Amber Archive May 2017: by subject

[AMBER-Developers] [AMBER] A9 tutorial analyse.sh problem
- David Case (Sat May 20 2017 - 21:38:52 PDT)
[AMBER] .prmtop file not saved
- Shafaq Muzammal (Tue May 30 2017 - 01:40:28 PDT)
- David Case (Tue May 23 2017 - 20:34:18 PDT)
- Shafaq Muzammal (Tue May 23 2017 - 05:33:51 PDT)
[AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16
- Charles Lin (Tue May 09 2017 - 09:02:45 PDT)
- Pratul K. Agarwal (Tue May 09 2017 - 08:36:26 PDT)
- Charles Lin (Tue May 09 2017 - 08:24:56 PDT)
- Paul Westphaelinger (Tue May 09 2017 - 01:00:06 PDT)
[AMBER] <Na 1> Could not find vdW (or other) parameters for type: Na
- Bill Ross (Mon May 15 2017 - 11:52:00 PDT)
- Thakur, Abhishek (Mon May 15 2017 - 09:01:42 PDT)
- David A Case (Fri May 12 2017 - 05:33:34 PDT)
- Thakur, Abhishek (Thu May 11 2017 - 14:37:54 PDT)
- David A Case (Thu May 11 2017 - 12:02:00 PDT)
- Thakur, Abhishek (Thu May 11 2017 - 09:10:52 PDT)
[AMBER] [Amber16]"cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol"
- Scott Le Grand (Thu May 18 2017 - 15:16:01 PDT)
- Ross Walker (Thu May 18 2017 - 14:46:15 PDT)
- Scott Brozell (Thu May 18 2017 - 11:57:11 PDT)
- David A Case (Thu May 18 2017 - 06:42:34 PDT)
- Elvis Martis (Thu May 18 2017 - 05:58:15 PDT)
- 冯国强 (Wed May 17 2017 - 23:23:58 PDT)
- 冯国强 (Wed May 17 2017 - 23:18:10 PDT)
[AMBER] A9 tutorial analyse.sh problem
- Robert Wohlhueter (Sun May 21 2017 - 08:40:55 PDT)
- Robert Wohlhueter (Sat May 20 2017 - 09:06:58 PDT)
- David Case (Sat May 20 2017 - 06:31:19 PDT)
- Hai Nguyen (Fri May 19 2017 - 18:05:47 PDT)
- Hai Nguyen (Fri May 19 2017 - 17:58:45 PDT)
- Robert Wohlhueter (Fri May 19 2017 - 17:37:18 PDT)
[AMBER] acdoctor: fatal error when reading carboxylates from .mol2 files
- Scott Brozell (Tue May 02 2017 - 00:20:56 PDT)
- Niel Henriksen (Mon May 01 2017 - 15:09:32 PDT)
[AMBER] add ligand parameters
- Loris Moretti (Tue May 30 2017 - 05:39:59 PDT)
- Brent Krueger (Fri May 26 2017 - 04:04:53 PDT)
- Bill Ross (Fri May 26 2017 - 03:37:43 PDT)
- Loris Moretti (Fri May 26 2017 - 03:19:32 PDT)
- Bill Ross (Fri May 26 2017 - 01:50:10 PDT)
- Loris Moretti (Fri May 26 2017 - 01:45:01 PDT)
[AMBER] addions doubt
- Bill Ross (Wed May 17 2017 - 01:13:54 PDT)
- Mary Varughese (Wed May 17 2017 - 00:05:22 PDT)
[AMBER] AddToBox Failure
- David Case (Wed May 03 2017 - 10:20:16 PDT)
- David Cerutti (Tue May 02 2017 - 19:50:52 PDT)
- David Case (Tue May 02 2017 - 18:24:55 PDT)
- sylvester kisembo (Tue May 02 2017 - 07:21:22 PDT)
[AMBER] AMBER Digest, Vol 1932, Issue 1
- Elvis Martis (Tue May 23 2017 - 01:27:02 PDT)
- Garima Singh (Tue May 23 2017 - 00:17:18 PDT)
[AMBER] AMBER error
- Neha Gandhi (Thu May 25 2017 - 17:11:20 PDT)
- David Case (Thu May 25 2017 - 07:54:44 PDT)
- Bill Ross (Wed May 24 2017 - 21:01:42 PDT)
- Neha Gandhi (Wed May 24 2017 - 20:28:10 PDT)
- David Case (Thu May 18 2017 - 19:00:52 PDT)
- Bill Ross (Thu May 18 2017 - 13:00:19 PDT)
- Jerrano Bowleg (Thu May 18 2017 - 12:48:22 PDT)
[AMBER] Amber parameters for CPD and 6-4PP
- Elvis Martis (Tue May 09 2017 - 04:21:58 PDT)
- p.kartheek (Tue May 09 2017 - 02:50:28 PDT)
[AMBER] Ambertools coulomb constant
- David Case (Wed May 03 2017 - 10:30:22 PDT)
- Gard Nelson (Tue May 02 2017 - 16:55:28 PDT)
[AMBER] aMD and cpH-MD
- Hofer, Florian (Thu May 04 2017 - 01:45:42 PDT)
[AMBER] amino-cyclopropyl parameters
- David A Case (Wed May 31 2017 - 05:20:21 PDT)
- Loris Moretti (Wed May 31 2017 - 00:32:48 PDT)
- David A Case (Tue May 30 2017 - 06:52:05 PDT)
- Loris Moretti (Tue May 30 2017 - 05:39:51 PDT)
- Thakur, Abhishek (Fri May 26 2017 - 06:00:04 PDT)
- Loris Moretti (Fri May 26 2017 - 00:32:30 PDT)
[AMBER] Ante_R.E.D script files.
