Amber Archive Oct 2018: by subject

[AMBER] .gesp file is not generated for Antechamber
- M RCC (Wed Oct 10 2018 - 09:43:37 PDT)
[AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16
- Charles Lin (Mon Oct 08 2018 - 07:19:11 PDT)
- Paul Westphälinger (Thu Oct 04 2018 - 02:34:30 PDT)
- Paul Westphälinger (Tue Oct 02 2018 - 02:33:18 PDT)
[AMBER] acpype_error
- Antonio Amber Carlesso (Fri Oct 05 2018 - 14:25:39 PDT)
- Alan (Fri Oct 05 2018 - 13:25:38 PDT)
- Antonio Amber Carlesso (Fri Oct 05 2018 - 12:15:38 PDT)
- dhaval patel (Fri Oct 05 2018 - 11:49:08 PDT)
- Antonio Amber Carlesso (Fri Oct 05 2018 - 11:11:06 PDT)
[AMBER] add12_6_4 Parmed error
- Nikolay N. Kuzmich (Thu Oct 04 2018 - 04:26:08 PDT)
- Pengfei Li (Tue Oct 02 2018 - 12:03:46 PDT)
- Nikolay N. Kuzmich (Tue Oct 02 2018 - 10:06:28 PDT)
[AMBER] Alternative way to do targeted MD
- Feng Pan (Sun Oct 28 2018 - 12:41:07 PDT)
- Xiaoling Leng (Fri Oct 26 2018 - 13:49:09 PDT)
- Feng Pan (Thu Oct 25 2018 - 13:47:46 PDT)
- Xiaoling Leng (Thu Oct 25 2018 - 12:43:42 PDT)
- Feng Pan (Wed Oct 24 2018 - 11:01:35 PDT)
- Xiaoling Leng (Wed Oct 24 2018 - 07:55:15 PDT)
- Feng Pan (Thu Oct 18 2018 - 15:17:34 PDT)
- Xiaoling Leng (Thu Oct 18 2018 - 11:53:33 PDT)
[AMBER] AMBER 18 INSTALLATION ON CLUSTER - ERROR
- David A Case (Thu Oct 11 2018 - 06:30:27 PDT)
- Midhun K Madhu (Wed Oct 10 2018 - 22:32:49 PDT)
[AMBER] Amber 18 installation problem
- MR. RABINDRANATH PAUL (Thu Oct 04 2018 - 22:02:46 PDT)
- Bill Ross (Thu Oct 04 2018 - 10:35:25 PDT)
- Hai Nguyen (Thu Oct 04 2018 - 08:42:47 PDT)
- MR. RABINDRANATH PAUL (Thu Oct 04 2018 - 08:41:08 PDT)
- Daniel Roe (Thu Oct 04 2018 - 05:45:34 PDT)
- MR. RABINDRANATH PAUL (Thu Oct 04 2018 - 01:25:10 PDT)
- Bill Ross (Thu Oct 04 2018 - 01:08:05 PDT)
- MR. RABINDRANATH PAUL (Thu Oct 04 2018 - 00:44:25 PDT)
[AMBER] AMBER and plumed
- Pierre GIRARD (Wed Oct 10 2018 - 14:03:31 PDT)
- Qinghua Liao (Wed Oct 10 2018 - 13:42:21 PDT)
- Pierre GIRARD (Wed Oct 10 2018 - 13:35:26 PDT)
- Qinghua Liao (Wed Oct 10 2018 - 12:23:24 PDT)
- Pierre GIRARD (Wed Oct 10 2018 - 11:05:05 PDT)
[AMBER] AMBER Digest, Vol 2436, Issue 1
- Midhun K Madhu (Fri Oct 12 2018 - 01:36:25 PDT)
[AMBER] Amber Error (an illegal memory access)
- Avirup Ghosh (Tue Oct 30 2018 - 21:22:45 PDT)
[AMBER] Amber force field for non-natural amino acids
- Carlos Simmerling (Tue Oct 23 2018 - 15:06:35 PDT)
- Thomas Fox (Tue Oct 23 2018 - 14:53:01 PDT)
- Carlos Simmerling (Tue Oct 23 2018 - 14:44:15 PDT)
- Thomas Fox (Tue Oct 23 2018 - 14:24:20 PDT)
- Mijiddorj B (Mon Oct 22 2018 - 06:46:19 PDT)
- Carlos Simmerling (Sat Oct 20 2018 - 03:11:19 PDT)
- Mijiddorj B (Fri Oct 19 2018 - 21:53:42 PDT)
[AMBER] Amber Install on Mojave
- David A Case (Fri Oct 12 2018 - 05:13:45 PDT)
[AMBER] Amber Install on Mojave (ld: library not found for -lmc) Fix
- Andrew Schaub (Mon Oct 08 2018 - 09:39:51 PDT)
- Andrew Schaub (Mon Oct 08 2018 - 09:33:00 PDT)
- Gustaf Olsson (Mon Oct 08 2018 - 07:54:11 PDT)
- Andrew Schaub (Mon Oct 08 2018 - 06:09:28 PDT)
- Andrew Schaub (Sun Oct 07 2018 - 17:02:03 PDT)
[AMBER] Amber to gromacs topology
- David A Case (Thu Oct 04 2018 - 08:27:43 PDT)
- Saikat Pal (Thu Oct 04 2018 - 08:20:09 PDT)
- Matias Machado (Thu Oct 04 2018 - 08:16:21 PDT)
- Saikat Pal (Thu Oct 04 2018 - 07:34:34 PDT)
- Matias Machado (Thu Oct 04 2018 - 07:19:12 PDT)
- Saikat Pal (Thu Oct 04 2018 - 04:37:46 PDT)
[AMBER] Amber workshop in Europe?
