
    - Re: [AMBER] Force field interfaces Carlos Simmerling via AMBER (Fri Jun 17 2022 - 06:33:32 PDT)
- Re: [AMBER] Force field interfaces Maria Nagan via AMBER (Fri Jun 17 2022 - 06:37:28 PDT)
Re: [AMBER] [EXTERNAL] Calculation of RDF around a fixed position in space Roe, Daniel \(NIH/NHLBI\) \[E\] via AMBER (Fri Jun 17 2022 - 09:48:16 PDT)
[AMBER] PIP2 lipids in Amber FF Ryan Woltz via AMBER (Fri Jun 17 2022 - 12:56:59 PDT)
- Re: [AMBER] PIP2 lipids in Amber FF Stephan Schott via AMBER (Tue Jun 21 2022 - 09:57:54 PDT)
[AMBER] In the QM/MM MD with g09, the Fe which in the QM region, is written as F (and the atomic number is written as 9) in gau_job.log and gau_job.Inp. 冯时 via AMBER (Sun Jun 19 2022 - 20:01:47 PDT)
- Re: [AMBER] {SPAM?} In the QM/MM MD with g09, the Fe which in the QM region, is written as F (and the atomic number is written as 9) in gau_job.log and gau_job.Inp. Matthew Guberman-Pfeffer via AMBER (Mon Jun 20 2022 - 06:16:27 PDT)
  - Re: [AMBER] {SPAM?} In the QM/MM MD with g09, the Fe which in the QM region, is written as F (and the atomic number is written as 9) in gau_job.log and gau_job.Inp. 冯时 via AMBER (Tue Jun 21 2022 - 19:39:28 PDT)
[AMBER] CPPTRAJ, Total H-Bond Count Question Matthew Guberman-Pfeffer via AMBER (Sun Jun 19 2022 - 14:11:38 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Daniel Roe via AMBER (Fri Jun 24 2022 - 11:51:23 PDT)
[AMBER] tleap problem with spc water Giulia Sormani via AMBER (Mon Jun 20 2022 - 06:24:53 PDT)
- Re: [AMBER] tleap problem with spc water Carlos Simmerling via AMBER (Mon Jun 20 2022 - 07:51:48 PDT)
- Re: [AMBER] tleap problem with spc water Petr Stadlbauer via AMBER (Mon Jun 20 2022 - 10:14:48 PDT)
[AMBER] Amber Beatriz Goncalves via AMBER (Mon Jun 20 2022 - 12:09:29 PDT)
[AMBER] Reproducibility issues for Umbrella Sampling simulations using NFE for different AMBER versions Till El Harrar via AMBER (Tue Jun 21 2022 - 09:58:33 PDT)
[AMBER] Simulating hot water in super-cold gas under 0 pressure Erdem Yeler via AMBER (Tue Jun 21 2022 - 02:08:28 PDT)
[AMBER] In the QM/MM MD with g09, the Fe which in the QM region, is written as F (and the atomic number is written as 9) in gau_job.log and gau_job.Inp. David Poole via AMBER (Mon Jun 20 2022 - 12:16:40 PDT)
- Re: [AMBER] In the QM/MM MD with g09, the Fe which in the QM region, is written as F (and the atomic number is written as 9) in gau_job.log and gau_job.Inp. 冯时 via AMBER (Tue Jun 21 2022 - 19:51:41 PDT)
[AMBER] no new update for ambertool 21 in ubuntu 22.04 Setyanto Md via AMBER (Mon Jun 20 2022 - 17:51:56 PDT)
[AMBER] Segmentation Fault During Minimization in Sander.MPI Nathan Black via AMBER (Tue Jun 21 2022 - 10:45:26 PDT)
[AMBER] Nudged Elastic Band for a enzymatic reaction in explicit solvent Simone Fioccola via AMBER (Wed Jun 22 2022 - 01:34:26 PDT)
[AMBER] cholorform solvent very high energy Fabian Glaser via AMBER (Wed Jun 22 2022 - 04:12:39 PDT)
Re: [AMBER] GIST calculation on OpenMM trajectory Franz Waibl via AMBER (Thu Jun 23 2022 - 08:00:50 PDT)
[AMBER] Issues when running minimization with ParmEd under Amber20 installation EMANUELE CASALI via AMBER (Fri Jun 24 2022 - 01:53:35 PDT)
- Re: [AMBER] Issues when running minimization with ParmEd under Amber20 installation Hai Nguyen via AMBER (Fri Jun 24 2022 - 07:19:40 PDT)
[AMBER] Amber22 GCC8/CUDA10.2 compile issue Hashemi, Mohtadin via AMBER (Fri Jun 24 2022 - 22:17:19 PDT)
- Re: [AMBER] Amber22 GCC8/CUDA10.2 compile issue Scott Brozell via AMBER (Fri Jun 24 2022 - 23:50:42 PDT)
  - Re: [AMBER] Amber22 GCC8/CUDA10.2 compile issue Hashemi, Mohtadin via AMBER (Sat Jun 25 2022 - 10:12:28 PDT)
    - Re: [AMBER] Amber22 GCC8/CUDA10.2 compile issue Hashemi, Mohtadin via AMBER (Tue Jun 28 2022 - 09:46:34 PDT)
