Amber Archive Aug 2017: by subject

[AMBER] (kein Betreff)
- Traeg, Johannes (Thu Aug 31 2017 - 01:11:33 PDT)
- Junmei Wang (Wed Aug 30 2017 - 08:27:44 PDT)
- Traeg, Johannes (Wed Aug 30 2017 - 02:28:48 PDT)
- Junmei Wang (Tue Aug 29 2017 - 07:02:48 PDT)
- Junmei Wang (Tue Aug 29 2017 - 06:54:03 PDT)
- David A Case (Tue Aug 22 2017 - 05:14:16 PDT)
- Traeg, Johannes (Tue Aug 22 2017 - 03:31:48 PDT)
- Hannes Loeffler (Tue Aug 22 2017 - 01:56:40 PDT)
- Traeg, Johannes (Tue Aug 22 2017 - 01:47:49 PDT)
[AMBER] -rem flags in string method with swarms of trajectories amber
- Chunli Yan (Wed Aug 02 2017 - 19:02:31 PDT)
- Feng Pan (Wed Aug 02 2017 - 15:24:59 PDT)
- Feng Pan (Wed Aug 02 2017 - 15:18:46 PDT)
- Chunli Yan (Wed Aug 02 2017 - 14:49:22 PDT)
[AMBER] ... RESTARTED DUE TO LINMIN FAILURE ...
- Jason Swails (Mon Aug 28 2017 - 19:02:11 PDT)
- Malay Raul (Wed Aug 09 2017 - 08:23:31 PDT)
[AMBER] A bug with unperturbed charge during tleap processing
- Bill Ross (Wed Aug 09 2017 - 04:03:29 PDT)
- James Starlight (Wed Aug 09 2017 - 02:21:12 PDT)
- James Starlight (Mon Aug 07 2017 - 11:07:31 PDT)
- Daniel Roe (Mon Aug 07 2017 - 09:29:37 PDT)
- James Starlight (Mon Aug 07 2017 - 09:28:15 PDT)
- Daniel Roe (Mon Aug 07 2017 - 09:13:32 PDT)
- James Starlight (Mon Aug 07 2017 - 08:00:19 PDT)
- Bill Ross (Fri Aug 04 2017 - 12:00:01 PDT)
- James Starlight (Fri Aug 04 2017 - 11:50:25 PDT)
- James Starlight (Fri Aug 04 2017 - 05:34:02 PDT)
- James Starlight (Fri Aug 04 2017 - 00:19:27 PDT)
- David A Case (Thu Aug 03 2017 - 18:07:42 PDT)
- James Starlight (Thu Aug 03 2017 - 06:38:34 PDT)
- David A Case (Thu Aug 03 2017 - 04:55:44 PDT)
- James Starlight (Thu Aug 03 2017 - 01:27:19 PDT)
- Bill Ross (Wed Aug 02 2017 - 21:31:28 PDT)
- James Starlight (Wed Aug 02 2017 - 11:16:02 PDT)
[AMBER] A restrain mask for membrane protein simulation
- James Starlight (Fri Aug 18 2017 - 07:34:41 PDT)
- ABEL Stephane (Fri Aug 18 2017 - 07:31:24 PDT)
- James Starlight (Fri Aug 18 2017 - 07:17:05 PDT)
[AMBER] About common Gromacs and Amber Benchmarks
- Hannes Loeffler (Tue Aug 08 2017 - 00:45:01 PDT)
- Vlad (Tue Aug 08 2017 - 00:38:55 PDT)
[AMBER] adQMMM overheating
- Goetz, Andreas (Thu Aug 10 2017 - 00:41:04 PDT)
- Artur Przydacz (Wed Aug 09 2017 - 05:28:39 PDT)
- Goetz, Andreas (Tue Aug 08 2017 - 14:58:20 PDT)
- Artur Przydacz (Tue Aug 08 2017 - 14:03:40 PDT)
[AMBER] Amber Atom Types for Non-standard Residue
- david kastner (Sat Aug 05 2017 - 18:08:23 PDT)
[AMBER] AMBER Digest, Vol 2042, Issue 1
- Suchetana Gupta (Thu Aug 31 2017 - 03:13:38 PDT)
[AMBER] amber frcmod file
- Neha Gandhi (Thu Aug 03 2017 - 01:51:40 PDT)
[AMBER] amber install
- David A Case (Thu Aug 03 2017 - 05:02:01 PDT)