- Albert (Wed Oct 17 2018 - 23:31:44 PDT)
[AMBER] AMBER18 compilation using intel compiler
- pavel.banas.upol.cz (Wed Oct 03 2018 - 08:35:38 PDT)
- David A Case (Wed Oct 03 2018 - 07:03:17 PDT)
- pavel.banas.upol.cz (Wed Oct 03 2018 - 06:13:47 PDT)
[AMBER] amber18 installation problem
- David A Case (Wed Oct 31 2018 - 05:06:00 PDT)
- David A Case (Wed Oct 31 2018 - 05:04:17 PDT)
- Mary Dutta (Wed Oct 31 2018 - 03:48:13 PDT)
[AMBER] AMBER18: user-defined reaction coordinate in umbrella sampling
- 李耀 (Tue Oct 30 2018 - 07:06:20 PDT)
[AMBER] Antechamber on unknown residue
- David Case (Mon Oct 08 2018 - 06:29:41 PDT)
- Keiran Corbett (Mon Oct 08 2018 - 03:44:25 PDT)
[AMBER] Ca ion bond distances restraints with chelator ?
- David A Case (Thu Oct 25 2018 - 07:26:03 PDT)
- Michael Shokhen (Thu Oct 25 2018 - 05:25:35 PDT)
[AMBER] calculation of free binding energy when a residue is mutated to residues other than alanine?
- ali akbar (Thu Oct 11 2018 - 05:08:27 PDT)
[AMBER] Cationic dummy Zinc atom in accelerated molecular dynamics
- M RCC (Wed Oct 10 2018 - 06:06:18 PDT)
[AMBER] Commented AmberTools functions
- Ruben Ramos Horta (Thu Oct 11 2018 - 10:09:21 PDT)
[AMBER] constant pH pmemd.cuda error
- Cruzeiro,Vinicius Wilian D (Mon Oct 08 2018 - 14:20:08 PDT)
- andreas.tosstorff.cup.uni-muenchen.de (Mon Oct 08 2018 - 14:03:26 PDT)
- Cruzeiro,Vinicius Wilian D (Mon Oct 08 2018 - 13:34:09 PDT)
- andreas.tosstorff.cup.uni-muenchen.de (Mon Oct 08 2018 - 13:20:30 PDT)
[AMBER] Constrained QM.MM minimization
- Vito GENNA (Fri Oct 19 2018 - 13:37:02 PDT)
- David Case (Fri Oct 19 2018 - 11:50:53 PDT)
- Vito GENNA (Fri Oct 19 2018 - 09:12:31 PDT)
- Vito GENNA (Fri Oct 19 2018 - 08:20:41 PDT)
- Timothy Schutt (Fri Oct 19 2018 - 08:01:28 PDT)
- Timothy Schutt (Fri Oct 19 2018 - 07:52:17 PDT)
- Vito GENNA (Fri Oct 19 2018 - 07:28:37 PDT)
- Zuo, Zhicheng (Fri Oct 19 2018 - 07:23:00 PDT)
- Vito GENNA (Fri Oct 19 2018 - 06:29:12 PDT)
[AMBER] Cpptraj bond deforming
- Aashish Bhatt (Wed Oct 03 2018 - 22:56:42 PDT)
- Daniel Roe (Wed Oct 03 2018 - 10:59:53 PDT)
- Aashish Bhatt (Wed Oct 03 2018 - 10:41:53 PDT)
- Daniel Roe (Wed Oct 03 2018 - 10:16:34 PDT)
- Aashish Bhatt (Wed Oct 03 2018 - 10:10:15 PDT)
- Daniel Roe (Wed Oct 03 2018 - 09:43:33 PDT)
- Aashish Bhatt (Wed Oct 03 2018 - 07:52:42 PDT)
[AMBER] CUDA 10.0 vs CUDA 9.2 for Amber18&1080Ti GTX - any gain in performance?
- Ross Walker (Wed Oct 31 2018 - 13:12:54 PDT)
- Nikolay N. Kuzmich (Wed Oct 31 2018 - 07:31:56 PDT)
[AMBER] does surf command use for stripped trajectory?
