Amber Archive Sep 2018: by author

accuratefreeenergy.gmail.com
- [AMBER] nVidia Webinar: Achievable Free Energy Calculations through GPU-Accelerated AMBER (Mon Sep 24 2018 - 10:28:14 PDT)
Adrian Roitberg
- Re: [AMBER] Question about Amber. (Fri Sep 14 2018 - 05:39:51 PDT)
- Re: [AMBER] KDE analysis, (P) greater than one (Mon Sep 03 2018 - 06:34:24 PDT)
Alain Chaumont
- [AMBER] NVIDIA GPU RTX 2080 / RTX 2080 Ti (Thu Sep 27 2018 - 09:55:11 PDT)
Albert
- Re: [AMBER] why not free QM software？ (Sun Sep 16 2018 - 12:23:19 PDT)
- [AMBER] why not free QM software？ (Sat Sep 15 2018 - 07:42:01 PDT)
Alex Schwartz
- [AMBER] Problem in testing the Zinc enzyme example using MCPB.py (Tue Sep 18 2018 - 20:55:07 PDT)
Antonio Amber Carlesso
- Re: [AMBER] Clustering_distance_metric_option_general_rule (Thu Sep 27 2018 - 14:07:15 PDT)
- [AMBER] Clustering_distance_metric_option_general_rule (Sun Sep 16 2018 - 01:26:25 PDT)
Anuja Ware
- Re: [AMBER] Parameters for non-standard residues (Mon Sep 03 2018 - 04:10:19 PDT)
Aravind Ravichandran
- [AMBER] Error while creating topology file(HMassRepartition) in parmed (Mon Sep 24 2018 - 03:39:09 PDT)
- [AMBER] Leap: Nuleotides addition (Sat Sep 08 2018 - 04:32:36 PDT)
Asier Zorrilla
- Re: [AMBER] Question about Amber. (Fri Sep 21 2018 - 05:00:42 PDT)
- Re: [AMBER] Question about Amber. (Mon Sep 17 2018 - 01:25:00 PDT)
- [AMBER] Question about Amber. (Fri Sep 14 2018 - 05:08:37 PDT)
Avirup Ghosh
- [AMBER] atomic fluctuation vs residue (Tue Sep 18 2018 - 19:26:19 PDT)
Benjamin Clausen
- Re: [AMBER] Residue mutation and side chains (Thu Sep 13 2018 - 00:15:57 PDT)
- [AMBER] Residue mutation and side chains (Wed Sep 12 2018 - 04:01:50 PDT)
Bharat Manna
- Re: [AMBER] How to calculate Coordination number from RDF Profile using CPPTRAJ ? (Thu Sep 20 2018 - 20:30:19 PDT)
- [AMBER] Seeking clarification regarding Calculation of Linear Interaction Energy (lie) (Thu Sep 20 2018 - 20:25:51 PDT)
- [AMBER] How to calculate Coordination number from RDF Profile using CPPTRAJ ? (Thu Sep 13 2018 - 11:48:48 PDT)
- Re: [AMBER] Need help regarding calculation of Coordination number from RDF Profile (Tue Sep 04 2018 - 06:35:59 PDT)
Bill Ross
- Re: [AMBER] AMBER ntslim limit (Fri Sep 21 2018 - 02:46:10 PDT)
- Re: [AMBER] Unknown keyword (Wed Sep 19 2018 - 03:04:48 PDT)
- Re: [AMBER] Question about Amber. (Mon Sep 17 2018 - 01:40:01 PDT)
- Re: [AMBER] Error in umbrella sampling (Fri Sep 14 2018 - 09:47:11 PDT)
- Re: [AMBER] Residue mutation and side chains (Thu Sep 13 2018 - 00:23:03 PDT)
- Re: [AMBER] Query for umbrella sampling (Wed Sep 12 2018 - 13:41:32 PDT)
- Re: [AMBER] more about gfortran8.2 and clang9.1: no cpptraj problems here (Wed Sep 12 2018 - 13:38:55 PDT)
- Re: [AMBER] more about gfortran8.2 and clang9.1: no cpptraj problems here (Wed Sep 12 2018 - 13:35:08 PDT)
- Re: [AMBER] Question about configure Ambertool18 on Mac (Wed Sep 12 2018 - 01:06:26 PDT)
- Re: [AMBER] Question about configure Ambertool18 on Mac (Wed Sep 12 2018 - 00:38:43 PDT)
- Re: [AMBER] Question about configure Ambertool18 on Mac (Tue Sep 11 2018 - 22:46:11 PDT)
- Re: [AMBER] Restraining forces for atoms (Thu Sep 06 2018 - 09:07:23 PDT)
