Amber Archive Jun 2022: by author

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

Amber Archive Jun 2022 by author