- Daniel Roe (Wed Oct 17 2018 - 07:27:56 PDT)
- g.bakrani.sci.ui.ac.ir (Wed Oct 17 2018 - 04:30:56 PDT)
[AMBER] Effective born radii calculations - No correct statistics returned at the end of the mdout file
- Eric Lang (Wed Oct 24 2018 - 02:00:08 PDT)
- David A Case (Tue Oct 23 2018 - 09:48:40 PDT)
- Eric Lang (Tue Oct 23 2018 - 08:28:16 PDT)
[AMBER] error in distance restraint input file
- Michael Shokhen (Fri Oct 26 2018 - 05:34:53 PDT)
- David A Case (Fri Oct 26 2018 - 05:12:09 PDT)
- Michael Shokhen (Fri Oct 26 2018 - 03:31:12 PDT)
[AMBER] error in Resp
- fateme haghighi (Wed Oct 17 2018 - 05:33:22 PDT)
[AMBER] error in RESP calculation
- David A Case (Thu Oct 11 2018 - 06:35:22 PDT)
- fateme haghighi (Thu Oct 11 2018 - 00:36:23 PDT)
[AMBER] Error in Running tLEaP for Protein File
- David A Case (Mon Oct 22 2018 - 11:55:09 PDT)
- Amartya Pradhan (Mon Oct 22 2018 - 11:30:00 PDT)
[AMBER] Errors when installing with MPI
- David Case (Mon Oct 08 2018 - 18:09:39 PDT)
- Felipe Franco Gonzalez (Mon Oct 08 2018 - 13:49:03 PDT)
[AMBER] Fondaparinux Amber Force Field
- Marcelo Andrade Chagas (Sun Oct 14 2018 - 07:31:42 PDT)
[AMBER] Fortran runtime error: Bad value during integer read
- Carlos Simmerling (Wed Oct 31 2018 - 04:42:00 PDT)
- Thomas Evangelidis (Wed Oct 31 2018 - 04:36:17 PDT)
- Carlos Simmerling (Wed Oct 31 2018 - 04:22:24 PDT)
- Thomas Evangelidis (Wed Oct 31 2018 - 04:14:06 PDT)
- David Case (Tue Oct 30 2018 - 18:45:37 PDT)
- Thomas Evangelidis (Tue Oct 30 2018 - 15:55:14 PDT)
[AMBER] Full: Parameters for atom CE in lj_1264_pol.dat
- Nikolay N. Kuzmich (Fri Oct 12 2018 - 08:42:16 PDT)
- Pengfei Li (Tue Oct 09 2018 - 16:59:30 PDT)
- Nikolay N. Kuzmich (Mon Oct 08 2018 - 02:29:17 PDT)
[AMBER] Fwd: Lipid Order Parameters
- somdev pahari (Wed Oct 10 2018 - 08:39:36 PDT)
[AMBER] Fwd: The results of your email commands
- Charu Sharma (JRF) (Mon Oct 08 2018 - 21:35:22 PDT)
[AMBER] GAMD not running in CPU cluster
- Midhun K Madhu (Mon Oct 15 2018 - 04:19:18 PDT)
[AMBER] get energy of some residues of the molecule
- Johannes Kalliauer (Wed Oct 03 2018 - 07:13:44 PDT)
[AMBER] GLYCAM Amber Force Field to Fondaparinux...?
- Lachele Foley (Tue Oct 16 2018 - 07:11:20 PDT)
- Marcelo Andrade Chagas (Mon Oct 15 2018 - 13:24:14 PDT)
[AMBER] GPU memory usage with center-of-mass restratints
- David Case (Mon Oct 08 2018 - 06:08:03 PDT)
[AMBER] How to run the test in HPC cluster and GPU
- Charles Lin (Fri Oct 05 2018 - 08:14:49 PDT)
- Saikat Pal (Thu Oct 04 2018 - 04:15:53 PDT)
[AMBER] How to use ff99SB-ILDN in Amber16
- Vito GENNA (Fri Oct 12 2018 - 15:02:02 PDT)
- Qinghua Liao (Fri Oct 12 2018 - 14:29:28 PDT)
- Yang, Tianyi (Fri Oct 12 2018 - 14:26:13 PDT)
[AMBER] hydrogen bond analysis
- Qinghua Liao (Wed Oct 10 2018 - 08:40:03 PDT)
- Daniel Roe (Wed Oct 10 2018 - 05:23:13 PDT)
- Qinghua Liao (Wed Oct 10 2018 - 02:51:39 PDT)
- Zuo, Zhicheng (Tue Oct 09 2018 - 17:15:22 PDT)
- Qinghua Liao (Tue Oct 09 2018 - 16:03:44 PDT)
[AMBER] Installation issues on Mac OSX 10.14
- Matthew Fisher (Mon Oct 15 2018 - 07:49:28 PDT)
- Gustaf Olsson (Thu Oct 11 2018 - 23:17:04 PDT)
- David Case (Thu Oct 11 2018 - 19:15:10 PDT)
- Matthew Fisher (Thu Oct 11 2018 - 10:02:18 PDT)
[AMBER] Interplane angles using vector and vectormath in cpptraj
- Daniel Roe (Tue Oct 30 2018 - 05:53:35 PDT)
- Wesley Michael Botello-Smith (Mon Oct 29 2018 - 17:45:48 PDT)
- Matthew Turner (Mon Oct 29 2018 - 15:35:09 PDT)
[AMBER] ligand_preparation_general_rule
- Antonio Amber Carlesso (Fri Oct 05 2018 - 13:02:33 PDT)
- David A Case (Thu Oct 04 2018 - 05:43:46 PDT)
- Antonio Amber Carlesso (Wed Oct 03 2018 - 07:07:05 PDT)