- Re: [AMBER] Fwd: Problem with energy minimization sander.MPI (Wed Sep 05 2018 - 02:03:25 PDT)
- Re: [AMBER] Restraining forces for atoms (Wed Sep 05 2018 - 01:17:52 PDT)
Carlos Simmerling
- Re: [AMBER] Protein "jumping" during SMD run (Fri Sep 14 2018 - 13:32:53 PDT)
- Re: [AMBER] Question about Amber. (Fri Sep 14 2018 - 05:17:15 PDT)
- Re: [AMBER] Residue mutation and side chains (Thu Sep 13 2018 - 08:41:48 PDT)
- Re: [AMBER] Residue mutation and side chains (Wed Sep 12 2018 - 09:25:16 PDT)
Charles-Alexandre Mattelaer
- Re: [AMBER] why not free QM software？ (Sat Sep 15 2018 - 07:47:41 PDT)
Charo del Genio
- Re: [AMBER] Format of cpptraj pairwise distance file when clustering (Tue Sep 04 2018 - 01:00:48 PDT)
- [AMBER] Format of cpptraj pairwise distance file when clustering (Mon Sep 03 2018 - 07:18:02 PDT)
- Re: [AMBER] cpptraj segmentation fault when using avgout in cluster (Mon Sep 03 2018 - 07:07:27 PDT)
Christina Bergonzo
- Re: [AMBER] Clustering_distance_metric_option_general_rule (Thu Sep 20 2018 - 08:47:55 PDT)
Cory Ayres
- [AMBER] Protein "jumping" during SMD run (Fri Sep 14 2018 - 08:13:16 PDT)
Cruzeiro,Vinicius Wilian D
- [AMBER] Constant pH and Redox Potential MD tutorial (Sat Sep 01 2018 - 05:41:44 PDT)
Daniel Roe
- Re: [AMBER] Reducing memory usage in lifetime analyses (Wed Sep 26 2018 - 12:14:10 PDT)
- Re: [AMBER] Calculating residence times with cpptraj (Wed Sep 26 2018 - 12:08:57 PDT)
- Re: [AMBER] Contact Map (Mon Sep 24 2018 - 08:48:33 PDT)
- Re: [AMBER] Contact Map (Mon Sep 24 2018 - 08:46:58 PDT)
- Re: [AMBER] Running GIST calculation in parallel (Fri Sep 21 2018 - 10:18:41 PDT)
- Re: [AMBER] Regarding nastruct command in cpptraj (Fri Sep 21 2018 - 09:09:47 PDT)
- Re: [AMBER] CPPTRAJ: extracting the restraining forces (Thu Sep 20 2018 - 08:45:32 PDT)
- Re: [AMBER] Running GIST calculation in parallel (Thu Sep 20 2018 - 08:37:37 PDT)
- Re: [AMBER] RMS rotate about z-axis only (Thu Sep 20 2018 - 08:25:03 PDT)
- Re: [AMBER] Clustering_distance_metric_option_general_rule (Thu Sep 20 2018 - 08:21:26 PDT)
- Re: [AMBER] Distance based energy calculation (Thu Sep 20 2018 - 08:13:41 PDT)
- Re: [AMBER] atomic fluctuation vs residue (Thu Sep 20 2018 - 07:42:08 PDT)
- Re: [AMBER] Regarding nastruct command in cpptraj (Thu Sep 20 2018 - 07:40:39 PDT)
- Re: [AMBER] Contact Map (Thu Sep 20 2018 - 06:00:58 PDT)
- Re: [AMBER] Problem with stripping with a condition (Thu Sep 20 2018 - 05:49:44 PDT)
- Re: [AMBER] rdf in one dimmension (Mon Sep 17 2018 - 04:22:57 PDT)
- Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis (Mon Sep 17 2018 - 04:21:51 PDT)
- Re: [AMBER] H-bond between the substrate molecule and protein in the MD traj (Thu Sep 13 2018 - 06:09:18 PDT)
- Re: [AMBER] difference of distances using cpptraj in free energy plot (Wed Sep 12 2018 - 10:55:23 PDT)
- Re: [AMBER] Format of cpptraj pairwise distance file when clustering (Tue Sep 04 2018 - 12:26:16 PDT)
- Re: [AMBER] Format of cpptraj pairwise distance file when clustering (Tue Sep 04 2018 - 08:02:53 PDT)
- Re: [AMBER] Format of cpptraj pairwise distance file when clustering (Mon Sep 03 2018 - 11:49:34 PDT)
- Re: [AMBER] KDE analysis, (P) greater than one (Sat Sep 01 2018 - 05:48:25 PDT)
