Amber Archive Jul 2020: by subject

[AMBER] "Does not have a type" error in tleap
- Jatin Kashyap (Wed Jul 01 2020 - 10:00:14 PDT)
- David A Case (Wed Jul 01 2020 - 08:43:20 PDT)
[AMBER] ABMD with RMSD and RoG: ** NFE-Error ** : Cannot read &colvar namelist!
- Diego Morone (Thu Jul 23 2020 - 08:22:09 PDT)
- Feng Pan (Wed Jul 22 2020 - 18:21:51 PDT)
- Diego Morone (Mon Jul 20 2020 - 06:37:31 PDT)
[AMBER] About time-dependent positional restraints
- David Sáez (Mon Jul 13 2020 - 08:34:33 PDT)
- Christina Bergonzo (Mon Jul 13 2020 - 05:42:04 PDT)
- David Sáez (Fri Jul 10 2020 - 18:40:27 PDT)
- David Sáez (Fri Jul 10 2020 - 18:37:45 PDT)
[AMBER] Accelerated Molecular Dynamics and convergence
- Rosellen, Martin (Wed Jul 08 2020 - 06:58:20 PDT)
[AMBER] Accounting for PBC in Density Plots
- An Ta (Mon Jul 06 2020 - 10:46:41 PDT)
- An Ta (Mon Jul 06 2020 - 10:44:06 PDT)
[AMBER] Adding ions to implicit solvent models
- Bill Ross (Thu Jul 30 2020 - 02:00:18 PDT)
- Conrad F Li (Wed Jul 29 2020 - 18:17:34 PDT)
[AMBER] Amber 20 - Support Multi GPU
- Adriano José Ferruzzi (Thu Jul 23 2020 - 07:11:26 PDT)
- David A Case (Wed Jul 22 2020 - 17:36:38 PDT)
- Adriano José Ferruzzi (Wed Jul 22 2020 - 12:31:29 PDT)
[AMBER] Amber 20 on Google Colab
- Suchetana Gupta (Wed Jul 01 2020 - 22:54:07 PDT)
[AMBER] Amber installation error
- Gustaf Olsson (Wed Jul 01 2020 - 22:46:33 PDT)
- ankita mehta (Wed Jul 01 2020 - 11:10:40 PDT)
[AMBER] Amber nc trajectory file analysis by x3dna
- Daniel Roe (Fri Jul 31 2020 - 08:28:19 PDT)
- Maria Nagan (Fri Jul 31 2020 - 08:22:17 PDT)
- Jenny 148 (Fri Jul 31 2020 - 08:05:56 PDT)
[AMBER] Amber prmtop and inpcrd of complex file with a water molecular cutoff
- David A Case (Thu Jul 09 2020 - 05:36:15 PDT)
- 辛志宏 (Wed Jul 08 2020 - 21:11:32 PDT)
- David A Case (Tue Jul 07 2020 - 10:56:07 PDT)
- 辛志宏 (Tue Jul 07 2020 - 07:54:04 PDT)
[AMBER] Amber SHAKE error when running REMD
- 변진영 (Sun Jul 19 2020 - 23:56:58 PDT)
[AMBER] AMBER trajectory analysis in MINT package
- Jisha B (Thu Jul 23 2020 - 05:40:18 PDT)
[AMBER] amber trajectory nc file to pdb ensemble
- Rodrigo Galindo-Murillo (Fri Jul 31 2020 - 10:54:29 PDT)
- Rodrigo Galindo-Murillo (Fri Jul 31 2020 - 10:53:30 PDT)
- Rodrigo Galindo-Murillo (Fri Jul 31 2020 - 10:04:00 PDT)
- Thomas Cheatham (Fri Jul 31 2020 - 09:45:45 PDT)
- Athena N (Fri Jul 31 2020 - 09:28:26 PDT)
[AMBER] Amber vs Namd energy values are different.
- David A Case (Sun Jul 12 2020 - 18:23:52 PDT)
- Vishal Reddy (Sun Jul 12 2020 - 14:24:50 PDT)
[AMBER] amber website down?