- David Case (Wed Oct 03 2018 - 04:50:35 PDT)
- David Case (Wed Oct 03 2018 - 04:40:13 PDT)
- Antonio Amber Carlesso (Wed Oct 03 2018 - 02:51:37 PDT)
- David Case (Tue Oct 02 2018 - 04:37:58 PDT)
- Bill Ross (Tue Oct 02 2018 - 00:52:14 PDT)
- Antonio Amber Carlesso (Tue Oct 02 2018 - 00:31:14 PDT)
[AMBER] Lipid Order Parameters
- Daniel Roe (Wed Oct 10 2018 - 09:07:20 PDT)
- somdev pahari (Sat Oct 06 2018 - 08:03:48 PDT)
[AMBER] Material simulation using Amber and Interface FF
- Pengfei Li (Fri Oct 26 2018 - 14:48:46 PDT)
- Sundar (Tue Oct 23 2018 - 14:42:51 PDT)
[AMBER] MD_Box_size_and_counterions_counting_general_rule
- Matias Machado (Wed Oct 31 2018 - 07:04:29 PDT)
- David A Case (Thu Oct 25 2018 - 07:18:59 PDT)
- Antonio Amber Carlesso (Thu Oct 25 2018 - 04:54:55 PDT)
[AMBER] Measuring Membrane Curvature
- somdev pahari (Thu Oct 25 2018 - 11:31:05 PDT)
[AMBER] more on building Amber18 on Mojave
- Gustaf Olsson (Thu Oct 18 2018 - 22:56:29 PDT)
- Daniel Roe (Thu Oct 18 2018 - 16:07:57 PDT)
- Gustaf Olsson (Thu Oct 18 2018 - 00:00:14 PDT)
- David A Case (Wed Oct 17 2018 - 10:25:29 PDT)
- Gustaf Olsson (Tue Oct 16 2018 - 03:47:06 PDT)
- David A Case (Mon Oct 15 2018 - 07:39:27 PDT)
[AMBER] Na+ ion got stuck at one C-terminal end
- Rakesh Srivastava (Fri Oct 26 2018 - 21:30:09 PDT)
- Pengfei Li (Fri Oct 26 2018 - 15:03:42 PDT)
- Rakesh Srivastava (Thu Oct 25 2018 - 23:25:13 PDT)
[AMBER] NFE _Lib error
- Feng Pan (Wed Oct 03 2018 - 07:02:12 PDT)
- Hugo Macdermott-Opeskin (Tue Oct 02 2018 - 17:19:16 PDT)
[AMBER] non-bonded params
- Matias Machado (Fri Oct 26 2018 - 11:23:36 PDT)
- hosein geraili (Fri Oct 26 2018 - 09:30:36 PDT)
[AMBER] Number of inter-conversions between minima on a FEL
- Daniel Roe (Wed Oct 03 2018 - 08:03:06 PDT)
- Chetna Tyagi (Wed Oct 03 2018 - 04:59:35 PDT)
[AMBER] number of reaction coordinate in a ASMD run
- sangita kachhap (Fri Oct 05 2018 - 06:14:38 PDT)
[AMBER] Parametarization error
- senal dinuka (Thu Oct 18 2018 - 20:47:59 PDT)
- David Case (Thu Oct 18 2018 - 11:09:55 PDT)
- Bill Ross (Thu Oct 18 2018 - 02:19:37 PDT)
- senal dinuka (Thu Oct 18 2018 - 00:58:25 PDT)
- Bill Ross (Thu Oct 18 2018 - 00:29:49 PDT)
- senal dinuka (Thu Oct 18 2018 - 00:18:16 PDT)
- Bill Ross (Wed Oct 17 2018 - 21:45:59 PDT)
- senal dinuka (Wed Oct 17 2018 - 21:34:09 PDT)
[AMBER] Parameters for atom CE in lj_1264_pol.dat
- Nikolay N. Kuzmich (Mon Oct 08 2018 - 02:20:52 PDT)
[AMBER] parmchk2 frcmod file
- Jon Uranga (Fri Oct 26 2018 - 05:57:34 PDT)
- David A Case (Fri Oct 26 2018 - 05:30:45 PDT)
- Jon Uranga (Fri Oct 26 2018 - 03:36:12 PDT)
[AMBER] Part of protein going out of the box
- Daniel Roe (Wed Oct 03 2018 - 10:21:38 PDT)
- Leena Aggarwal (Wed Oct 03 2018 - 07:57:32 PDT)
[AMBER] pi-pi And Aromatic Interactions
- Jiri Sponer (Fri Oct 19 2018 - 16:25:06 PDT)
- Jiri Sponer (Fri Oct 19 2018 - 15:56:19 PDT)
- Carlos Simmerling (Fri Oct 19 2018 - 14:21:48 PDT)
- Chris Neale (Fri Oct 19 2018 - 14:15:23 PDT)
- Carlos Simmerling (Fri Oct 19 2018 - 14:03:26 PDT)
- Chris Neale (Fri Oct 19 2018 - 13:37:57 PDT)
- Christina Bergonzo (Fri Oct 19 2018 - 05:49:58 PDT)
- Chris Neale (Thu Oct 18 2018 - 20:27:05 PDT)
- Meng Wu (Thu Oct 18 2018 - 19:11:02 PDT)
[AMBER] pmemd.MPI won't work in Amber 18
- Ross Walker (Thu Oct 04 2018 - 05:31:06 PDT)
- Hai Long (Wed Oct 03 2018 - 19:57:17 PDT)
[AMBER] Post-process calculation of atomic forces
- SARAH JEANNE LEFAVE (Wed Oct 31 2018 - 10:58:35 PDT)
- Daniel Roe (Tue Oct 30 2018 - 08:20:34 PDT)
- SARAH JEANNE LEFAVE (Fri Oct 26 2018 - 17:00:10 PDT)
[AMBER] Problem in saving amber prmtop file from DNA pdb file creacted using server http://structure.usc.edu/make-na/server.html) ?