- Hai Nguyen (Wed Aug 02 2017 - 21:34:18 PDT)
- liu junjun (Wed Aug 02 2017 - 20:00:36 PDT)
- Mohammad Zahidul Hossain Khan (Wed Aug 02 2017 - 19:06:31 PDT)
- Mohammad Zahidul Hossain Khan (Wed Aug 02 2017 - 15:04:19 PDT)
[AMBER] Amber Install Failure - update does not work
- Leandro Bortot (Thu Aug 17 2017 - 06:21:43 PDT)
- James Kress (Wed Aug 16 2017 - 08:45:27 PDT)
- David A Case (Wed Aug 16 2017 - 07:06:32 PDT)
- David A Case (Tue Aug 15 2017 - 20:41:03 PDT)
- James Kress (Tue Aug 15 2017 - 15:47:52 PDT)
[AMBER] Amber TI accuracy
- Adrian Roitberg (Tue Aug 15 2017 - 08:42:38 PDT)
- Nikolay N. Kuzmich (Tue Aug 15 2017 - 08:36:59 PDT)
[AMBER] Amber web site is back up
- David A Case (Tue Aug 15 2017 - 06:49:49 PDT)
[AMBER] Amber workshop?
- Ross Walker (Thu Aug 24 2017 - 09:54:28 PDT)
- Georg Kuenze (Wed Aug 23 2017 - 14:51:23 PDT)
[AMBER] Amber16/DFTB and bromine
- Amani Eshtiwi (Fri Aug 18 2017 - 19:32:43 PDT)
- Amani Eshtiwi (Fri Aug 18 2017 - 19:11:18 PDT)
- Gustavo Seabra (Fri Aug 18 2017 - 19:06:32 PDT)
- Amani Eshtiwi (Fri Aug 18 2017 - 19:04:12 PDT)
- Gustavo Seabra (Fri Aug 18 2017 - 18:51:19 PDT)
- Amani Eshtiwi (Fri Aug 18 2017 - 16:44:18 PDT)
- Amani Eshtiwi (Fri Aug 18 2017 - 16:26:55 PDT)
- Amani Eshtiwi (Fri Aug 18 2017 - 15:46:46 PDT)
- Amani Eshtiwi (Fri Aug 18 2017 - 15:37:35 PDT)
- Gustavo Seabra (Fri Aug 18 2017 - 13:02:26 PDT)
- Goetz, Andreas (Fri Aug 18 2017 - 12:19:55 PDT)
- Amani Eshtiwi (Thu Aug 17 2017 - 13:20:17 PDT)
- Goetz, Andreas (Thu Aug 17 2017 - 12:53:05 PDT)
- Amani Eshtiwi (Thu Aug 17 2017 - 12:32:01 PDT)
[AMBER] An equilibration of the membrane protein prepared by charmm-gui
- James Kress (Thu Aug 31 2017 - 13:28:38 PDT)
- James Starlight (Thu Aug 31 2017 - 09:57:38 PDT)
- James Starlight (Thu Aug 31 2017 - 09:31:12 PDT)
- Amy Rice (Thu Aug 31 2017 - 08:23:31 PDT)
- James Starlight (Thu Aug 31 2017 - 07:52:04 PDT)
- James Starlight (Fri Aug 25 2017 - 14:26:46 PDT)
- James Starlight (Wed Aug 23 2017 - 08:50:58 PDT)
- James Starlight (Tue Aug 22 2017 - 07:26:11 PDT)
- ABEL Stephane (Fri Aug 18 2017 - 07:51:13 PDT)
- James Starlight (Fri Aug 18 2017 - 07:33:21 PDT)
- ABEL Stephane (Fri Aug 18 2017 - 07:28:23 PDT)
- James Starlight (Fri Aug 18 2017 - 06:36:28 PDT)
- ABEL Stephane (Fri Aug 18 2017 - 03:30:45 PDT)
- James Starlight (Fri Aug 18 2017 - 00:23:24 PDT)
[AMBER] Analyzing the aMD results - Tutorial 22
- carmine marco morgillo (Sat Aug 19 2017 - 08:51:37 PDT)
[AMBER] angle of domain movement calculation
- Carlos Simmerling (Wed Aug 23 2017 - 08:58:53 PDT)
- sangita kachhap (Wed Aug 23 2017 - 03:05:29 PDT)
[AMBER] Applying external force along a particular direction
- Sanjib Paul (Thu Aug 03 2017 - 05:45:29 PDT)