- Vatsal Purohit (Mon May 15 2017 - 11:10:25 PDT)
[AMBER] Antechamber can't transform Gaussian output file into *.mol2
- Scott Brozell (Wed May 31 2017 - 11:24:36 PDT)
- Bill Ross (Wed May 31 2017 - 05:09:59 PDT)
- Nikolay N. Kuzmich (Wed May 31 2017 - 05:06:28 PDT)
[AMBER] Atom type assignment by Antechamber
- Matsuura, Azuma (Mon May 08 2017 - 18:14:22 PDT)
- Junmei Wang (Mon May 08 2017 - 08:19:48 PDT)
- Matsuura, Azuma (Sun May 07 2017 - 22:13:13 PDT)
[AMBER] Building distributable executable
- Scott Brozell (Thu May 18 2017 - 12:07:07 PDT)
- Scott Brozell (Wed May 17 2017 - 18:40:22 PDT)
- D'Auria, Raffaella (Wed May 17 2017 - 18:05:47 PDT)
- Daniel Roe (Wed May 17 2017 - 11:49:49 PDT)
- Scott Brozell (Wed May 17 2017 - 11:20:26 PDT)
- Jason Swails (Wed May 17 2017 - 10:40:08 PDT)
- Scott Brozell (Wed May 17 2017 - 09:21:59 PDT)
- David Case (Wed May 17 2017 - 05:52:30 PDT)
- D'Auria, Raffaella (Tue May 16 2017 - 12:24:09 PDT)
[AMBER] calculation of the binding energy in amber 12 or 14
- David Case (Thu May 25 2017 - 10:28:42 PDT)
- Saikat Pal (Tue May 23 2017 - 22:09:30 PDT)
- David A Case (Sat May 20 2017 - 06:26:27 PDT)
- Saikat Pal (Thu May 18 2017 - 22:33:30 PDT)
[AMBER] Cellulose simulation
- luca maggi (Mon May 08 2017 - 01:17:52 PDT)
- Lachele Foley (Mon May 08 2017 - 01:06:26 PDT)
- luca maggi (Sun May 07 2017 - 07:37:18 PDT)
[AMBER] Citation for frcmod.parmbsc0, frcmod.ionsjc_tip3p
- Ramin Salimi (Wed May 31 2017 - 05:41:36 PDT)
- David A Case (Wed May 31 2017 - 05:25:43 PDT)
- Saeed Izadi (Tue May 30 2017 - 18:12:58 PDT)
- Ramin Salimi (Tue May 30 2017 - 17:33:58 PDT)
[AMBER] convergence question about xmin
- David Case (Mon May 29 2017 - 13:06:40 PDT)
- Scott Brozell (Wed May 17 2017 - 11:30:05 PDT)
- liu junjun (Wed May 17 2017 - 10:22:00 PDT)
- liu junjun (Tue May 16 2017 - 02:53:21 PDT)
[AMBER] Could not find vdW (or other) parameters for type: Na+
- David A Case (Thu May 18 2017 - 06:51:14 PDT)
- Elvis Martis (Thu May 18 2017 - 05:56:25 PDT)
- Michael Shokhen (Thu May 18 2017 - 04:13:40 PDT)
[AMBER] Cpptraj calculates only three PHI-PSI angles in a 18-residue long peptide
- Daniel Roe (Mon May 08 2017 - 13:04:18 PDT)
- Chetna Tyagi (Mon May 08 2017 - 10:37:53 PDT)
- Elvis Martis (Mon May 08 2017 - 09:51:27 PDT)
- Daniel Roe (Mon May 08 2017 - 08:14:26 PDT)
- Chetna Tyagi (Mon May 08 2017 - 08:07:34 PDT)
[AMBER] cpptraj GIST
- Tom Kurtzman (Wed May 31 2017 - 05:52:27 PDT)
- Daniel Roe (Fri May 26 2017 - 10:54:29 PDT)
- Gabriel Jara (Fri May 26 2017 - 10:49:54 PDT)
[AMBER] cpptraj nastruct local helical vectors?
- Daniel Roe (Fri May 19 2017 - 08:33:55 PDT)
- Kenneth Huang (Thu May 18 2017 - 12:03:55 PDT)
[AMBER] CX1 missing connect0 atom._MCPB
- Pengfei Li (Wed May 10 2017 - 15:45:08 PDT)
- Thakur, Abhishek (Wed May 10 2017 - 12:24:55 PDT)
[AMBER] dimer rmsd issue.