- David A Case (Mon Jul 20 2020 - 18:26:01 PDT)
- Gustaf Olsson (Mon Jul 20 2020 - 14:18:29 PDT)
- Wim R. Cardoen (Mon Jul 20 2020 - 14:07:08 PDT)
[AMBER] amber14 gpu installation failed
- Carlos (Mon Jul 13 2020 - 12:08:47 PDT)
- David A Case (Wed Jul 08 2020 - 05:16:50 PDT)
- Carlos (Tue Jul 07 2020 - 20:42:57 PDT)
[AMBER] Amber20 Compiling problem with b2 and Boost.Regex
- Amanda Buyan (Wed Jul 29 2020 - 16:40:29 PDT)
- Amanda Buyan (Mon Jul 27 2020 - 15:50:37 PDT)
- David A Case (Mon Jul 27 2020 - 06:10:37 PDT)
- Amanda Buyan (Sun Jul 26 2020 - 18:35:07 PDT)
[AMBER] AMBER20 Error: No package metadata was found for pdb4amber
- Huang Tao (Wed Jul 22 2020 - 05:14:41 PDT)
- David A Case (Wed Jul 22 2020 - 04:55:10 PDT)
- Huang Tao (Tue Jul 21 2020 - 19:39:21 PDT)
[AMBER] Amber20 installation
- Daniel Roe (Tue Jul 07 2020 - 05:48:48 PDT)
- Gustaf Olsson (Wed Jul 01 2020 - 23:06:29 PDT)
- Kliuchnikov, Evgenii (Wed Jul 01 2020 - 11:16:21 PDT)
[AMBER] Amber20 Performance on RTX (Turing): known problems, with a patch forthcoming
- Tim Travers (Tue Jul 21 2020 - 09:40:40 PDT)
- David Cerutti (Tue Jul 21 2020 - 09:06:31 PDT)
- Tim Travers (Tue Jul 21 2020 - 08:17:07 PDT)
[AMBER] Amber20: Error in the linking of the pysander
- Gustaf Olsson (Sat Jul 18 2020 - 12:39:37 PDT)
- Wim R. Cardoen (Fri Jul 17 2020 - 13:54:04 PDT)
[AMBER] AMD parameter: protein residue should count ligand or not
- Lod King (Tue Jul 28 2020 - 10:55:43 PDT)
[AMBER] Asking for help: cross linking polymer
- Dr. Anselm Horn (Wed Jul 08 2020 - 00:56:29 PDT)
- SAKO MIRZAIE (Tue Jul 07 2020 - 20:31:21 PDT)
- David A Case (Tue Jul 07 2020 - 18:42:53 PDT)
- SAKO MIRZAIE (Tue Jul 07 2020 - 17:28:10 PDT)
[AMBER] ASMD equil4 not producing output files
- Hantz, Eric R. (Wed Jul 29 2020 - 13:11:18 PDT)
- Adrian Roitberg (Tue Jul 28 2020 - 09:56:35 PDT)
- Hantz, Eric R. (Tue Jul 28 2020 - 06:51:23 PDT)
[AMBER] Atomic Polarizability
- Dr. Anselm Horn (Tue Jul 07 2020 - 14:24:55 PDT)
- David A Case (Tue Jul 07 2020 - 10:58:39 PDT)
- Thakur, Abhishek (Tue Jul 07 2020 - 09:58:48 PDT)
[AMBER] attach pull release method exploration for free energy calculations
- Niel Henriksen (Thu Jul 09 2020 - 16:34:55 PDT)
- Carlos Simmerling (Thu Jul 09 2020 - 13:24:12 PDT)
- Debarati DasGupta (Thu Jul 09 2020 - 12:40:32 PDT)
[AMBER] Barostat and thermostat for membrane protein-ligand simulation
- ANDREA PASQUADIBISCEGLIE (Sat Jul 11 2020 - 00:11:29 PDT)
- Sally Pias (Thu Jul 09 2020 - 18:27:40 PDT)
- Andrea Pasquadibisceglie (Thu Jul 09 2020 - 02:32:05 PDT)
- Sally Pias (Tue Jul 07 2020 - 20:16:56 PDT)
- ANDREA PASQUADIBISCEGLIE (Mon Jul 06 2020 - 08:49:36 PDT)
[AMBER] bulding a monosaccharide with N-acetylation
- Lachele Foley (Wed Jul 01 2020 - 04:55:06 PDT)
[AMBER] calculating methane parameters using RISM
- David A Case (Thu Jul 02 2020 - 05:14:52 PDT)
- angad sharma (Thu Jul 02 2020 - 01:31:03 PDT)
[AMBER] Caping error
- Elvis Martis (Tue Jun 30 2020 - 21:48:01 PDT)
- mohamed marzouk (Tue Jun 30 2020 - 21:38:15 PDT)
[AMBER] carboxylated Lys
- Dr. Anselm Horn (Fri Jul 24 2020 - 07:46:10 PDT)
- Állan Ferrari (Thu Jul 23 2020 - 14:30:32 PDT)
[AMBER] Charges for modified DNA base at the termini?