- David A Case (Thu Oct 04 2018 - 05:54:50 PDT)
- Bill Ross (Thu Oct 04 2018 - 01:09:22 PDT)
- Subrata Paul (Thu Oct 04 2018 - 00:37:08 PDT)
[AMBER] Problem regarding radial command
- Saikat Pal (Wed Oct 31 2018 - 05:01:13 PDT)
[AMBER] Problem with antechamber/acdoctor
- David Case (Sat Oct 06 2018 - 05:54:35 PDT)
[AMBER] Problem with tleap
- Bill Ross (Wed Oct 17 2018 - 11:22:43 PDT)
- Ali Khodayari (Wed Oct 17 2018 - 11:05:01 PDT)
[AMBER] Problems with MPI compilation gb_force.F90
- Ruben Ramos Horta (Wed Oct 03 2018 - 10:10:58 PDT)
[AMBER] Provisional RTX2080 AMBER 18 Performance Numbers
- Marek Maly (Tue Oct 09 2018 - 06:18:29 PDT)
- Ross Walker (Tue Oct 09 2018 - 06:14:20 PDT)
- Marek Maly (Tue Oct 09 2018 - 02:39:23 PDT)
- David Cerutti (Mon Oct 08 2018 - 12:46:47 PDT)
- Marek Maly (Mon Oct 08 2018 - 11:44:13 PDT)
- David Cerutti (Mon Oct 08 2018 - 04:28:08 PDT)
- Marek Maly (Mon Oct 08 2018 - 03:15:37 PDT)
- David Cerutti (Sat Oct 06 2018 - 14:53:43 PDT)
- Ross Walker (Sat Oct 06 2018 - 14:03:11 PDT)
- Ross Walker (Sat Oct 06 2018 - 08:30:40 PDT)
- David Cerutti (Fri Oct 05 2018 - 07:11:14 PDT)
- Ross Walker (Fri Oct 05 2018 - 06:39:30 PDT)
- Marek Maly (Fri Oct 05 2018 - 06:17:19 PDT)
- Ross Walker (Fri Oct 05 2018 - 05:32:07 PDT)
[AMBER] Query regarding Amber installation
- Rakesh Srivastava (Thu Oct 04 2018 - 22:07:38 PDT)
- Rakesh Srivastava (Mon Oct 01 2018 - 09:21:31 PDT)
- David A Case (Mon Oct 01 2018 - 08:42:49 PDT)
- Hai Nguyen (Mon Oct 01 2018 - 05:59:23 PDT)
- Rakesh Srivastava (Mon Oct 01 2018 - 05:49:29 PDT)
[AMBER] Question about stripping waters
- Maria Clelia Milletti (Tue Oct 23 2018 - 08:24:37 PDT)
- David Case (Sat Oct 20 2018 - 14:23:30 PDT)
- Maria Clelia Milletti (Fri Oct 19 2018 - 13:42:24 PDT)
- Daniel Roe (Thu Oct 18 2018 - 16:00:58 PDT)
- Maria Clelia Milletti (Thu Oct 18 2018 - 10:22:31 PDT)
[AMBER] Question Regarding GRID
- Saikat Pal (Fri Oct 26 2018 - 07:44:09 PDT)
[AMBER] questions on pmemd.cuda for thermodynamic integration
- Song-Ho Chong (Fri Oct 05 2018 - 08:06:49 PDT)
[AMBER] R.E.D. Server is down
- Stéphane Téletchéa (Thu Oct 04 2018 - 07:43:25 PDT)
[AMBER] Reducing memory usage in lifetime analyses
- Gustaf Olsson (Wed Oct 03 2018 - 03:23:52 PDT)
- Daniel Roe (Tue Oct 02 2018 - 11:20:34 PDT)
[AMBER] Regarding calculation of RMSD
- DHEERAJ CHITARA (Mon Oct 01 2018 - 05:38:49 PDT)
[AMBER] Regarding calculation of RMSD using AMBER-18 CPPTRAJ V-18.01
- Daniel Roe (Thu Oct 11 2018 - 05:13:17 PDT)
- DHEERAJ CHITARA (Thu Oct 11 2018 - 01:23:10 PDT)
- Daniel Roe (Wed Oct 10 2018 - 05:20:11 PDT)
- DHEERAJ CHITARA (Tue Oct 09 2018 - 23:15:50 PDT)
[AMBER] Regarding Leap
- Charu Sharma (JRF) (Tue Oct 30 2018 - 09:40:38 PDT)
- Charu Sharma (JRF) (Tue Oct 30 2018 - 09:40:15 PDT)
- David A Case (Tue Oct 30 2018 - 09:24:46 PDT)