- Daniel Roe (Tue May 16 2017 - 08:16:36 PDT)
- Bill Ross (Sun May 14 2017 - 12:16:55 PDT)
- Elvis Martis (Sun May 14 2017 - 10:44:13 PDT)
- Saman Yousuf ali (Sun May 14 2017 - 10:13:54 PDT)
[AMBER] Distance based mask and reference
- Marion, Antoine (Sat May 20 2017 - 06:44:48 PDT)
- David Case (Sat May 20 2017 - 06:19:52 PDT)
- Marion, Antoine (Fri May 19 2017 - 09:15:21 PDT)
[AMBER] Distance regarding to interface between two solvents
- Habib Rozale (Wed May 10 2017 - 02:00:40 PDT)
[AMBER] DNA Tutorial B1 - Temperature Drop
- David Case (Wed May 03 2017 - 05:37:42 PDT)
- Johannes Kalliauer (Wed May 03 2017 - 03:57:37 PDT)
[AMBER] does not have a type
- David Case (Mon May 01 2017 - 07:59:23 PDT)
- Thakur, Abhishek (Mon May 01 2017 - 07:58:44 PDT)
- Sowmya Indrakumar (Mon May 01 2017 - 07:56:14 PDT)
[AMBER] Doubt about EVB/LES-PIMD
- David A Case (Thu May 18 2017 - 06:30:40 PDT)
- Stregone (Wed May 17 2017 - 11:06:07 PDT)
[AMBER] Dummy atoms when running antechamber in B4 (sustiva) tutorial
- David A Case (Wed May 31 2017 - 05:15:22 PDT)
- Nikolay N. Kuzmich (Wed May 31 2017 - 04:43:20 PDT)
- David Case (Mon May 29 2017 - 09:17:56 PDT)
- Nikolay N. Kuzmich (Mon May 29 2017 - 06:08:32 PDT)
[AMBER] early bird deadline extended
- Thomas Exner (Wed May 17 2017 - 08:56:52 PDT)
[AMBER] EEL and VDW Notification on minimization with sander/pmemd
- David Case (Sun May 14 2017 - 05:29:46 PDT)
- Elvis Martis (Sat May 13 2017 - 01:11:17 PDT)
- Charles Mariasoosai (Fri May 12 2017 - 09:57:53 PDT)
[AMBER] Error when running MMPBSA calculation using Force field from CHARMM GUI membrane builder running on amber.
- Daniel Roe (Fri May 05 2017 - 11:29:08 PDT)
- Miguel Rivera (Thu May 04 2017 - 15:18:54 PDT)
[AMBER] Error while upgrading to AmberTools 17
- Hai Nguyen (Thu May 25 2017 - 05:56:30 PDT)
- Chetna Tyagi (Thu May 25 2017 - 04:15:11 PDT)
- Hai Nguyen (Wed May 24 2017 - 06:03:55 PDT)
- Chetna Tyagi (Wed May 24 2017 - 03:29:51 PDT)
[AMBER] Error with 'surf' and acetonitrile-water solvent mixture
- Marcel Passon (Fri May 05 2017 - 07:43:06 PDT)
- Daniel Roe (Thu May 04 2017 - 08:54:32 PDT)
- Daniel Roe (Thu May 04 2017 - 08:00:55 PDT)
- Daniel Roe (Tue May 02 2017 - 10:45:28 PDT)
[AMBER] error: At line 551 of file mdin_ctrl_dat.F90 (unit = 5, file = 'heat.mdin')
- Elvis Martis (Sat May 13 2017 - 07:33:06 PDT)
- Ramin Salimi (Sat May 13 2017 - 06:43:56 PDT)
- Elvis Martis (Sat May 13 2017 - 06:21:00 PDT)
- Elvis Martis (Sat May 13 2017 - 06:17:22 PDT)
- Ramin Salimi (Sat May 13 2017 - 05:21:35 PDT)
[AMBER] ERROR: Could not read coords from .rst file
- Szymon Żaczek (Thu May 11 2017 - 01:01:36 PDT)
- Vishal Nemaysh (Thu May 11 2017 - 00:23:45 PDT)
[AMBER] external electric field in Amber 16
- Bill Ross (Wed May 31 2017 - 17:00:06 PDT)
- michal biler (Wed May 31 2017 - 14:22:24 PDT)
- Bill Ross (Tue May 30 2017 - 14:46:57 PDT)
- michal biler (Tue May 30 2017 - 14:06:04 PDT)
- Carlos Simmerling (Tue May 30 2017 - 07:43:23 PDT)
- michal biler (Tue May 30 2017 - 07:39:20 PDT)
[AMBER] External electric fields on CUDA enabled PMEMD
- Charles Lin (Wed May 10 2017 - 21:37:02 PDT)
- Neville Bethel (Wed May 10 2017 - 18:54:11 PDT)