- Kenneth Huang (Sun Jul 26 2020 - 23:50:39 PDT)
[AMBER] Clarification of Amber Post on Heating Protocol
- David A Case (Tue Jul 14 2020 - 19:11:44 PDT)
- Robert Molt (Tue Jul 14 2020 - 14:46:25 PDT)
[AMBER] Command for making atoms rigid
- Dr. Anselm Horn (Wed Jul 15 2020 - 08:38:56 PDT)
- Pinky Mazumder (Tue Jul 14 2020 - 15:55:40 PDT)
[AMBER] Cores, CPU RAM, GPU RAM
- James Kress (Wed Jul 22 2020 - 15:19:25 PDT)
- James Kress (Fri Jul 17 2020 - 15:28:37 PDT)
[AMBER] CPPTRAJ: Time Correlation Function (TCF)
- Daniel Roe (Mon Jul 20 2020 - 07:54:56 PDT)
- emanuele falbo (Thu Jul 16 2020 - 01:55:57 PDT)
- Souvik (Wed Jul 15 2020 - 09:06:15 PDT)
- emanuele falbo (Wed Jul 15 2020 - 07:29:40 PDT)
[AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol
- Andrea Cavalli (Sat Jul 25 2020 - 07:26:42 PDT)
- mirzo (Sat Jul 25 2020 - 06:36:52 PDT)
- David Cerutti (Sat Jul 25 2020 - 05:40:36 PDT)
- venkat (Sat Jul 25 2020 - 05:02:26 PDT)
[AMBER] Default temperature regulation during production run: Missed to declare ntt option
- David A Case (Wed Jul 15 2020 - 05:08:42 PDT)
- Jorden Cabal (Tue Jul 14 2020 - 20:29:20 PDT)
- Jorden Cabal (Tue Jul 14 2020 - 20:22:14 PDT)
- Carlos Simmerling (Tue Jul 14 2020 - 09:41:37 PDT)
- David A Case (Tue Jul 14 2020 - 09:38:56 PDT)
- Jorden Cabal (Tue Jul 14 2020 - 04:26:02 PDT)
[AMBER] Defining new atoms in AMBER
- David A Case (Fri Jul 03 2020 - 06:41:54 PDT)
- Kolattukudy P. Santo (Thu Jul 02 2020 - 13:18:28 PDT)
- David A Case (Thu Jul 02 2020 - 10:20:11 PDT)
- Kolattukudy P. Santo (Thu Jul 02 2020 - 08:47:00 PDT)
[AMBER] Download link for AmberTools17
- David A Case (Thu Jul 23 2020 - 05:08:06 PDT)
- Casalini Tommaso (Thu Jul 23 2020 - 01:44:20 PDT)
[AMBER] EAMD_BOOST and reweighting of AMD runs
- Rosellen, Martin (Tue Jul 14 2020 - 08:00:51 PDT)
[AMBER] Erro Amber18 GPU
- Renato Araujo (Thu Jul 30 2020 - 18:07:17 PDT)
- David A Case (Thu Jul 30 2020 - 17:29:39 PDT)
- Renato Araujo (Thu Jul 30 2020 - 12:55:42 PDT)
[AMBER] Error building Amber
- Gustaf Olsson (Thu Jul 30 2020 - 09:56:12 PDT)
- David A Case (Thu Jul 30 2020 - 04:54:10 PDT)
- David A Case (Wed Jul 29 2020 - 18:21:11 PDT)
- Walton Smith (Wed Jul 29 2020 - 17:57:21 PDT)
- Walton Smith (Wed Jul 29 2020 - 17:09:55 PDT)
- Gustaf Olsson (Wed Jul 29 2020 - 12:50:32 PDT)
- Walton Smith (Wed Jul 29 2020 - 07:26:19 PDT)
- Walton Smith (Wed Jul 29 2020 - 06:31:31 PDT)
- Gustaf Olsson (Wed Jul 29 2020 - 04:58:32 PDT)
- David A Case (Tue Jul 28 2020 - 20:17:05 PDT)
- David A Case (Tue Jul 28 2020 - 18:57:44 PDT)
- Gustaf Olsson (Tue Jul 28 2020 - 14:35:15 PDT)
- Walton Smith (Tue Jul 28 2020 - 07:03:42 PDT)
- David A Case (Tue Jul 28 2020 - 06:43:52 PDT)
- Gustaf Olsson (Tue Jul 28 2020 - 02:14:47 PDT)
- Walton Smith (Mon Jul 27 2020 - 12:50:54 PDT)
- David A Case (Mon Jul 27 2020 - 10:48:48 PDT)
- David A Case (Mon Jul 27 2020 - 10:15:14 PDT)
- Walton Smith (Mon Jul 27 2020 - 07:04:33 PDT)
[AMBER] error in 3d rism calculation
- Tyler Luchko (Lists) (Mon Jul 20 2020 - 13:25:09 PDT)
- angad sharma (Mon Jul 20 2020 - 10:27:05 PDT)
[AMBER] Error in Gausian file preparation using MCPB.py
- Preeti Pandey (Fri Jul 31 2020 - 14:20:16 PDT)
- gagandeep singh (Fri Jul 24 2020 - 14:55:47 PDT)
[AMBER] Error in incprd file while performing steered molecular dynamics simulation
- Pinky Mazumder (Sat Jul 18 2020 - 00:09:30 PDT)
[AMBER] Error in Installing Amber 20 on GPU