Re: [AMBER] writing dna-ligand topology using amber t-leap David A Case via AMBER (Sat Jun 25 2022 - 05:04:04 PDT)
[AMBER] ParmEd, Trouble with timerge Matthew Guberman-Pfeffer via AMBER (Sat Jun 25 2022 - 19:05:19 PDT)
[AMBER] Postdoc Position (immediately available) Ilyas Yildirim via AMBER (Sat Jun 25 2022 - 23:57:01 PDT)
[AMBER] Should I Perform Docking Before Simulation To Find Realistic Binding Score With MMPBSA ? Erdem Yeler via AMBER (Sun Jun 26 2022 - 02:48:20 PDT)
[AMBER] metatwist error Muhammad Ayoub Waqas via AMBER (Sun Jun 26 2022 - 07:18:22 PDT)
- Re: [AMBER] metatwist error David A Case via AMBER (Sun Jun 26 2022 - 12:56:03 PDT)
[AMBER] REMD trajectory visualisation help Suchetana Gupta via AMBER (Sun Jun 26 2022 - 12:00:43 PDT)
- Re: [AMBER] REMD trajectory visualisation help Suchetana Gupta via AMBER (Sun Jun 26 2022 - 13:04:58 PDT)
  - Re: [AMBER] REMD trajectory visualisation help Suchetana Gupta via AMBER (Sun Jun 26 2022 - 13:45:18 PDT)
- Re: [AMBER] REMD trajectory visualisation help Adrian Roitberg via AMBER (Mon Jun 27 2022 - 10:12:32 PDT)
[AMBER] PPI-GaMD error in amber22 Yeng-Tseng Wang via AMBER (Sun Jun 26 2022 - 13:14:35 PDT)
[AMBER] Spurious protein distortion in Thermodynamic Integration Ali Morshedifard via AMBER (Sun Jun 26 2022 - 18:00:49 PDT)
[AMBER] mdin files problem in REMD CHEN Huifeng via AMBER (Mon Jun 27 2022 - 00:56:03 PDT)
- Re: [AMBER] mdin files problem in REMD David A Case via AMBER (Mon Jun 27 2022 - 04:52:25 PDT)
  - [AMBER] 回复: [Ext] Re: mdin files problem in REMD CHEN Huifeng via AMBER (Mon Jun 27 2022 - 09:17:51 PDT)
    - Re: [AMBER] 回复: [Ext] Re: mdin files problem in REMD Carlos Simmerling via AMBER (Mon Jun 27 2022 - 10:13:30 PDT)
[AMBER] KeyError:"M"(MCPB.py) for four Mn3+ Yutian Song via AMBER (Mon Jun 27 2022 - 01:46:20 PDT)
[AMBER] Amber22 installation issues Gao Zhenting via AMBER (Tue Jun 28 2022 - 02:13:02 PDT)
- Re: [AMBER] Amber22 installation issues Gao Zhenting via AMBER (Tue Jun 28 2022 - 08:05:25 PDT)
- Re: [AMBER] Amber22 installation issues David A Case via AMBER (Tue Jun 28 2022 - 13:08:23 PDT)
  - Re: [AMBER] Amber22 installation issues Gustavo Seabra via AMBER (Tue Jun 28 2022 - 15:25:02 PDT)
[AMBER] Visualizing rism3d.snglpnt output Brian Radak via AMBER (Tue Jun 28 2022 - 11:04:11 PDT)
- Re: [AMBER] Visualizing rism3d.snglpnt output Brian Radak via AMBER (Wed Jun 29 2022 - 05:21:33 PDT)
  - Re: [AMBER] Visualizing rism3d.snglpnt output Brian Radak via AMBER (Wed Jun 29 2022 - 08:44:36 PDT)
[AMBER] Slightly misleading error message: "mcbarint is greater than the number of steps" Neale, Christopher Andrew via AMBER (Tue Jun 28 2022 - 12:34:44 PDT)
[AMBER] cpptraj doesn't read c4 term of LJ 12-6-4 potential Giulia Sormani via AMBER (Wed Jun 29 2022 - 01:59:55 PDT)
- Re: [AMBER] cpptraj doesn't read c4 term of LJ 12-6-4 potential Daniel Roe via AMBER (Wed Jun 29 2022 - 02:57:19 PDT)
- Re: [AMBER] cpptraj doesn't read c4 term of LJ 12-6-4 potential Daniel Roe via AMBER (Wed Jun 29 2022 - 11:43:29 PDT)
[AMBER] hydrophobic interactions analysis Hector A. Baldoni via AMBER (Wed Jun 29 2022 - 10:36:02 PDT)
[AMBER] KeyError:"M"(MCPB.py) for more than one MN Yutian Song via AMBER (Thu Jun 30 2022 - 00:22:53 PDT)
[AMBER] acetonitrile Fabian Glaser via AMBER (Thu Jun 30 2022 - 01:21:42 PDT)
- Re: [AMBER] acetonitrile Fabian Glaser via AMBER (Thu Jun 30 2022 - 05:36:36 PDT)
[AMBER] ParmEd, Trouble with timerge Matthew Guberman-Pfeffer via AMBER (Thu Jun 30 2022 - 07:05:12 PDT)
[AMBER] RDF vs, Coordination numbers Damiano Spadoni via AMBER (Thu Jun 30 2022 - 09:46:51 PDT)

Amber Archive Jun 2022 by thread