[AMBER] Barostat options for membrane protein simulations in NPT
- James Starlight (Wed Aug 02 2017 - 08:21:15 PDT)
[AMBER] Binding free energy for dimeric form
- Maryam Hamzehee (Wed Aug 23 2017 - 04:55:07 PDT)
[AMBER] Building of beta strand
- Rajarshi Roy (Tue Aug 08 2017 - 03:40:34 PDT)
- Hai Nguyen (Mon Aug 07 2017 - 12:23:58 PDT)
- Daniel Roe (Mon Aug 07 2017 - 07:28:37 PDT)
- Rajarshi Roy (Wed Aug 02 2017 - 21:34:08 PDT)
- Hai Nguyen (Wed Aug 02 2017 - 10:24:54 PDT)
- Rajarshi Roy (Wed Aug 02 2017 - 09:32:52 PDT)
- Hai Nguyen (Wed Aug 02 2017 - 09:27:47 PDT)
- Rajarshi Roy (Wed Aug 02 2017 - 07:51:19 PDT)
[AMBER] Calculate lateral self-diffusion coefficient for POPE embedded protein system
- Daniel Roe (Thu Aug 31 2017 - 06:03:18 PDT)
- carmine marco morgillo (Wed Aug 30 2017 - 15:51:20 PDT)
[AMBER] calculate PMF in string methods
- Feng Pan (Sat Aug 19 2017 - 00:28:35 PDT)
- Chunli Yan (Fri Aug 18 2017 - 14:43:41 PDT)
- Carlos Simmerling (Fri Aug 18 2017 - 12:40:19 PDT)
- Chunli Yan (Thu Aug 17 2017 - 19:25:57 PDT)
- Chunli Yan (Thu Aug 17 2017 - 19:22:45 PDT)
- Feng Pan (Thu Aug 17 2017 - 15:48:55 PDT)
- Chunli Yan (Wed Aug 16 2017 - 16:42:03 PDT)
[AMBER] Calculation the Area per lipids using cpptraj
- James Starlight (Wed Aug 30 2017 - 01:00:03 PDT)
- Daniel Roe (Tue Aug 29 2017 - 12:35:33 PDT)
- James Starlight (Wed Aug 23 2017 - 06:33:35 PDT)
- Daniel Roe (Mon Aug 21 2017 - 06:28:04 PDT)
- James Starlight (Mon Aug 21 2017 - 01:19:35 PDT)
[AMBER] Can pmemd.cuda.MPI do SMD on GPUs?
- Xing (Thu Aug 17 2017 - 13:59:12 PDT)
- Adrian Roitberg (Wed Aug 16 2017 - 14:55:10 PDT)
- Xing (Wed Aug 16 2017 - 14:16:47 PDT)
[AMBER] charmmlipid2amber.py with Charm-gui lipids
- James Starlight (Thu Aug 17 2017 - 04:25:35 PDT)
- ABEL Stephane (Thu Aug 17 2017 - 04:16:30 PDT)
- James Starlight (Thu Aug 17 2017 - 01:44:42 PDT)
- ABEL Stephane (Wed Aug 16 2017 - 11:07:34 PDT)
- James Starlight (Wed Aug 16 2017 - 10:57:40 PDT)
- ABEL Stephane (Wed Aug 16 2017 - 09:18:54 PDT)
- James Starlight (Wed Aug 16 2017 - 08:54:01 PDT)
[AMBER] Clarification about Gnp settings in MM/PBSA
- Guqin Shi (Tue Aug 29 2017 - 13:00:47 PDT)
- Guqin Shi (Tue Aug 29 2017 - 11:35:51 PDT)
[AMBER] Closest velocities
- Daniel Roe (Tue Aug 29 2017 - 12:26:03 PDT)
- Pär Håkansson (Tue Aug 29 2017 - 00:31:23 PDT)
- Daniel Roe (Thu Aug 24 2017 - 13:00:49 PDT)
- Pär Håkansson (Thu Aug 24 2017 - 12:20:04 PDT)
[AMBER] Compilation of Amber 14
- Milo Westler (Fri Aug 04 2017 - 12:44:56 PDT)
- Daniel Roe (Fri Aug 04 2017 - 11:24:34 PDT)
- Milo Westler (Fri Aug 04 2017 - 09:00:39 PDT)
- David A Case (Thu Aug 03 2017 - 18:20:59 PDT)
- Milo Westler (Thu Aug 03 2017 - 13:01:10 PDT)
[AMBER] convert .mae topology to .prmtop topology?