- Re: [AMBER] Temperature calculaton by CPPTRAJ (Sat Sep 01 2018 - 05:46:25 PDT)
David A Case
- Re: [AMBER] Error while creating topology file(HMassRepartition) in parmed (Mon Sep 24 2018 - 04:42:28 PDT)
- Re: [AMBER] Error while creating topology file(HMassRepartition) in parmed (Mon Sep 24 2018 - 04:39:26 PDT)
- Re: [AMBER] Options for nonpolar solvation free energy calculation with mm_pbsa.pl (Mon Sep 24 2018 - 04:32:26 PDT)
- Re: [AMBER] Amber on GPU (Thu Sep 20 2018 - 04:14:54 PDT)
- Re: [AMBER] Error in umbrella sampling (Mon Sep 17 2018 - 10:10:20 PDT)
- Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis (Sun Sep 16 2018 - 17:59:18 PDT)
- Re: [AMBER] Question about Amber. (Fri Sep 14 2018 - 05:53:49 PDT)
- Re: [AMBER] a error about MMPBSA.PY (Fri Sep 14 2018 - 05:40:24 PDT)
- Re: [AMBER] Compression of CDF coordinate files to gzip AMBER18. (Thu Sep 13 2018 - 04:39:00 PDT)
- Re: [AMBER] Some questions about mmpbsa.py (Thu Sep 13 2018 - 04:32:04 PDT)
- [AMBER] more about gfortran8.2 and clang9.1: no cpptraj problems here (Wed Sep 12 2018 - 13:28:34 PDT)
- Re: [AMBER] Question about configure Ambertool18 on Mac (Wed Sep 12 2018 - 05:08:42 PDT)
- Re: [AMBER] A error about Minimize structure and calc entropy IN MM_PBSA.PL (Tue Sep 11 2018 - 09:11:25 PDT)
- Re: [AMBER] CUDA and driver version for Nvidia Titan Black and Titan Z GPUs cluster (Mon Sep 10 2018 - 08:20:55 PDT)
- Re: [AMBER] Leap: Nuleotides addition (Sat Sep 08 2018 - 07:31:39 PDT)
- Re: [AMBER] Energy uints in mden file and mdout_analyzer.py (Thu Sep 06 2018 - 11:59:39 PDT)
- Re: [AMBER] Fwd: Problem with energy minimization sander.MPI (Wed Sep 05 2018 - 05:10:03 PDT)
- Re: [AMBER] Reg: antechamber net charge calculation -nc (Tue Sep 04 2018 - 10:46:58 PDT)
- Re: [AMBER] Coordinate messed up after tleap set box (Tue Sep 04 2018 - 10:37:20 PDT)
- [AMBER] [david.case.rutgers.edu: Re: Coordinate messed up after tleap set box] (Tue Sep 04 2018 - 05:31:36 PDT)
- Re: [AMBER] Coordinate messed up after tleap set box (Tue Sep 04 2018 - 05:28:36 PDT)
- Re: [AMBER] Distance HH TIP3P (Mon Sep 03 2018 - 04:47:40 PDT)
- Re: [AMBER] Normal mode calculation on a truncated system (Mon Sep 03 2018 - 04:46:07 PDT)
David Case
- Re: [AMBER] How to computing peptide partial charges with antechamber? (Sat Sep 29 2018 - 10:54:01 PDT)
- Re: [AMBER] Problems with MPI compilation gb_force.F90 (Fri Sep 28 2018 - 04:28:31 PDT)
- Re: [AMBER] Counter Ions in X-Ray structure. (Thu Sep 27 2018 - 13:29:38 PDT)
- Re: [AMBER] annoying elapsed time in mdout of amber18 (Thu Sep 27 2018 - 13:36:36 PDT)
- Re: [AMBER] Counter Ions in X-Ray structure. (Thu Sep 27 2018 - 05:53:16 PDT)
- Re: [AMBER] test errors of amber18 (Thu Sep 27 2018 - 04:51:59 PDT)
- Re: [AMBER] Critical Isoform selectivity in MD (Thu Sep 27 2018 - 04:46:52 PDT)
- Re: [AMBER] Re-scaling masses and kinetic energy in TI calculations (Thu Sep 27 2018 - 04:42:42 PDT)
- Re: [AMBER] Error while creating topology file(HMassRepartition) in parmed (Mon Sep 24 2018 - 16:11:47 PDT)
- Re: [AMBER] Amber Installation Error (Tue Sep 18 2018 - 06:21:49 PDT)
- Re: [AMBER] Amber16 cuda compiling error (Tue Sep 18 2018 - 06:18:54 PDT)
David Cerutti