- Charu Sharma (JRF) (Tue Oct 30 2018 - 08:49:49 PDT)
- Chetna Tyagi (Wed Oct 17 2018 - 05:52:03 PDT)
- Charu Sharma (JRF) (Wed Oct 17 2018 - 05:05:22 PDT)
- Chetna Tyagi (Wed Oct 17 2018 - 04:42:37 PDT)
- Charu Sharma (JRF) (Wed Oct 17 2018 - 04:50:56 PDT)
- Charu Sharma (JRF) (Wed Oct 17 2018 - 04:49:02 PDT)
- Chetna Tyagi (Wed Oct 17 2018 - 04:24:19 PDT)
- Charu Sharma (JRF) (Wed Oct 17 2018 - 04:30:14 PDT)
- Elvis Martis (Sun Oct 14 2018 - 00:58:56 PDT)
- Charu Sharma (JRF) (Sat Oct 13 2018 - 03:46:17 PDT)
- Elvis Martis (Sat Oct 13 2018 - 00:31:40 PDT)
- Charu Sharma (JRF) (Fri Oct 12 2018 - 22:58:52 PDT)
- Elvis Martis (Wed Oct 10 2018 - 08:15:02 PDT)
- Charu Sharma (JRF) (Wed Oct 10 2018 - 04:01:24 PDT)
- Elvis Martis (Mon Oct 08 2018 - 22:41:36 PDT)
- Charu Sharma (JRF) (Mon Oct 08 2018 - 21:33:15 PDT)
[AMBER] Restrain distance for Umbrella Sampling
- emanuele falbo (Mon Oct 08 2018 - 08:28:08 PDT)
- David A Case (Mon Oct 08 2018 - 08:08:08 PDT)
- emanuele falbo (Mon Oct 08 2018 - 07:03:44 PDT)
[AMBER] Rigid body simulation of Nitrogenase's FeMo cluster
- David A Case (Tue Oct 09 2018 - 05:17:47 PDT)
- Sadra Aghajani (Tue Oct 09 2018 - 00:32:17 PDT)
[AMBER] RTX 2080 Benchmarks
- Bisignano, Paola (Mon Oct 08 2018 - 13:21:24 PDT)
- David Cerutti (Mon Oct 08 2018 - 13:13:40 PDT)
- Bisignano, Paola (Mon Oct 08 2018 - 13:05:14 PDT)
[AMBER] RTX2080 Performance Update for AMBER 18
- Ross Walker (Wed Oct 10 2018 - 20:15:37 PDT)
[AMBER] RTX2080TI Performance
- Ross Walker (Fri Oct 12 2018 - 07:27:59 PDT)
- Marek Maly (Thu Oct 11 2018 - 09:58:50 PDT)
- David Cerutti (Thu Oct 11 2018 - 07:46:21 PDT)
- Ross Walker (Thu Oct 11 2018 - 04:19:47 PDT)
[AMBER] Sander and Thermodynamic integration and softcore
- David A Case (Fri Oct 26 2018 - 05:06:55 PDT)
- Khabiri, Morteza (Thu Oct 25 2018 - 12:07:24 PDT)
[AMBER] Selecting specific set of molecules for output trajectory
- David A Case (Tue Oct 09 2018 - 05:20:53 PDT)
- anu chandra (Tue Oct 09 2018 - 04:29:36 PDT)
[AMBER] Setting up parameters for a simulation at 350K
- David Cerutti (Thu Oct 04 2018 - 10:35:28 PDT)
- Bill Ross (Thu Oct 04 2018 - 10:30:05 PDT)
- Dmitry Suplatov (Thu Oct 04 2018 - 08:54:02 PDT)
- David Cerutti (Thu Oct 04 2018 - 08:45:24 PDT)
- Dmitry Suplatov (Thu Oct 04 2018 - 08:39:51 PDT)
[AMBER] Simulating a covalently bound ligand
- senal dinuka (Fri Oct 26 2018 - 04:03:22 PDT)
- David A Case (Tue Oct 23 2018 - 04:39:42 PDT)
- senal dinuka (Mon Oct 22 2018 - 21:48:53 PDT)
[AMBER] SIRAH 2.0: a finer taste in coarse-grained protiens
- Matias Machado (Thu Oct 11 2018 - 08:17:17 PDT)
[AMBER] Striping distance based water residues
- Kshatresh Dutta Dubey (Wed Oct 10 2018 - 08:48:06 PDT)
- Daniel Roe (Wed Oct 10 2018 - 05:17:50 PDT)
- Kshatresh Dutta Dubey (Wed Oct 10 2018 - 03:29:30 PDT)
[AMBER] Struggling to convert AMBER .frcmod and .mol2 to GROMACS for HEME