- Daniel Roe (Thu Aug 31 2017 - 06:15:31 PDT)
- Marcelo Andrade Chagas (Wed Aug 30 2017 - 20:14:56 PDT)
[AMBER] cphstats Error: Could not open or parse cpin file
- Jason Swails (Mon Aug 28 2017 - 18:52:15 PDT)
- Vincent Ustach (Thu Aug 24 2017 - 20:22:28 PDT)
[AMBER] Cpptraj to center molecules
- Aseel Bala Ahmed (Sun Aug 13 2017 - 13:27:22 PDT)
- David A Case (Sun Aug 13 2017 - 05:32:15 PDT)
- Aseel Bala Ahmed (Sat Aug 12 2017 - 14:38:56 PDT)
- Bill Ross (Sat Aug 12 2017 - 13:22:38 PDT)
- Aseel Bala Ahmed (Sat Aug 12 2017 - 13:13:49 PDT)
- Bill Ross (Sat Aug 12 2017 - 13:09:27 PDT)
- Bill Ross (Sat Aug 12 2017 - 13:04:17 PDT)
- Aseel Bala Ahmed (Sat Aug 12 2017 - 12:55:32 PDT)
- Daniel Roe (Sat Aug 12 2017 - 10:50:17 PDT)
- Aseel Bala (Fri Aug 11 2017 - 12:36:06 PDT)
[AMBER] Creation of coordinate and topology file for protei-ligand complex
- David A Case (Mon Aug 28 2017 - 10:42:34 PDT)
- Bill Ross (Mon Aug 28 2017 - 09:08:38 PDT)
- Bill Ross (Mon Aug 28 2017 - 09:06:28 PDT)
- Ashok Kumar (Mon Aug 28 2017 - 09:03:00 PDT)
[AMBER] Decomposition Energy Problem with Aspartic Acid only
- Jag Silwal (Fri Aug 11 2017 - 09:18:45 PDT)
[AMBER] Deprotonation of Tyr
- pancham lal Gupta (Wed Aug 30 2017 - 08:40:08 PDT)
- Marcos Serrou do Amaral (Mon Aug 21 2017 - 16:25:46 PDT)
- Sowmya Indrakumar (Mon Aug 21 2017 - 13:19:15 PDT)
- Marcos Serrou do Amaral (Mon Aug 21 2017 - 12:34:52 PDT)
- Sowmya Indrakumar (Mon Aug 21 2017 - 08:37:54 PDT)
- Sowmya Indrakumar (Sun Aug 20 2017 - 06:45:32 PDT)
- Sowmya Indrakumar (Fri Aug 18 2017 - 08:57:44 PDT)
- Adrian Roitberg (Fri Aug 18 2017 - 08:38:10 PDT)
- Sowmya Indrakumar (Fri Aug 18 2017 - 08:24:46 PDT)
[AMBER] Deprotonation of Tyr using Parmed
- Jason Swails (Mon Aug 28 2017 - 18:57:59 PDT)
- Sowmya Indrakumar (Thu Aug 24 2017 - 06:04:32 PDT)
- Jason Swails (Thu Aug 24 2017 - 02:01:16 PDT)
- Sowmya Indrakumar (Tue Aug 22 2017 - 07:08:06 PDT)
- Sowmya Indrakumar (Tue Aug 22 2017 - 06:41:11 PDT)
[AMBER] different crd format?