- David A Case (Sat Jul 04 2020 - 05:01:40 PDT)
- Suchetana Gupta (Sat Jul 04 2020 - 02:43:47 PDT)
- David A Case (Fri Jul 03 2020 - 06:37:24 PDT)
- Suchetana Gupta (Thu Jul 02 2020 - 21:51:54 PDT)
- David A Case (Thu Jul 02 2020 - 10:11:24 PDT)
- Gustaf Olsson (Thu Jul 02 2020 - 05:58:40 PDT)
- Gustaf Olsson (Thu Jul 02 2020 - 05:56:29 PDT)
- Suchetana Gupta (Thu Jul 02 2020 - 05:22:52 PDT)
- David A Case (Thu Jul 02 2020 - 05:07:02 PDT)
- Gustaf Olsson (Wed Jul 01 2020 - 23:44:09 PDT)
- Suchetana Gupta (Wed Jul 01 2020 - 22:57:41 PDT)
- Gustaf Olsson (Wed Jul 01 2020 - 22:55:21 PDT)
- Suchetana Gupta (Wed Jul 01 2020 - 11:13:29 PDT)
- Suchetana Gupta (Wed Jul 01 2020 - 10:39:51 PDT)
- David A Case (Wed Jul 01 2020 - 08:45:01 PDT)
- Suchetana Gupta (Tue Jun 30 2020 - 22:28:23 PDT)
[AMBER] Error in partial MINIMIZATION STEP
- Elvis Martis (Sat Jul 04 2020 - 09:53:33 PDT)
- Shreeramesh (Sat Jul 04 2020 - 09:39:01 PDT)
[AMBER] Error in SMD running
- David A Case (Thu Jul 09 2020 - 05:32:53 PDT)
- PRITI ROY (Wed Jul 08 2020 - 19:05:50 PDT)
[AMBER] Error pmemd.cuda amber 20 GPU
- David Cerutti (Thu Jul 09 2020 - 09:44:51 PDT)
- David Cerutti (Thu Jul 09 2020 - 09:30:28 PDT)
- Camila Clemente (Thu Jul 09 2020 - 07:11:29 PDT)
[AMBER] Error while running Antechamber
- David A Case (Fri Jul 03 2020 - 14:12:24 PDT)
- Shreeramesh (Fri Jul 03 2020 - 11:02:15 PDT)
[AMBER] fatal error in 3D RISM calculation
- Tyler Luchko (Wed Jul 22 2020 - 09:32:05 PDT)
- Daniel Roe (Tue Jul 21 2020 - 10:34:04 PDT)
- Leena Aggarwal (Tue Jul 21 2020 - 04:39:21 PDT)
- angad sharma (Tue Jul 21 2020 - 01:57:07 PDT)
[AMBER] fixatomorder
- Thakur, Abhishek (Tue Jul 07 2020 - 10:38:56 PDT)
[AMBER] Force Trajectory Output ABMD
- Jonathon Ferrell (Mon Jul 06 2020 - 09:56:24 PDT)
[AMBER] Forcefield for 5' phosphate in RNA
- David A Case (Thu Jul 09 2020 - 05:42:51 PDT)
- dnlfr1994.gmail.com (Thu Jul 09 2020 - 05:01:36 PDT)
[AMBER] Fortran error in constant pH MD
- Cruzeiro,Vinicius Wilian D (Fri Jul 03 2020 - 08:23:37 PDT)
- Paul Meister (Thu Jul 02 2020 - 09:28:56 PDT)
[AMBER] gamess/MCPB.py tutorial
- Pengfei Li (Mon Jul 20 2020 - 11:14:55 PDT)
- Arthur Glasfeld (Sat Jul 04 2020 - 11:03:32 PDT)
[AMBER] generating methane parameters for rism
- Tyler Luchko (Lists) (Sun Jul 05 2020 - 15:02:14 PDT)
- Leena Aggarwal (Sun Jul 05 2020 - 11:05:20 PDT)
- angad sharma (Sat Jul 04 2020 - 05:22:17 PDT)
[AMBER] generating parameters of methane for RISM
- angad sharma (Sun Jul 05 2020 - 04:25:07 PDT)
[AMBER] GPU compatible with AMBER
- David A Case (Fri Jul 10 2020 - 05:04:24 PDT)
- Isabelle Navizet (Thu Jul 09 2020 - 05:34:06 PDT)
[AMBER] Hoogsteen H-bond
- Jisha B (Wed Jul 01 2020 - 08:18:10 PDT)
[AMBER] How to calculate velocity in steered simulation
- Pinky Mazumder (Fri Jul 24 2020 - 20:58:05 PDT)
[AMBER] how to create nice animated videos to show simulations
- Rodrigo Galindo-Murillo (Wed Jul 01 2020 - 06:57:01 PDT)
- Chetna Tyagi (Wed Jul 01 2020 - 04:54:35 PDT)
- Raman Preet Singh (Wed Jul 01 2020 - 04:56:06 PDT)
- Carlos Simmerling (Wed Jul 01 2020 - 03:40:47 PDT)
- Elvis Martis (Wed Jul 01 2020 - 03:39:08 PDT)
- Suchetana Gupta (Wed Jul 01 2020 - 03:34:48 PDT)
- Chetna Tyagi (Wed Jul 01 2020 - 03:31:34 PDT)
[AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450)
- Pengfei Li (Mon Jul 20 2020 - 10:53:34 PDT)
- Thirakorn Mokkawes (Thu Jul 09 2020 - 03:59:16 PDT)
[AMBER] How to install Amber20 with pmemd.amoeba?