- Charles Lin (Sun Apr 30 2017 - 19:32:00 PDT)
[AMBER] Fast 3-point water residue error for coordinates
- Sadegh Faramarzi Ganjabad (Mon May 08 2017 - 13:09:40 PDT)
- Song-Ho Chong (Mon May 08 2017 - 08:22:53 PDT)
- Sadegh Faramarzi Ganjabad (Sun May 07 2017 - 23:46:54 PDT)
[AMBER] Fast 3-point water residue error for coordinates generated with parmed
- Daniel Roe (Fri May 05 2017 - 12:15:57 PDT)
- Sadegh Faramarzi Ganjabad (Fri May 05 2017 - 11:32:46 PDT)
[AMBER] fcc_metals.lib is not a valid databae
- Sohag Biswas (Wed May 10 2017 - 04:58:24 PDT)
[AMBER] fcc_metals.lib not found
- Pengfei Li (Tue May 30 2017 - 10:40:09 PDT)
- Sohag Biswas (Mon May 29 2017 - 21:24:47 PDT)
[AMBER] ff parameters
- Jason Swails (Mon May 08 2017 - 05:39:40 PDT)
- David Case (Sat May 06 2017 - 05:19:20 PDT)
- Hai Nguyen (Fri May 05 2017 - 13:17:49 PDT)
- Andrea Spitaleri (Fri May 05 2017 - 12:46:19 PDT)
- Jason Swails (Fri May 05 2017 - 11:31:13 PDT)
- David Case (Fri May 05 2017 - 05:05:31 PDT)
- Andrea Spitaleri (Fri May 05 2017 - 00:38:28 PDT)
[AMBER] Find entropy from non-equilibrium free energy calculation
- Ramin Salimi (Tue May 02 2017 - 00:53:18 PDT)
- Hannes Loeffler (Tue May 02 2017 - 00:08:52 PDT)
- Ramin Salimi (Mon May 01 2017 - 10:50:48 PDT)
[AMBER] finding number of atoms within a radius
- Elvis Martis (Wed May 24 2017 - 05:54:34 PDT)
- Debodyuti Dutta (Wed May 24 2017 - 04:45:20 PDT)
[AMBER] Fwd: Error while preparing docked complex for minimization
- NADIA RAHMAH (Mon May 29 2017 - 16:03:23 PDT)
- Bill Ross (Sun May 28 2017 - 13:53:17 PDT)
- David Case (Sun May 28 2017 - 09:09:10 PDT)
- Elvis Martis (Sun May 28 2017 - 04:40:29 PDT)
- NADIA RAHMAH (Sun May 28 2017 - 03:59:59 PDT)
[AMBER] Fwd: failed to generate parameter and topology file for protein-ligand complex containing zinc
- Elvis Martis (Tue May 02 2017 - 07:24:02 PDT)
- Sharon D. Morris (Tue May 02 2017 - 05:22:55 PDT)
[AMBER] Fwd: Problem in splitting mdcrd file with cpptraj
- Manjula Saravanan (Thu May 11 2017 - 22:20:31 PDT)
[AMBER] Fwd: Request for troubleshoot in MAWS (igem software from Heidelberg) based on AMBER
- Abudhahir Buhari (Mon May 15 2017 - 01:24:23 PDT)
[AMBER] GAFF parameters in amber16 and amber14
- Hannes Loeffler (Fri May 19 2017 - 00:21:17 PDT)
- Meiting Wang (Fri May 19 2017 - 00:14:19 PDT)
[AMBER] glycoprotein
- Neha Gandhi (Tue May 02 2017 - 00:08:48 PDT)
- Neha Gandhi (Mon May 01 2017 - 23:49:10 PDT)
[AMBER] GPUs parallel problem
- Ross Walker (Fri May 05 2017 - 05:05:58 PDT)
- Meng Wu (Fri May 05 2017 - 02:36:59 PDT)
- Ross Walker (Thu May 04 2017 - 08:16:03 PDT)
- Gulsevin,Alican (Thu May 04 2017 - 02:29:26 PDT)
- Andreas Tosstorff (Thu May 04 2017 - 02:21:41 PDT)
- Meng Wu (Thu May 04 2017 - 01:26:20 PDT)
[AMBER] Has Hessian printing been added?
- David Case (Sun May 14 2017 - 05:36:43 PDT)
- Eric Hansen (Fri May 12 2017 - 12:47:17 PDT)
[AMBER] Help with PB simulations using MPI
- Ray Luo (Thu May 18 2017 - 14:11:25 PDT)
- Jake (Thu May 18 2017 - 12:34:54 PDT)
[AMBER] High pressure fluctuation in isothermal-isobaric ensemble
- Daniel Roe (Wed May 31 2017 - 12:09:44 PDT)
- Ramin Salimi (Wed May 31 2017 - 09:12:03 PDT)
[AMBER] how to draw Radial Distribution Functions?