- Re: [AMBER] NVIDIA GPU RTX 2080 / RTX 2080 Ti (Thu Sep 27 2018 - 10:18:50 PDT)
- Re: [AMBER] cuda 10 support (Fri Sep 21 2018 - 08:41:57 PDT)
- Re: [AMBER] Amber16 cuda compiling error (Mon Sep 17 2018 - 21:33:00 PDT)
- Re: [AMBER] Amber16 cuda compiling error (Mon Sep 17 2018 - 20:47:11 PDT)
- Re: [AMBER] CUDA and driver version for Nvidia Titan Black and Titan Z GPUs cluster (Fri Sep 07 2018 - 10:46:41 PDT)
- Re: [AMBER] GTX-2080 benchmarks (Tue Sep 04 2018 - 10:24:06 PDT)
Deepika Sardana
- [AMBER] Adding 12_6_4 LJ parameters in prmtop file (Sun Sep 16 2018 - 09:33:18 PDT)
dhaval patel
- [AMBER] Regarding error in MCPB.py (Sun Sep 02 2018 - 02:18:23 PDT)
DHEERAJ CHITARA
- [AMBER] Compression of CDF coordinate files to gzip AMBER18. (Thu Sep 13 2018 - 01:12:44 PDT)
Dwight McGee
- Re: [AMBER] Installing fortran in Ubuntu-64 for Sander (Sat Sep 15 2018 - 17:35:31 PDT)
emanuele falbo
- Re: [AMBER] Umbrella sampling scripts (Thu Sep 27 2018 - 11:43:50 PDT)
- Re: [AMBER] Umbrella sampling scripts (Thu Sep 27 2018 - 07:14:28 PDT)
- Re: [AMBER] Umbrella sampling scripts (Thu Sep 27 2018 - 06:56:58 PDT)
- [AMBER] Umbrella sampling scripts (Thu Sep 27 2018 - 06:33:59 PDT)
- Re: [AMBER] QM/MM Thermodynamic Integration (Thu Sep 20 2018 - 04:29:22 PDT)
- Re: [AMBER] Amber on GPU (Thu Sep 20 2018 - 04:23:04 PDT)
- [AMBER] Amber on GPU (Thu Sep 20 2018 - 03:13:40 PDT)
Eric Lang
- Re: [AMBER] PBC error. Amber force field in NAMD (Tue Sep 25 2018 - 06:34:28 PDT)
Feng Pan
- Re: [AMBER] SMD free energy inferred from work (Mon Sep 24 2018 - 08:38:09 PDT)
Goetz, Andreas
- Re: [AMBER] QM/MM Thermodynamic Integration (Thu Sep 20 2018 - 09:50:57 PDT)
Gustaf Olsson
- Re: [AMBER] Reducing memory usage in lifetime analyses (Fri Sep 28 2018 - 00:20:42 PDT)
- [AMBER] Reducing memory usage in lifetime analyses (Tue Sep 25 2018 - 23:15:29 PDT)
- Re: [AMBER] H-bond between the substrate molecule and protein in the MD traj (Wed Sep 12 2018 - 23:16:14 PDT)
Gustavo Seabra
- Re: [AMBER] why not free QM software？ (Sun Sep 16 2018 - 12:33:38 PDT)
- Re: [AMBER] why not free QM software？ (Sun Sep 16 2018 - 11:49:33 PDT)
Hadi Rahmaninejad
- [AMBER] Problem with stripping with a condition (Wed Sep 19 2018 - 08:56:43 PDT)
- Re: [AMBER] rdf in one dimmension (Sun Sep 16 2018 - 17:32:30 PDT)
- [AMBER] rdf in one dimmension (Fri Sep 14 2018 - 13:29:25 PDT)
- Re: [AMBER] RMS is zero (Tue Sep 04 2018 - 14:19:08 PDT)
- [AMBER] RMS is zero (Tue Sep 04 2018 - 13:34:23 PDT)
Hai Nguyen
- Re: [AMBER] Newbie question about installing AmberTool18 in Linux (VirtualBox) (Sun Sep 16 2018 - 15:00:46 PDT)
- Re: [AMBER] RMS rotate about z-axis only (Fri Sep 14 2018 - 08:07:01 PDT)
hosein geraili
- [AMBER] covalently bonded ligand (Wed Sep 05 2018 - 05:40:54 PDT)
- [AMBER] parameterizing the covalently bonded ligand (Mon Sep 03 2018 - 09:25:24 PDT)
Ikuo KURISAKI
- Re: [AMBER] Temperature calculaton by CPPTRAJ (Mon Sep 03 2018 - 06:38:34 PDT)
- [AMBER] Temperature calculaton by CPPTRAJ (Sat Sep 01 2018 - 03:32:08 PDT)
- [AMBER] Temperature calculaton by CPPTRAJ (Sat Sep 01 2018 - 01:34:48 PDT)
James Kress
- Re: [AMBER] annoying elapsed time in mdout of amber18 (Fri Sep 28 2018 - 09:18:53 PDT)