- ABEL Stephane (Wed Oct 24 2018 - 01:45:55 PDT)
- David Case (Tue Oct 23 2018 - 17:08:56 PDT)
- Bill Ross (Tue Oct 23 2018 - 14:47:38 PDT)
- Matthew Fisher (Tue Oct 23 2018 - 14:10:32 PDT)
[AMBER] sugar derivatives parametrization
- Lachele Foley (Thu Oct 25 2018 - 08:29:58 PDT)
- Bisignano, Paola (Fri Oct 19 2018 - 08:34:14 PDT)
- Lachele Foley (Thu Oct 18 2018 - 20:00:27 PDT)
- Lachele Foley (Thu Oct 18 2018 - 19:58:32 PDT)
- David Case (Thu Oct 18 2018 - 11:09:42 PDT)
- Bisignano, Paola (Wed Oct 17 2018 - 15:49:34 PDT)
[AMBER] Temperature-Replica Exchange MD
- Cruzeiro,Vinicius Wilian D (Wed Oct 24 2018 - 08:00:01 PDT)
- Alessandro Contini (Wed Oct 24 2018 - 07:53:00 PDT)
- Gilberto Pereira (Wed Oct 24 2018 - 07:26:32 PDT)
[AMBER] Testing C++11 support: Not present
- Gustaf Olsson (Fri Oct 12 2018 - 05:55:23 PDT)
- Daniel Roe (Fri Oct 12 2018 - 05:41:29 PDT)
- Gustaf Olsson (Fri Oct 12 2018 - 00:54:13 PDT)
- Gustaf Olsson (Thu Oct 11 2018 - 23:28:25 PDT)
- Andrew Schaub (Thu Oct 11 2018 - 13:20:57 PDT)
- Daniel Roe (Wed Oct 10 2018 - 06:52:17 PDT)
- Gustaf Olsson (Tue Oct 09 2018 - 23:00:52 PDT)
- Daniel Roe (Tue Oct 09 2018 - 08:45:09 PDT)
- Gustaf Olsson (Tue Oct 09 2018 - 07:34:55 PDT)
- Daniel Roe (Tue Oct 09 2018 - 07:17:27 PDT)
- Gustaf Olsson (Mon Oct 08 2018 - 22:52:45 PDT)
- Gustaf Olsson (Mon Oct 08 2018 - 07:55:10 PDT)
- Gustaf Olsson (Mon Oct 08 2018 - 05:21:10 PDT)
- Gustaf Olsson (Mon Oct 08 2018 - 04:25:00 PDT)
- Gustaf Olsson (Mon Oct 08 2018 - 02:07:32 PDT)
- Bill Ross (Mon Oct 08 2018 - 01:54:37 PDT)
- Gustaf Olsson (Mon Oct 08 2018 - 01:04:12 PDT)
[AMBER] The make_na web service, and corresponding code
- David A Case (Mon Oct 22 2018 - 06:27:48 PDT)
[AMBER] the unperturbed charge of the unit is not zero
- Charu Sharma (JRF) (Tue Oct 30 2018 - 09:26:11 PDT)
- David A Case (Tue Oct 30 2018 - 08:52:25 PDT)
- soukaina louerdi (Tue Oct 30 2018 - 05:18:04 PDT)
- David A Case (Tue Oct 30 2018 - 05:08:03 PDT)
- soukaina louerdi (Tue Oct 30 2018 - 03:59:25 PDT)
- David A Case (Mon Oct 29 2018 - 05:07:46 PDT)
- soukaina louerdi (Sun Oct 28 2018 - 11:37:32 PDT)
- David Case (Sat Oct 27 2018 - 18:10:49 PDT)
- soukaina louerdi (Sat Oct 27 2018 - 16:17:49 PDT)
[AMBER] tleap gamma-carboxyglutamic acid linkage error
- Matias Machado (Wed Oct 31 2018 - 10:26:15 PDT)
- Bill Ross (Wed Oct 31 2018 - 02:40:02 PDT)
- Bill Ross (Wed Oct 31 2018 - 02:30:25 PDT)
- Rajbinder Kaur Virk (Wed Oct 31 2018 - 02:13:58 PDT)
- David Case (Tue Oct 30 2018 - 18:40:59 PDT)
- Rajbinder Kaur Virk (Tue Oct 30 2018 - 10:27:15 PDT)
- Matias Machado (Fri Oct 26 2018 - 11:45:20 PDT)
- Rajbinder Kaur Virk (Wed Oct 24 2018 - 22:39:03 PDT)
- Matias Machado (Tue Oct 23 2018 - 15:26:52 PDT)
- Rajbinder Kaur Virk (Sun Oct 21 2018 - 20:06:30 PDT)
[AMBER] Topological error for Mg in .prepin file.