- Daniel Roe (Wed May 10 2017 - 10:11:19 PDT)
- Yang Jinpeng (Wed May 10 2017 - 05:15:30 PDT)
[AMBER] How to restart MD
- Elvis Martis (Thu May 04 2017 - 00:12:58 PDT)
- Andreas Tosstorff (Thu May 04 2017 - 00:11:52 PDT)
- Garima Singh (Wed May 03 2017 - 23:48:32 PDT)
[AMBER] How to use Amber GAFF force field for methylated DNA
- Hannes Loeffler (Fri May 19 2017 - 00:36:15 PDT)
- MINGREN SHEN (Thu May 18 2017 - 20:03:15 PDT)
[AMBER] How to use Amber in HPC
- Elvis Martis (Fri May 12 2017 - 04:40:31 PDT)
- Garima Singh (Fri May 12 2017 - 03:53:49 PDT)
[AMBER] Implicit solvation method giving the error number of triangulated 3-point waters found: 0
- David Case (Wed May 17 2017 - 18:17:40 PDT)
- David Case (Wed May 17 2017 - 18:14:31 PDT)
- Ramin Salimi (Wed May 17 2017 - 13:25:19 PDT)
- Adrian Roitberg (Wed May 17 2017 - 12:53:28 PDT)
- Ramin Salimi (Wed May 17 2017 - 12:51:28 PDT)
[AMBER] Input case causing NaN in sander
- David Case (Wed May 31 2017 - 19:10:34 PDT)
[AMBER] Input case causing NaN in sander (and possibly pmemd) (Ambertools17)
- David Case (Mon May 29 2017 - 16:32:38 PDT)
- Åke Sandgren (Mon May 29 2017 - 13:18:48 PDT)
- David Case (Mon May 29 2017 - 12:43:31 PDT)
- Åke Sandgren (Fri May 19 2017 - 00:32:43 PDT)
[AMBER] Installation of AMBER 16
- Hai Nguyen (Tue May 23 2017 - 07:01:39 PDT)
- Nhai (Tue May 23 2017 - 06:37:06 PDT)
- Vidhya Srivatsan (Tue May 23 2017 - 06:26:15 PDT)
[AMBER] intra-residue water bridge with cpptraj
- Daniel Roe (Fri May 05 2017 - 06:00:04 PDT)
- Joanna Sarzynska (Fri May 05 2017 - 01:17:20 PDT)
[AMBER] KeyError: 'A' (MCPB.py)
- Pengfei Li (Wed May 31 2017 - 14:58:21 PDT)
- Sushi Shilpa (Tue May 30 2017 - 21:15:34 PDT)
- Pengfei Li (Tue May 30 2017 - 10:09:52 PDT)
- Sushi Shilpa (Mon May 29 2017 - 05:35:33 PDT)
[AMBER] LEaP failing after update to AmberTools17
- Charles-Alexandre Mattelaer (Wed May 03 2017 - 11:39:08 PDT)
- David Case (Wed May 03 2017 - 11:18:10 PDT)
- Charles-Alexandre Mattelaer (Wed May 03 2017 - 10:35:19 PDT)
[AMBER] Libgfortran error during amber tools install
- Hai Nguyen (Tue May 23 2017 - 20:52:19 PDT)
- David Case (Tue May 23 2017 - 20:41:10 PDT)
- Hai Nguyen (Tue May 23 2017 - 15:24:41 PDT)
- Van Rompaey Dries (Tue May 23 2017 - 10:57:43 PDT)
[AMBER] MCPB and Can not run MD simulation; some residue move out of protein
- Pengfei Li (Thu May 18 2017 - 09:45:22 PDT)
- David Case (Sun May 14 2017 - 05:42:31 PDT)
- Bill Ross (Sat May 13 2017 - 23:51:19 PDT)
- kungking Hanpaibool (Sat May 13 2017 - 23:36:57 PDT)
- Elvis Martis (Sat May 13 2017 - 22:11:16 PDT)
- kungking Hanpaibool (Sat May 13 2017 - 13:05:59 PDT)
[AMBER] MD Simulation of chemical complex
- David Case (Thu May 25 2017 - 10:31:59 PDT)
- ruqaiya khalil (Mon May 22 2017 - 06:18:15 PDT)
[AMBER] MD under external electric field & GPUs parallel problem
- 吴萌 (Tue May 02 2017 - 02:28:29 PDT)
[AMBER] mdgx configuration sampling
- CA gmail (Mon May 22 2017 - 00:36:22 PDT)
- David Cerutti (Fri May 19 2017 - 10:23:13 PDT)
- David Cerutti (Fri May 19 2017 - 08:33:34 PDT)
- CA gmail (Fri May 19 2017 - 04:55:05 PDT)
[AMBER] MG angle parameter
- Tommaso Biagini (Wed May 10 2017 - 22:47:11 PDT)
- Elvis Martis (Wed May 10 2017 - 21:48:00 PDT)
- Tommaso Biagini (Wed May 10 2017 - 21:17:17 PDT)
- kungking Hanpaibool (Wed May 10 2017 - 08:25:07 PDT)
- Tommaso Biagini (Wed May 10 2017 - 08:15:22 PDT)
- Elvis Martis (Wed May 10 2017 - 07:21:49 PDT)
- Tommaso Biagini (Wed May 10 2017 - 05:37:58 PDT)
[AMBER] Minimisation of a complex
- Nikita Devnarain (Mon May 22 2017 - 01:34:07 PDT)
- Bill Ross (Mon May 22 2017 - 01:27:23 PDT)
- Nikita Devnarain (Mon May 22 2017 - 01:19:04 PDT)
- Bill Ross (Mon May 22 2017 - 01:12:00 PDT)
- Nikita Devnarain (Mon May 22 2017 - 00:54:09 PDT)
[AMBER] Missing File: charmmlipid2amber.csv
- Elvis Martis (Mon May 01 2017 - 00:03:57 PDT)
- Alexander Adams (Sun Apr 30 2017 - 23:28:02 PDT)
[AMBER] MMGBSA energy decomposition per frame
- Jason Swails (Tue May 30 2017 - 07:47:17 PDT)
- Thomas Evangelidis (Sun May 28 2017 - 06:29:19 PDT)
[AMBER] Molecule with glyco - single amino acid linkage?