- Re: [AMBER] Problems with MPI compilation gb_force.F90 (Fri Sep 28 2018 - 09:16:49 PDT)
- Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 (Tue Sep 25 2018 - 09:49:54 PDT)
Jason Swails
- Re: [AMBER] parmed pdb to crd (Fri Sep 07 2018 - 20:09:32 PDT)
- Re: [AMBER] Couldn't find VdW parameters (Thu Sep 06 2018 - 05:56:23 PDT)
- Re: [AMBER] KDE analysis, (P) greater than one (Wed Sep 05 2018 - 20:49:34 PDT)
jinfeng liu
- Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis (Sun Sep 16 2018 - 18:47:44 PDT)
- Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis (Sun Sep 16 2018 - 18:21:31 PDT)
- [AMBER] unwrap problem in the liquid water dynamics trajectory analysis (Sat Sep 15 2018 - 22:43:13 PDT)
Keiran Corbett
- Re: [AMBER] Counter Ions in X-Ray structure. (Thu Sep 27 2018 - 07:38:52 PDT)
- Re: [AMBER] Counter Ions in X-Ray structure. (Thu Sep 27 2018 - 07:08:27 PDT)
- [AMBER] Counter Ions in X-Ray structure. (Thu Sep 27 2018 - 04:55:35 PDT)
Leena Aggarwal
- [AMBER] Query regarding the number of cores for running sander.MPI (Fri Sep 14 2018 - 01:25:42 PDT)
Lei Zhao
- [AMBER] test errors of amber18 (Mon Sep 17 2018 - 06:41:34 PDT)
leifepeterson.sbcglobal.net
- [AMBER] RESOLVED: AMBER Alanine tutorial (need to replace .mdcrd with .nc) (Mon Sep 17 2018 - 06:36:34 PDT)
- [AMBER] AMBER Alanine tutorial (different outputs from AMBER15 and AMBER18) (Sun Sep 16 2018 - 12:30:24 PDT)
- [AMBER] RESOLVED: peek_ewald_inpcrd: Box info not found in inpcrd (Sat Sep 15 2018 - 20:24:35 PDT)
- [AMBER] Sander 01_Min.out error (Sat Sep 15 2018 - 19:23:44 PDT)
- [AMBER] RESOLVED: Installing fortran in Ubuntu-64 for Sander (Sat Sep 15 2018 - 19:15:25 PDT)
- [AMBER] Installing fortran in Ubuntu-64 for Sander (Sat Sep 15 2018 - 13:03:50 PDT)
- [AMBER] Newbie question about installing AmberTool18 in Linux (VirtualBox) (Sat Sep 15 2018 - 09:28:16 PDT)
M RCC
- [AMBER] PBC error. Amber force field in NAMD (Tue Sep 25 2018 - 04:34:54 PDT)
- [AMBER] Critical Isoform selectivity in MD (Sun Sep 23 2018 - 23:15:49 PDT)
- Re: [AMBER] Running GIST calculation in parallel (Fri Sep 21 2018 - 07:53:03 PDT)
- [AMBER] Running GIST calculation in parallel (Thu Sep 20 2018 - 02:57:44 PDT)
- [AMBER] Help in COM pulling (Sun Sep 02 2018 - 09:25:52 PDT)
- Re: [AMBER] NCSU_SMD for protein-ligand complex pulling (Sat Sep 01 2018 - 03:25:20 PDT)
- [AMBER] Constant velocity pulling in SMD (Fri Aug 31 2018 - 23:49:50 PDT)
Mac Kevin Braza
- Re: [AMBER] KDE analysis, (P) greater than one (Mon Sep 03 2018 - 18:25:25 PDT)
- [AMBER] KDE analysis, (P) greater than one (Fri Aug 31 2018 - 20:24:19 PDT)
Marcos Serrou do Amaral
- Re: [AMBER] Umbrella sampling scripts (Thu Sep 27 2018 - 07:54:03 PDT)
- Re: [AMBER] Umbrella sampling scripts (Thu Sep 27 2018 - 06:51:27 PDT)
Markowska
- Re: [AMBER] CUDA and driver version for Nvidia Titan Black and Titan Z GPUs cluster (Fri Sep 07 2018 - 11:17:42 PDT)
- [AMBER] CUDA and driver version for Nvidia Titan Black and Titan Z GPUs cluster (Fri Sep 07 2018 - 10:37:06 PDT)
maryam azimzadehirani
- Re: [AMBER] Fwd: Problem with energy minimization sander.MPI (Wed Sep 05 2018 - 07:03:20 PDT)
- Re: [AMBER] Fwd: Problem with energy minimization sander.MPI (Wed Sep 05 2018 - 02:34:17 PDT)