- Kliuchnikov, Evgenii (Sat Jul 25 2020 - 21:46:59 PDT)
- David A Case (Sat Jul 25 2020 - 17:36:21 PDT)
- Kliuchnikov, Evgenii (Sat Jul 25 2020 - 12:29:56 PDT)
[AMBER] How to make pass extra argument "--bind-to none" to mpirun for ORCA when running QMMM from sander?
- Goetz, Andreas (Fri Jul 31 2020 - 03:12:22 PDT)
- Francesca Lønstad Bleken (Fri Jul 31 2020 - 02:42:32 PDT)
[AMBER] How to set salt concentration
- Nada Afiva (Sat Jul 04 2020 - 11:42:11 PDT)
- Matias Machado (Sat Jul 04 2020 - 11:17:07 PDT)
- Nada Afiva (Fri Jul 03 2020 - 12:58:26 PDT)
- Clorice Reinhardt (Fri Jul 03 2020 - 12:10:18 PDT)
- Nada Afiva (Fri Jul 03 2020 - 12:00:43 PDT)
- Dr. Anselm Horn (Fri Jul 03 2020 - 08:59:08 PDT)
- David A Case (Fri Jul 03 2020 - 06:44:48 PDT)
- Nada Afiva (Fri Jul 03 2020 - 02:49:24 PDT)
- Matias Machado (Thu Jul 02 2020 - 06:17:27 PDT)
- Nada Afiva (Thu Jul 02 2020 - 01:34:28 PDT)
- Aashish Bhatt (Wed Jul 01 2020 - 21:15:29 PDT)
- Suchetana Gupta (Wed Jul 01 2020 - 20:59:37 PDT)
- Gerardo Zerbetto De Palma (Wed Jul 01 2020 - 20:57:37 PDT)
- Nada Afiva (Wed Jul 01 2020 - 20:54:44 PDT)
[AMBER] how to use triclinic box shape
- Nada Afiva (Thu Jul 02 2020 - 17:38:11 PDT)
- David Cerutti (Thu Jul 02 2020 - 05:48:10 PDT)
- David A Case (Thu Jul 02 2020 - 05:35:14 PDT)
- Nada Afiva (Thu Jul 02 2020 - 01:47:46 PDT)
[AMBER] Install broke and compilation fails
- Gustaf Olsson (Tue Jul 07 2020 - 14:12:51 PDT)
- Gustaf Olsson (Tue Jul 07 2020 - 06:58:10 PDT)
[AMBER] Installing Amber20 with cuda9
- Schröder, David Christopher (Thu Jul 02 2020 - 10:22:44 PDT)
- Schröder, David Christopher (Thu Jul 02 2020 - 08:11:36 PDT)
- Schröder, David Christopher (Thu Jul 02 2020 - 06:58:38 PDT)
[AMBER] Interaction of cellulose-hemicellulose
- Lachele Foley (Wed Jul 29 2020 - 00:17:07 PDT)
- Pinky Mazumder (Tue Jul 28 2020 - 08:48:49 PDT)
[AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..."