- Pengfei Li (Fri Oct 26 2018 - 14:57:39 PDT)
- David Case (Wed Oct 24 2018 - 17:58:31 PDT)
- ABEL Stephane (Wed Oct 24 2018 - 07:11:39 PDT)
- Anuja Ware (Wed Oct 24 2018 - 06:54:19 PDT)
- ABEL Stephane (Wed Oct 24 2018 - 06:41:03 PDT)
- Anuja Ware (Wed Oct 24 2018 - 06:22:55 PDT)
[AMBER] torsion angles of carbon allotropes
- Ibrahim Said (Tue Oct 09 2018 - 03:56:34 PDT)
- David Case (Mon Oct 08 2018 - 18:04:27 PDT)
- Ibrahim Said (Mon Oct 08 2018 - 11:57:08 PDT)
[AMBER] Total system charge and TI simulations
- David Case (Mon Oct 01 2018 - 16:49:24 PDT)
- Veenis, Andrew Jay (Mon Oct 01 2018 - 12:29:05 PDT)
[AMBER] TR : Struggling to convert AMBER .frcmod and .mol2 to GROMACS for HEME
- ABEL Stephane (Wed Oct 24 2018 - 01:50:20 PDT)
[AMBER] Unkown residue to AMBER
- David A Case (Wed Oct 10 2018 - 04:31:27 PDT)
- Keiran Corbett (Wed Oct 10 2018 - 00:55:52 PDT)
[AMBER] Using custom non-bonding potential, drude oscillator in Amber18
- Kyeong-jun Jeong (Tue Oct 16 2018 - 10:11:42 PDT)
- David A Case (Tue Oct 16 2018 - 06:22:43 PDT)
- Kyeong-jun Jeong (Mon Oct 15 2018 - 15:46:22 PDT)
[AMBER] using parmed (python api) to merge two parm7 files for TI
- Jason Swails (Fri Oct 19 2018 - 11:39:27 PDT)
- Wesley Michael Botello-Smith (Tue Oct 16 2018 - 13:43:22 PDT)
- Wesley Michael Botello-Smith (Tue Oct 16 2018 - 13:35:33 PDT)
[AMBER] viscosity calculation
- Arun Srikanth (Fri Oct 12 2018 - 10:59:25 PDT)
- David A Case (Fri Oct 12 2018 - 04:56:52 PDT)
- Lorenzo Gontrani (Tue Oct 09 2018 - 07:48:45 PDT)
[AMBER] Warning for MMPBSA.py calculation
- maryam azimzadehirani (Sat Oct 06 2018 - 00:01:19 PDT)
[AMBER] Water Density
- Seibold, Steve Allan (Tue Oct 02 2018 - 05:57:30 PDT)
- David Case (Mon Oct 01 2018 - 16:32:22 PDT)
- Seibold, Steve Allan (Mon Oct 01 2018 - 12:03:00 PDT)
[AMBER] Water do not see the system....
- Vito GENNA (Thu Oct 11 2018 - 10:25:29 PDT)
- Daniel Roe (Thu Oct 11 2018 - 09:20:19 PDT)
- Daniel Roe (Thu Oct 11 2018 - 08:59:04 PDT)
- Vito GENNA (Thu Oct 11 2018 - 08:56:10 PDT)
- Matias Machado (Thu Oct 11 2018 - 08:48:45 PDT)
- Vito GENNA (Thu Oct 11 2018 - 01:48:44 PDT)
- Vito GENNA (Wed Oct 10 2018 - 13:48:20 PDT)
- David A Case (Wed Oct 10 2018 - 13:16:03 PDT)
- Vito GENNA (Wed Oct 10 2018 - 09:18:40 PDT)
fatal error in Resp
- David Case (Fri Oct 19 2018 - 04:28:03 PDT)
- fateme haghighi (Thu Oct 18 2018 - 14:33:00 PDT)
- fateme haghighi (Thu Oct 18 2018 - 00:52:22 PDT)
Fatal error in RESP calculation
- David A Case (Wed Oct 10 2018 - 07:40:02 PDT)
- fateme haghighi (Wed Oct 10 2018 - 06:52:52 PDT)
Problem running the adqmmm test, one mdcrd file only
- Dreab, Ana (Sun Oct 07 2018 - 14:17:10 PDT)
- Goetz, Andreas (Sat Oct 06 2018 - 23:01:20 PDT)
- Dreab, Ana (Sat Oct 06 2018 - 20:46:47 PDT)
- David A Case (Thu Oct 04 2018 - 08:21:11 PDT)
- Dreab, Ana (Thu Oct 04 2018 - 06:17:30 PDT)

Amber Archive Oct 2018 by subject