- [AMBER] Fwd: Problem with energy minimization sander.MPI (Wed Sep 05 2018 - 01:54:14 PDT)
Matias Machado
- Re: [AMBER] Counter Ions in X-Ray structure. (Thu Sep 27 2018 - 10:25:17 PDT)
- Re: [AMBER] Counter Ions in X-Ray structure. (Thu Sep 27 2018 - 09:24:24 PDT)
- Re: [AMBER] Running GIST calculation in parallel (Sun Sep 23 2018 - 06:08:22 PDT)
- Re: [AMBER] Running GIST calculation in parallel (Fri Sep 21 2018 - 11:16:07 PDT)
- Re: [AMBER] setting of different concentration of Nacl (Fri Sep 21 2018 - 07:58:16 PDT)
- Re: [AMBER] setting of different concentration of Nacl (Fri Sep 21 2018 - 07:10:30 PDT)
- Re: [AMBER] AMBER ntslim limit (Fri Sep 21 2018 - 05:06:16 PDT)
- Re: [AMBER] Temperature RMS, ntslim limit (Thu Sep 20 2018 - 07:48:35 PDT)
- Re: [AMBER] AMBER Alanine tutorial (different outputs from AMBER15 and AMBER18) (Sun Sep 16 2018 - 13:18:29 PDT)
- Re: [AMBER] RESOLVED: peek_ewald_inpcrd: Box info not found in inpcrd (Sun Sep 16 2018 - 08:35:10 PDT)
- Re: [AMBER] How to calculate Coordination number from RDF Profile using CPPTRAJ ? (Sun Sep 16 2018 - 07:50:47 PDT)
- Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis (Sun Sep 16 2018 - 07:04:09 PDT)
- Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis (Sun Sep 16 2018 - 06:52:54 PDT)
Meng Wu
- [AMBER] H-bond between the substrate molecule and protein in the MD traj (Wed Sep 12 2018 - 18:30:49 PDT)
- Re: [AMBER] Energy uints in mden file and mdout_analyzer.py (Fri Sep 07 2018 - 20:42:52 PDT)
- Re: [AMBER] Energy uints in mden file and mdout_analyzer.py (Thu Sep 06 2018 - 19:14:59 PDT)
- [AMBER] Energy uints in mden file and mdout_analyzer.py (Thu Sep 06 2018 - 06:17:41 PDT)
MOHD HOMAIDUR RAHMAN
- [AMBER] Fwd: Distance based energy calculation (Tue Sep 18 2018 - 23:32:03 PDT)
- [AMBER] Distance based energy calculation (Thu Sep 13 2018 - 06:45:52 PDT)
Neha Gandhi
- [AMBER] parmed pdb to crd (Fri Sep 07 2018 - 02:04:34 PDT)
Nikolay N. Kuzmich
- Re: [AMBER] AMBER ntslim limit (Fri Sep 21 2018 - 02:34:30 PDT)
- [AMBER] Temperature RMS, ntslim limit (Thu Sep 20 2018 - 05:29:24 PDT)
- [AMBER] CPPTRAJ: extracting the restraining forces (Wed Sep 12 2018 - 06:02:47 PDT)
- Re: [AMBER] Restraining forces for atoms (Thu Sep 06 2018 - 05:46:42 PDT)
- [AMBER] Restraining forces for atoms (Wed Sep 05 2018 - 01:06:12 PDT)
- [AMBER] Subtracting the forces from harmonic restraints (Mon Sep 03 2018 - 01:52:57 PDT)
Nisha Amarnath Jonniya
- [AMBER] setting of different concentration of Nacl (Fri Sep 21 2018 - 05:40:52 PDT)
- Re: [AMBER] difference of distances using cpptraj in free energy plot (Thu Sep 13 2018 - 00:34:53 PDT)
- [AMBER] difference of distances using cpptraj in free energy plot (Wed Sep 12 2018 - 05:07:10 PDT)
Paul Westphälinger
- Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 (Wed Sep 26 2018 - 04:10:04 PDT)
- Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 (Tue Sep 25 2018 - 03:43:55 PDT)
Pengfei Li
- Re: [AMBER] Adding 12_6_4 LJ parameters in prmtop file (Sat Sep 22 2018 - 07:42:55 PDT)
- Re: [AMBER] Adding 12_6_4 LJ parameters in prmtop file (Sat Sep 22 2018 - 07:41:42 PDT)