- yunshi11 . (Mon May 08 2017 - 15:18:09 PDT)
- Lachele Foley (Sun May 07 2017 - 21:32:46 PDT)
- yunshi11 . (Sun May 07 2017 - 20:25:23 PDT)
[AMBER] NetCDF error: Invalid argument
- David Case (Mon May 22 2017 - 21:20:22 PDT)
- Daniel Roe (Mon May 22 2017 - 07:17:27 PDT)
- xu qingliang (Sun May 21 2017 - 23:28:03 PDT)
- David Case (Sat May 20 2017 - 21:45:58 PDT)
- xu qingliang (Sat May 20 2017 - 06:03:18 PDT)
[AMBER] No Torsion terms
- Elvis Martis (Tue May 30 2017 - 06:26:07 PDT)
- sylvester kisembo (Tue May 30 2017 - 06:15:39 PDT)
[AMBER] ntx=5 and ntx=7 (Sanderinput)
- David Case (Wed May 03 2017 - 05:27:41 PDT)
- Hannes Loeffler (Wed May 03 2017 - 00:31:05 PDT)
- Johannes Kalliauer (Wed May 03 2017 - 00:16:49 PDT)
[AMBER] Parameterization Ligand Boron
- Elvis Martis (Mon May 08 2017 - 07:45:48 PDT)
- Pedro Fernandes (Mon May 08 2017 - 06:09:46 PDT)
[AMBER] Partial Mini error
- David Case (Mon May 15 2017 - 19:15:50 PDT)
- Nikita Devnarain (Mon May 15 2017 - 05:33:02 PDT)
[AMBER] phosaa10 reference
- David A Case (Thu May 18 2017 - 08:06:13 PDT)
- Jacopo Sgrignani (Thu May 18 2017 - 07:30:39 PDT)
[AMBER] possible bug for reading &qmmm after &lmod
- David Case (Mon May 29 2017 - 12:34:07 PDT)
- Scott Brozell (Thu May 18 2017 - 11:34:07 PDT)
- liu junjun (Thu May 18 2017 - 09:00:01 PDT)
[AMBER] Possible bug in the GPU code
- David Case (Mon May 08 2017 - 18:14:57 PDT)
- Pratul K. Agarwal (Mon May 08 2017 - 15:35:44 PDT)
[AMBER] Problem in splitting mdcrd file with cpptraj
- Daniel Roe (Wed May 10 2017 - 08:48:56 PDT)
- Manjula Saravanan (Tue May 09 2017 - 23:11:11 PDT)
[AMBER] Problem with parmed
- Qinghua Liao (Wed May 17 2017 - 04:23:59 PDT)
- Jason Swails (Wed May 17 2017 - 04:17:00 PDT)
- Qinghua Liao (Wed May 17 2017 - 03:16:54 PDT)
- Hannes Loeffler (Wed May 17 2017 - 03:08:37 PDT)
- Qinghua Liao (Wed May 17 2017 - 03:00:42 PDT)
[AMBER] Query regarding energy calcuation using 3D-RISM
- David Case (Sat May 20 2017 - 21:23:57 PDT)
- Vertika Gautam (Sat May 20 2017 - 13:44:54 PDT)
[AMBER] question about commutation of sub-trajectories and frame aligning
- Gordon Richard Chalmers (Wed May 10 2017 - 10:36:08 PDT)
- Daniel Roe (Wed May 10 2017 - 08:46:12 PDT)
- Gordon Richard Chalmers (Wed May 10 2017 - 05:56:42 PDT)
[AMBER] Question about RMSD "jumps"
- Bill Ross (Sat May 27 2017 - 17:48:05 PDT)
- Ly, Thu Ngoc Anh (Sat May 27 2017 - 16:26:55 PDT)
[AMBER] Question about the pairwise option in cpptraj
- Daniel Roe (Fri May 05 2017 - 11:48:45 PDT)
- David Case (Wed May 03 2017 - 18:30:21 PDT)
[AMBER] Question on implementing igb=8, along with mbondi3
- Carlos Simmerling (Wed May 03 2017 - 03:28:58 PDT)
- Ramin Salimi (Wed May 03 2017 - 00:26:23 PDT)
[AMBER] random coil in the protein secondary structure analysis
- Daniel Roe (Tue May 30 2017 - 07:06:22 PDT)
- leila karami (Sat May 27 2017 - 09:04:03 PDT)
[AMBER] reference or custom GPUs?