- Daniel Roe (Fri Jul 31 2020 - 05:52:47 PDT)
- 辛志宏 (Thu Jul 30 2020 - 20:46:21 PDT)
- David A Case (Tue Jul 28 2020 - 06:59:16 PDT)
- 辛志宏 (Mon Jul 27 2020 - 18:48:41 PDT)
- David A Case (Sun Jul 26 2020 - 17:44:15 PDT)
- Elvis Martis (Sun Jul 26 2020 - 05:43:46 PDT)
- 辛志宏 (Sun Jul 26 2020 - 04:59:21 PDT)
[AMBER] Issue heating system in equilibration step
- Samuel A. Ratliff (Fri Jul 31 2020 - 13:14:09 PDT)
- Carlos Simmerling (Fri Jul 31 2020 - 12:19:23 PDT)
- Samuel A. Ratliff (Fri Jul 31 2020 - 12:16:01 PDT)
- Carlos Simmerling (Fri Jul 31 2020 - 12:10:07 PDT)
- Samuel A. Ratliff (Fri Jul 31 2020 - 09:58:44 PDT)
- Samuel A. Ratliff (Tue Jul 28 2020 - 10:05:00 PDT)
[AMBER] Issue while installing Amber20
- David A Case (Sat Jul 25 2020 - 05:37:24 PDT)
- Alejandro Cagnoni (Fri Jul 24 2020 - 13:44:29 PDT)
[AMBER] libnetcdf.so.7 needed by /usr/local/src/amber18/lib/libcpptraj.so, not found when upgrading AT18 to AT19
- Markowska (Mon Jul 20 2020 - 12:59:05 PDT)
- David A Case (Mon Jul 20 2020 - 10:05:00 PDT)
- Markowska (Mon Jul 20 2020 - 07:44:13 PDT)
- Daniel Roe (Mon Jul 20 2020 - 06:59:36 PDT)
- Markowska (Mon Jul 20 2020 - 06:56:26 PDT)
[AMBER] LJ potential for OPC water model
- David A Case (Wed Jul 08 2020 - 09:30:42 PDT)
- Loki (Fri Jul 03 2020 - 09:28:55 PDT)
- Loki (Fri Jul 03 2020 - 09:01:58 PDT)
- Matias Machado (Fri Jul 03 2020 - 09:35:32 PDT)
- Loki (Fri Jul 03 2020 - 05:07:04 PDT)
[AMBER] Mask behavior vs distance measurement?
- Kenneth Huang (Fri Jul 10 2020 - 10:31:28 PDT)
- Daniel Roe (Thu Jul 09 2020 - 19:06:18 PDT)
- Kenneth Huang (Thu Jul 09 2020 - 17:04:10 PDT)
[AMBER] matching paramters of methane
- David A Case (Thu Jul 16 2020 - 09:36:28 PDT)
- angad sharma (Thu Jul 16 2020 - 08:27:44 PDT)
[AMBER] Maximum system size
- David A Case (Sun Jul 26 2020 - 17:57:50 PDT)
- Jack Shepherd (Sat Jul 25 2020 - 17:57:01 PDT)
[AMBER] MBAR with Amber 18
- David A Case (Wed Jul 08 2020 - 05:19:59 PDT)
- Ulf Ryde (Wed Jul 01 2020 - 03:25:00 PDT)
[AMBER] Missing bond parameters after MCPB.py
- Pengfei Li (Mon Jul 20 2020 - 12:17:50 PDT)
[AMBER] MMGBSA and MMPBSA error (CalcError: failed with prmtop file complex.prmtop!)
- Nada Afiva (Mon Jul 06 2020 - 14:18:44 PDT)
- Ray Luo (Sun Jul 05 2020 - 11:31:34 PDT)
- Nada Afiva (Sat Jul 04 2020 - 20:17:36 PDT)
- Nada Afiva (Sat Jul 04 2020 - 14:58:44 PDT)
[AMBER] mmpbsa error
- MYRIAN TORRES RICO (Mon Jul 20 2020 - 00:45:27 PDT)
- Kshatresh Dutta Dubey (Sat Jul 18 2020 - 03:19:02 PDT)
- MYRIAN TORRES RICO (Fri Jul 17 2020 - 04:31:13 PDT)
[AMBER] Modified cysteine parameters
- Dr. Anselm Horn (Mon Jul 20 2020 - 01:46:00 PDT)
- David A Case (Sun Jul 19 2020 - 04:43:13 PDT)
- krishnendu sinha (Sun Jul 19 2020 - 00:49:40 PDT)
[AMBER] nmropt vs infe
- Feng Pan (Thu Jul 09 2020 - 22:01:21 PDT)
[AMBER] ntx and irest
- David A Case (Thu Jul 02 2020 - 04:55:35 PDT)
[AMBER] OT: Job Posting
- Lachele Foley (Thu Jul 16 2020 - 16:40:13 PDT)
[AMBER] Problem compiling Amber20 - undefined reference to 'plumedmain_create'
- David A Case (Thu Jul 23 2020 - 05:05:39 PDT)
- Amanda Buyan (Wed Jul 22 2020 - 23:07:39 PDT)
[AMBER] Problem installing AmberMD with MPI support on Cray XC40
- Jakub Jalowiec (Mon Jul 27 2020 - 15:27:13 PDT)
[AMBER] Problem of Steered MD Simulation for unfolding of RNA
- Souvik (Thu Jul 02 2020 - 09:34:22 PDT)
- Leena Aggarwal (Thu Jul 02 2020 - 07:43:04 PDT)
- Vishal Singh (Thu Jul 02 2020 - 04:46:22 PDT)
[AMBER] problem with pdb4amber
- Hai Nguyen (Wed Jul 22 2020 - 09:13:40 PDT)
- David A Case (Wed Jul 22 2020 - 07:59:02 PDT)
[AMBER] Problem with running Python script in AMBER environment.