- Re: [AMBER] Problem in testing the Zinc enzyme example using MCPB.py (Sat Sep 22 2018 - 07:31:16 PDT)
- Re: [AMBER] Au+++ ion parameter (Sat Sep 08 2018 - 12:49:12 PDT)
- Re: [AMBER] Au+++ ion parameter (Sat Sep 08 2018 - 12:18:52 PDT)
- Re: [AMBER] Arsenous acid (H3AsO3) parameterization (Sat Sep 08 2018 - 12:10:41 PDT)
- Re: [AMBER] metalParm2.xml or metalParm.xml (Sat Sep 08 2018 - 11:46:38 PDT)
- Re: [AMBER] MCPB.py error (not reading chk file) (Sat Sep 08 2018 - 11:38:13 PDT)
- Re: [AMBER] covalently bonded ligand (Sat Sep 08 2018 - 11:30:14 PDT)
- Re: [AMBER] Regarding error in MCPB.py (Tue Sep 04 2018 - 07:12:38 PDT)
Piotr Fajer
- [AMBER] GTX-2080 benchmarks (Tue Sep 04 2018 - 10:04:49 PDT)
Rajarshi Roy
- Re: [AMBER] Regarding nastruct command in cpptraj (Fri Sep 21 2018 - 22:01:54 PDT)
- Re: [AMBER] Regarding nastruct command in cpptraj (Fri Sep 21 2018 - 00:35:42 PDT)
- [AMBER] Regarding nastruct command in cpptraj (Tue Sep 18 2018 - 10:39:41 PDT)
- [AMBER] Regarding output file in REMD (Mon Sep 03 2018 - 21:47:10 PDT)
Ray Luo
- Re: [AMBER] pbsa:cannot match namelist object name mprob (Mon Sep 17 2018 - 10:15:21 PDT)
- Re: [AMBER] A confusion about the binding energy calculated by pbsa with implicit membrane model (Wed Sep 12 2018 - 10:35:32 PDT)
Ross Walker
- Re: [AMBER] CUDA and driver version for Nvidia Titan Black and Titan Z GPUs cluster (Mon Sep 10 2018 - 15:12:49 PDT)
Ruben Ramos Horta
- [AMBER] Problems with MPI compilation gb_force.F90 (Fri Sep 28 2018 - 01:05:10 PDT)
Ruth Helena Tichauer
- Re: [AMBER] SMD free energy inferred from work (Mon Sep 24 2018 - 13:16:10 PDT)
- [AMBER] SMD free energy inferred from work (Mon Sep 24 2018 - 06:46:42 PDT)
Ryan Novosielski
- Re: [AMBER] CUDA and driver version for Nvidia Titan Black and Titan Z GPUs cluster (Mon Sep 10 2018 - 13:33:09 PDT)
Saikat Pal
- [AMBER] Query on 2DRMSD (Fri Sep 21 2018 - 05:03:09 PDT)
- Re: [AMBER] Error in umbrella sampling (Tue Sep 18 2018 - 07:30:02 PDT)
- Re: [AMBER] Error in umbrella sampling (Mon Sep 17 2018 - 10:23:41 PDT)
- Re: [AMBER] Error in umbrella sampling (Mon Sep 17 2018 - 08:50:53 PDT)
- [AMBER] Error in umbrella sampling (Fri Sep 14 2018 - 07:26:14 PDT)
- [AMBER] Query for umbrella sampling (Wed Sep 12 2018 - 13:36:57 PDT)
- [AMBER] Query for umbrella sampling (Wed Sep 12 2018 - 00:09:01 PDT)
Samdani A
- [AMBER] Reg: antechamber net charge calculation -nc (Tue Sep 04 2018 - 07:22:40 PDT)
Sarah Fegan - UKRI STFC
- [AMBER] Problem with antechamber/acdoctor (Wed Sep 26 2018 - 03:15:11 PDT)
senal dinuka
- Re: [AMBER] Amber16 cuda compiling error (Mon Sep 17 2018 - 21:13:58 PDT)
- [AMBER] Amber16 cuda compiling error (Mon Sep 17 2018 - 20:43:19 PDT)
Simon Kit Sang Chu
- Re: [AMBER] Coordinate messed up after tleap set box (Tue Sep 04 2018 - 11:39:48 PDT)
- Re: [AMBER] Coordinate messed up after tleap set box (Tue Sep 04 2018 - 09:58:33 PDT)
- [AMBER] Coordinate messed up after tleap set box (Mon Sep 03 2018 - 12:31:32 PDT)
Song-Ho Chong
- Re: [AMBER] annoying elapsed time in mdout of amber18 (Fri Sep 28 2018 - 09:23:26 PDT)
- Re: [AMBER] annoying elapsed time in mdout of amber18 (Fri Sep 28 2018 - 00:15:24 PDT)
- Re: [AMBER] annoying elapsed time in mdout of amber18 (Thu Sep 27 2018 - 20:38:57 PDT)