- Ross Walker (Thu May 18 2017 - 17:22:11 PDT)
- Scott Le Grand (Thu May 18 2017 - 15:14:59 PDT)
- Ross Walker (Thu May 18 2017 - 14:50:10 PDT)
- Hadházi Ádám (Thu May 18 2017 - 03:00:57 PDT)
[AMBER] Reference structure for targeted MD
- Daniel Roe (Tue May 16 2017 - 09:02:15 PDT)
- David Case (Tue May 16 2017 - 05:28:30 PDT)
- Francesco Gentile (Mon May 15 2017 - 19:26:39 PDT)
[AMBER] Reg residue selection in trajectory
- Vidhya Srivatsan (Wed May 24 2017 - 12:08:24 PDT)
- Irfan Alibay (Wed May 24 2017 - 11:34:17 PDT)
- Vidhya Srivatsan (Wed May 24 2017 - 11:07:12 PDT)
[AMBER] Regarding amber-gaussian QM/MM problem
- Budhathoki, Dipesh (Fri May 05 2017 - 10:24:57 PDT)
- Goetz, Andreas (Tue May 02 2017 - 16:07:24 PDT)
- Budhathoki, Dipesh (Tue May 02 2017 - 15:35:08 PDT)
[AMBER] Regarding Native Contacts
- Daniel Roe (Mon May 22 2017 - 07:12:01 PDT)
- Suchetana Gupta (Mon May 22 2017 - 03:28:01 PDT)
[AMBER] RESP charge for protonated cytosine ribonucleotide
- David Case (Mon May 29 2017 - 12:46:34 PDT)
- xuzhh (Mon May 29 2017 - 03:42:02 PDT)
[AMBER] resp charges
- FyD (Thu May 18 2017 - 04:50:46 PDT)
- Jones de Andrade (Wed May 17 2017 - 06:01:45 PDT)
- David Cerutti (Wed May 17 2017 - 02:58:48 PDT)
- Andrea Spitaleri (Wed May 17 2017 - 01:50:22 PDT)
- Artem Shekhovtsov (Wed May 17 2017 - 01:34:05 PDT)
- Alessandro Contini (Wed May 17 2017 - 01:27:19 PDT)
- Jacopo Sgrignani (Wed May 17 2017 - 01:11:21 PDT)
[AMBER] Restraint in Steered MD/Jarzynski method
- Ramin Salimi (Mon May 01 2017 - 09:10:04 PDT)
- Hannes Loeffler (Mon May 01 2017 - 00:11:42 PDT)
[AMBER] sander API data structure
- Hai Nguyen (Mon May 22 2017 - 19:20:46 PDT)
- Brent Krueger (Mon May 22 2017 - 07:39:02 PDT)
- Bill Ross (Tue May 16 2017 - 10:52:24 PDT)
- Jason Swails (Tue May 16 2017 - 10:39:10 PDT)
- Brent Krueger (Tue May 16 2017 - 09:15:59 PDT)
- Hai Nguyen (Tue May 16 2017 - 08:32:34 PDT)
- Daniel Roe (Tue May 16 2017 - 08:03:21 PDT)
- Brent Krueger (Tue May 16 2017 - 06:43:26 PDT)
[AMBER] Spherical flat bottom restraint
- David Case (Sun May 28 2017 - 09:02:45 PDT)
- M. Wong (Sat May 27 2017 - 20:41:16 PDT)
[AMBER] Statistically estimating the error and data reliability for Jarzynski Method
- Hannes Loeffler (Thu May 18 2017 - 00:40:15 PDT)
- Ramin Salimi (Wed May 17 2017 - 13:26:41 PDT)
- Ramin Salimi (Wed May 17 2017 - 10:50:16 PDT)
- Adrian Roitberg (Wed May 17 2017 - 10:30:22 PDT)
- Ramin Salimi (Wed May 17 2017 - 10:21:41 PDT)
- Hannes Loeffler (Wed May 17 2017 - 02:12:44 PDT)
- Ramin Salimi (Wed May 17 2017 - 02:00:54 PDT)
- Hannes Loeffler (Wed May 17 2017 - 01:52:54 PDT)
- Ramin Salimi (Wed May 17 2017 - 01:24:54 PDT)
[AMBER] The problem for image tool in AMBER
- Daniel Roe (Fri May 05 2017 - 06:14:01 PDT)
- 鲁俊波 (Thu May 04 2017 - 09:37:35 PDT)
- Daniel Roe (Thu May 04 2017 - 08:49:53 PDT)
- 鲁俊波 (Wed May 03 2017 - 20:20:58 PDT)
[AMBER] Tip3p water box size for two different systems.