- David A Case (Thu Jul 09 2020 - 17:32:24 PDT)
- Hai Nguyen (Thu Jul 09 2020 - 14:36:02 PDT)
- Vishal Singh (Wed Jul 08 2020 - 23:51:52 PDT)
[AMBER] Problems deriving charges with RESP
- Lucas Bandeira (Mon Jul 27 2020 - 17:23:52 PDT)
[AMBER] Problems generating charges with RESP
- Lucas Bandeira (Mon Jul 27 2020 - 13:39:01 PDT)
[AMBER] Problems with MC barostat
- Yessica (Sun Jul 12 2020 - 16:53:08 PDT)
[AMBER] Question about SMD using polymer
- Carlos Simmerling (Mon Jul 13 2020 - 07:14:24 PDT)
- Pinky Mazumder (Fri Jul 10 2020 - 13:24:35 PDT)
- Carlos Simmerling (Mon Jul 06 2020 - 08:05:08 PDT)
- Pinky Mazumder (Mon Jul 06 2020 - 08:01:38 PDT)
[AMBER] Questions on random seed
- Nada Afiva (Thu Jul 16 2020 - 16:20:23 PDT)
- David A Case (Thu Jul 16 2020 - 05:25:17 PDT)
- Nada Afiva (Wed Jul 15 2020 - 20:35:37 PDT)
[AMBER] Refitting charges with MCPB destabilizes the active site
- Casalini Tommaso (Wed Jul 29 2020 - 04:23:44 PDT)
[AMBER] Reg. MMGBSA Calculations
- DHEERAJ CHITARA (Sat Jul 11 2020 - 11:26:52 PDT)
[AMBER] Reonstructing frames from PCA projection
- Daniel Roe (Mon Jul 20 2020 - 07:43:58 PDT)
- Michael F. Bruist (Fri Jul 17 2020 - 08:24:03 PDT)
[AMBER] REPEATED LINMIN FAILURE
- James Kress (Fri Jul 10 2020 - 15:05:27 PDT)
- Sharif Nada (Fri Jul 10 2020 - 14:39:32 PDT)
- Elvis Martis (Fri Jul 10 2020 - 04:27:55 PDT)
- Akshay Prabhakant (Fri Jul 10 2020 - 04:20:12 PDT)
[AMBER] running QM/MM calculations
- David A Case (Wed Jul 29 2020 - 04:40:51 PDT)
[AMBER] Seg fault with pmemd.cuda.MPI using plumed
- Jacob Remington (Sat Jul 11 2020 - 12:16:54 PDT)
[AMBER] Several tutorial not found
- Michael F. Bruist (Mon Jul 20 2020 - 09:22:13 PDT)
- David A Case (Fri Jul 17 2020 - 09:53:41 PDT)
- David Cerutti (Fri Jul 17 2020 - 08:59:27 PDT)
- Michael F. Bruist (Fri Jul 17 2020 - 08:19:56 PDT)
[AMBER] Size of Solvent Box
- David A Case (Wed Jul 22 2020 - 12:16:56 PDT)
- DHEERAJ CHITARA (Wed Jul 22 2020 - 11:14:20 PDT)
[AMBER] smooth soft core potentials
- David A Case (Thu Jul 23 2020 - 17:49:30 PDT)
- Debarati DasGupta (Thu Jul 23 2020 - 13:26:32 PDT)
[AMBER] Solvent excluded volume
- Shilpa Gupta (Sat Jul 04 2020 - 03:21:31 PDT)
[AMBER] SPLIT method doubt
- Camila Mara Clemente (Wed Jul 15 2020 - 12:24:44 PDT)
- Matias Machado (Wed Jul 15 2020 - 10:22:14 PDT)
- Camila Clemente (Wed Jul 15 2020 - 08:45:52 PDT)
- Dr. Anselm Horn (Wed Jul 15 2020 - 08:30:37 PDT)
- Camila Clemente (Tue Jul 14 2020 - 15:01:49 PDT)
[AMBER] steered MD with restraints on a selection
- Pinky Mazumder (Fri Jul 24 2020 - 19:51:46 PDT)
[AMBER] Steered molecular dynamics Simulation
- Pinky Mazumder (Sat Jul 25 2020 - 21:16:28 PDT)
- Vishal Singh (Fri Jul 24 2020 - 21:39:40 PDT)
- Pinky Mazumder (Fri Jul 24 2020 - 19:47:39 PDT)
[AMBER] Strip water job is killed after 10-40% completion
- Daniel Roe (Tue Jul 07 2020 - 07:11:16 PDT)
- Dr. Anselm Horn (Tue Jul 07 2020 - 07:08:38 PDT)