- [AMBER] annoying elapsed time in mdout of amber18 (Thu Sep 27 2018 - 05:57:00 PDT)
Sourav Purohit
- Re: [AMBER] Contact Map (Thu Sep 20 2018 - 11:24:01 PDT)
- [AMBER] Contact Map (Mon Sep 17 2018 - 15:59:06 PDT)
Stefan Ivanov
- [AMBER] Calculating residence times with cpptraj (Tue Sep 25 2018 - 21:52:54 PDT)
Stephan Schott
- Re: [AMBER] setting of different concentration of Nacl (Fri Sep 21 2018 - 08:13:31 PDT)
- Re: [AMBER] setting of different concentration of Nacl (Fri Sep 21 2018 - 07:49:30 PDT)
- Re: [AMBER] Query regarding the number of cores for running sander.MPI (Fri Sep 14 2018 - 01:43:18 PDT)
- Re: [AMBER] RMS is zero (Tue Sep 04 2018 - 13:58:04 PDT)
Sushi Shilpa
- [AMBER] Unknown keyword (Wed Sep 19 2018 - 02:55:54 PDT)
- Re: [AMBER] Couldn't find VdW parameters (Fri Sep 07 2018 - 01:51:10 PDT)
- [AMBER] Couldn't find VdW parameters (Thu Sep 06 2018 - 05:20:02 PDT)
- [AMBER] MCPB.py error (not reading chk file) (Thu Sep 06 2018 - 01:58:22 PDT)
tang.xiaping.outlook.com
- Re: [AMBER] Question about configure Ambertool18 on Mac (Wed Sep 12 2018 - 00:50:49 PDT)
- Re: [AMBER] Question about configure Ambertool18 on Mac (Wed Sep 12 2018 - 00:29:08 PDT)
- [AMBER] Question about configure Ambertool18 on Mac (Tue Sep 11 2018 - 22:35:25 PDT)
Thomas Cheatham
- Re: [AMBER] Query on 2DRMSD (Fri Sep 21 2018 - 17:09:41 PDT)
Tom Kurtzman
- Re: [AMBER] Re-scaling masses and kinetic energy in TI calculations (Thu Sep 27 2018 - 05:29:51 PDT)
- Re: [AMBER] Running GIST calculation in parallel (Fri Sep 21 2018 - 15:35:32 PDT)
- Re: [AMBER] rdf in one dimmension (Mon Sep 17 2018 - 19:49:35 PDT)
- Re: [AMBER] rdf in one dimmension (Fri Sep 14 2018 - 18:48:20 PDT)
- Re: [AMBER] rdf in one dimmension (Fri Sep 14 2018 - 18:36:17 PDT)
Waqas Takkar
- [AMBER] cuda 10 support (Fri Sep 21 2018 - 03:42:04 PDT)
Wesley Michael Botello-Smith
- [AMBER] RMS rotate about z-axis only (Tue Sep 11 2018 - 13:02:49 PDT)
yulongsun.nwpu.edu.cn
- [AMBER] How to computing peptide partial charges with antechamber? (Sat Sep 29 2018 - 06:59:53 PDT)
Yuthika Dholey
- [AMBER] Amber Installation Error (Mon Sep 17 2018 - 22:46:02 PDT)
李耀
- [AMBER] Amber constraint SMD (Wed Sep 12 2018 - 08:17:30 PDT)
高振梅
- [AMBER] pbsa:cannot match namelist object name mprob (Mon Sep 17 2018 - 07:00:46 PDT)
- [AMBER] A confusion about the binding energy calculated by pbsa with implicit membrane model (Fri Sep 14 2018 - 06:25:56 PDT)
- [AMBER] A confusion about the binding energy calculated by pbsa with implicit membrane model (Wed Sep 12 2018 - 06:15:50 PDT)
龚乾坤
- [AMBER] Options for nonpolar solvation free energy calculation with mm_pbsa.pl (Sun Sep 16 2018 - 19:50:56 PDT)
- [AMBER] a error about MMPBSA.PY (Thu Sep 13 2018 - 17:29:07 PDT)
- [AMBER] Some questions about mmpbsa.py (Thu Sep 13 2018 - 00:01:12 PDT)
- Re: [AMBER] A error about Minimize structure and calc entropy IN MM_PBSA.PL (Tue Sep 11 2018 - 23:59:41 PDT)
- Re: [AMBER] A error about Minimize structure and calc entropy IN MM_PBSA.PL (Tue Sep 11 2018 - 18:06:48 PDT)
- [AMBER] A error about Minimize structure and calc entropy IN MM_PBSA.PL (Tue Sep 11 2018 - 05:26:36 PDT)

Amber Archive Sep 2018 by author