- Bill Ross (Thu May 11 2017 - 22:52:06 PDT)
- Elvis Martis (Thu May 11 2017 - 22:42:34 PDT)
- Saman Yousuf ali (Thu May 11 2017 - 22:30:43 PDT)
- Elvis Martis (Thu May 11 2017 - 22:18:59 PDT)
- Saman Yousuf ali (Thu May 11 2017 - 07:57:17 PDT)
[AMBER] tleap-incorpoarating .frcmod, .prep files for unnatural nucleotides
- Elvis Martis (Mon May 08 2017 - 21:11:43 PDT)
- p.kartheek (Mon May 08 2017 - 10:33:43 PDT)
[AMBER] Too many iterations in routine! in RMSD calculation
- Daniel Roe (Mon May 01 2017 - 09:23:09 PDT)
- kungking Hanpaibool (Mon May 01 2017 - 09:09:42 PDT)
- kungking Hanpaibool (Mon May 01 2017 - 08:59:59 PDT)
- Daniel Roe (Mon May 01 2017 - 08:55:58 PDT)
- kungking Hanpaibool (Mon May 01 2017 - 08:50:42 PDT)
- Daniel Roe (Mon May 01 2017 - 08:29:09 PDT)
[AMBER] Translate the center of mass of the protein to the origin (0, 0, 0)
- Daniel Roe (Wed May 24 2017 - 06:23:32 PDT)
- Meng Wu (Wed May 24 2017 - 02:47:27 PDT)
[AMBER] Two questions for GAFF
- Matsuura, Azuma (Wed May 10 2017 - 18:01:15 PDT)
- Junmei Wang (Wed May 10 2017 - 05:39:55 PDT)
- Matsuura, Azuma (Wed May 10 2017 - 00:58:16 PDT)
[AMBER] Unable to view the box coordinates in VMD
- Ramin Salimi (Mon May 22 2017 - 08:35:12 PDT)
- David Case (Mon May 22 2017 - 06:06:28 PDT)
- Ramin Salimi (Sun May 21 2017 - 22:51:55 PDT)
- David Case (Sun May 21 2017 - 16:23:54 PDT)
- Ramin Salimi (Sun May 21 2017 - 10:55:32 PDT)
[AMBER] understanding results
- Carlos Romero (Thu May 18 2017 - 20:06:38 PDT)
- David A Case (Thu May 18 2017 - 06:35:19 PDT)
- Carlos Romero (Wed May 17 2017 - 11:46:28 PDT)
[AMBER] Unstable umbrella simulation with Amber16 in GTX1080
- David Case (Sun May 21 2017 - 16:31:08 PDT)
- kurisaki (Thu May 18 2017 - 15:41:03 PDT)
[AMBER] Virial and Kinetic energy
- Iain Bethune (Tue May 23 2017 - 03:47:10 PDT)
[AMBER] Water Analysis with SPAM
- Daniel Roe (Tue May 16 2017 - 09:08:23 PDT)
- julian.zachmann selvita.home.pl (Tue May 16 2017 - 08:40:07 PDT)
- Daniel Roe (Tue May 16 2017 - 08:19:50 PDT)
- julian.zachmann selvita.home.pl (Tue May 16 2017 - 08:09:24 PDT)
- Daniel Roe (Tue May 16 2017 - 07:49:58 PDT)
- Bill Ross (Mon May 15 2017 - 11:34:14 PDT)
- julian.zachmann selvita.home.pl (Mon May 15 2017 - 04:56:15 PDT)
- Bill Ross (Mon May 15 2017 - 04:47:34 PDT)
- julian.zachmann selvita.home.pl (Mon May 15 2017 - 04:27:48 PDT)
- Bill Ross (Mon May 15 2017 - 03:22:45 PDT)
- Bill Ross (Mon May 15 2017 - 03:16:53 PDT)
- Bill Ross (Mon May 15 2017 - 02:54:51 PDT)
- julian.zachmann selvita.home.pl (Mon May 15 2017 - 02:20:43 PDT)
- Bill Ross (Mon May 15 2017 - 02:09:32 PDT)
- julian.zachmann selvita.home.pl (Mon May 15 2017 - 01:55:38 PDT)
- julian.zachmann selvita.home.pl (Thu May 11 2017 - 07:29:58 PDT)
[AMBER] Water Geometry in SPCBOX Inconsistent with Literatures
- Chris Moth (Tue May 30 2017 - 09:57:04 PDT)
- David Cerutti (Mon May 29 2017 - 01:24:54 PDT)
- Changhao Wang (Mon May 29 2017 - 00:30:23 PDT)
[AMBER] Which Linux distro for Amber16?
- Bill Ross (Tue May 23 2017 - 21:33:47 PDT)
- Jason Swails (Tue May 23 2017 - 21:28:19 PDT)
- Hai Nguyen (Tue May 23 2017 - 20:57:18 PDT)
- Hadházi Ádám (Mon May 22 2017 - 05:00:20 PDT)
[AMBER] Wrong quotation marks in manual
- David Case (Mon May 29 2017 - 09:07:50 PDT)
[AMBER] Wrong Quotation marks in Manual in several examplecodes
- Hai Nguyen (Tue May 23 2017 - 21:06:28 PDT)
- Johannes Kalliauer (Mon May 22 2017 - 01:59:09 PDT)
consult about LEaP in amber
- 张壮壮 (Mon May 01 2017 - 07:28:07 PDT)
error: could not find mpi library for --enable-mpi
- David Case (Mon May 29 2017 - 16:55:42 PDT)
- Lucas (Mon May 29 2017 - 13:19:27 PDT)
NetCDF error: Invalid argument (David Case)
- David Case (Wed May 24 2017 - 17:26:42 PDT)
- xu qingliang (Wed May 24 2017 - 01:39:17 PDT)

Amber Archive May 2017 by subject