- Shreeramesh (Mon Jul 06 2020 - 09:23:26 PDT)
[AMBER] Structure Artifact After Autoimage
- Mikhael, Simoun (Fri Jul 31 2020 - 14:01:52 PDT)
[AMBER] The most update force fields for DNA and RNA
- Nada Afiva (Fri Jul 03 2020 - 18:10:18 PDT)
- David A Case (Fri Jul 03 2020 - 17:52:45 PDT)
- Nada Afiva (Fri Jul 03 2020 - 14:30:27 PDT)
[AMBER] tinker_to_amber force fields
- David A Case (Wed Jul 22 2020 - 17:28:48 PDT)
- David A Case (Wed Jul 22 2020 - 12:24:37 PDT)
- Kliuchnikov, Evgenii (Wed Jul 22 2020 - 12:10:14 PDT)
- Kliuchnikov, Evgenii (Wed Jul 22 2020 - 11:37:33 PDT)
[AMBER] Tinker_to_amber problem
- Kliuchnikov, Evgenii (Fri Jul 17 2020 - 17:59:00 PDT)
- David A Case (Fri Jul 17 2020 - 17:54:54 PDT)
- Kliuchnikov, Evgenii (Fri Jul 17 2020 - 12:50:01 PDT)
[AMBER] tleap does not recognize nonstandard residue from lib file
- JoAnne Babula (Wed Jul 22 2020 - 13:49:49 PDT)
- JoAnne Babula (Wed Jul 22 2020 - 12:43:59 PDT)
[AMBER] Tracking lifetime distance by closest of specific water IDs?
- Kenneth Huang (Tue Jul 28 2020 - 07:28:51 PDT)
[AMBER] Undefined angle parameter and torsion terms in Amber18
- Razil Tahir (Wed Jul 22 2020 - 08:13:08 PDT)
[AMBER] Undefined angle parameter and torsion terms in Antechamber
- Razil Tahir (Tue Jul 21 2020 - 21:03:20 PDT)
[AMBER] Units from quasiharmonic analysis of Principal Components
- German P. Barletta (Mon Jul 20 2020 - 12:25:23 PDT)
- David A Case (Sun Jul 19 2020 - 17:57:58 PDT)
- German P. Barletta (Sun Jul 19 2020 - 09:48:38 PDT)
[AMBER] Usage of the Density Peaks Algorithm.
- Gilberto Pereira (Thu Jul 02 2020 - 08:34:50 PDT)
[AMBER] Using multiple distance restraints or creating exclusion sphere
- Amanda Buyan (Sun Jul 12 2020 - 18:20:16 PDT)
[AMBER] Using ntt=10 in PMEMD
- Sharif Nada (Mon Jul 06 2020 - 03:29:40 PDT)
[AMBER] Using Orca to develop RESP Charges
- David Cerutti (Fri Jul 24 2020 - 11:08:22 PDT)
- Lucas Bandeira (Thu Jul 23 2020 - 13:37:56 PDT)
[AMBER] What would you like to see in visualization of chemical data?
- Robert Molt (Mon Jul 20 2020 - 04:31:50 PDT)
- Jan Mičan (Mon Jul 20 2020 - 03:48:06 PDT)
[AMBER] XMGRACE giving error
- Elvis Martis (Mon Jul 13 2020 - 22:53:37 PDT)
- Sumra Abbasi (Mon Jul 13 2020 - 22:33:20 PDT)
- Tru Huynh (Mon Jul 13 2020 - 04:27:48 PDT)
- Elvis Martis (Mon Jul 13 2020 - 04:07:40 PDT)
- Sumra Abbasi (Mon Jul 13 2020 - 03:37:50 PDT)
- Elvis Martis (Mon Jul 13 2020 - 03:19:43 PDT)
- Sumra Abbasi (Mon Jul 13 2020 - 03:07:36 PDT)
Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." (???)
- 辛志宏 (Wed Jul 29 2020 - 02:10:13 PDT)
restraint 10 kcal/mol
- Carlos Simmerling (Mon Jul 20 2020 - 07:23:54 PDT)
- Debarati DasGupta (Wed Jul 15 2020 - 14:50:24 PDT)
- Debarati DasGupta (Mon Jul 06 2020 - 15:57:38 PDT)
- Carlos Simmerling (Mon Jul 06 2020 - 08:32:00 PDT)
- Debarati DasGupta (Mon Jul 06 2020 - 08:16:07 PDT)

Amber Archive Jul 2020 by subject