- Daniel Roe (Mon Aug 07 2017 - 07:25:42 PDT)
- David A Case (Thu Aug 03 2017 - 05:06:31 PDT)
- Albert (Thu Aug 03 2017 - 00:46:25 PDT)
[AMBER] Discrepancies in MMPBSA calculations for the same trajectory
- Andrew.Warden.csiro.au (Thu Aug 24 2017 - 21:42:06 PDT)
[AMBER] Distance Restraint using COM for Umbrella Sampling
- Daniel Roe (Tue Aug 29 2017 - 12:29:06 PDT)
- Suchetana Gupta (Tue Aug 29 2017 - 05:56:49 PDT)
[AMBER] Error in Amber16 documentation
- Paul Westphälinger (Wed Aug 16 2017 - 07:32:18 PDT)
- Paul Westphälinger (Wed Aug 16 2017 - 03:30:01 PDT)
[AMBER] Error in hbond lifetime analysis
- Daniel Roe (Thu Aug 10 2017 - 12:29:17 PDT)
- Baig abdullah Al muhit (Tue Aug 08 2017 - 13:17:41 PDT)
[AMBER] Error in leap on using divalent ion
- David A Case (Wed Aug 09 2017 - 08:35:44 PDT)
- Chayya Bhargac (Wed Aug 09 2017 - 06:23:42 PDT)
[AMBER] Error while running antechamber for modified amino acid residue
- Rajarshi Roy (Sun Aug 27 2017 - 09:22:33 PDT)
- David A Case (Sun Aug 27 2017 - 05:57:40 PDT)
- Rajarshi Roy (Sun Aug 27 2017 - 04:50:28 PDT)
[AMBER] Error-Calculating distance between two atoms in CPPTRAJ
- Daniel Roe (Fri Aug 11 2017 - 10:03:44 PDT)
- Jag Silwal (Fri Aug 11 2017 - 10:00:21 PDT)
- Daniel Roe (Fri Aug 11 2017 - 09:52:39 PDT)
- Hai Nguyen (Fri Aug 11 2017 - 09:52:26 PDT)
- Jag Silwal (Fri Aug 11 2017 - 09:42:21 PDT)
[AMBER] External force apply along a particular direction
- Sanjib Paul (Wed Aug 02 2017 - 00:21:30 PDT)
[AMBER] fixing backbone dihedral angles in RNA structure
- Daniel Roe (Fri Aug 11 2017 - 10:08:09 PDT)
- Bill Ross (Thu Aug 10 2017 - 18:08:23 PDT)
- Asmita Gupta (Thu Aug 10 2017 - 17:58:58 PDT)
[AMBER] For restraint heating
- Saikat Pal (Tue Aug 29 2017 - 07:29:41 PDT)
- Bill Ross (Tue Aug 29 2017 - 07:13:34 PDT)
- Saikat Pal (Tue Aug 29 2017 - 07:06:08 PDT)
[AMBER] frcmod file format
- Pengfei Li (Thu Aug 31 2017 - 07:48:34 PDT)
- Lizelle Lubbe (Thu Aug 31 2017 - 03:03:45 PDT)
[AMBER] gaff2 atom type (cs) is not in PARMCHK.DAT
- Junmei Wang (Tue Aug 15 2017 - 04:51:09 PDT)
- David A Case (Wed Aug 09 2017 - 04:42:57 PDT)
- Scott Brozell (Tue Aug 08 2017 - 20:06:29 PDT)
- Scott Brozell (Tue Aug 08 2017 - 14:22:54 PDT)
- Tsai Kun-Lin (Mon Aug 07 2017 - 17:51:44 PDT)
[AMBER] GaMD
- Neha Gandhi (Tue Aug 01 2017 - 16:00:55 PDT)
[AMBER] grid command in cpptraj
- Daniel Roe (Wed Aug 16 2017 - 07:56:10 PDT)
- 沖本憲明 (Wed Aug 16 2017 - 07:23:10 PDT)
[AMBER] How best to build a solvent box for a solute with changing dimensions?
- Daniel Roe (Mon Aug 07 2017 - 09:26:13 PDT)
- Kasprzak, Wojciech (NIH/NCI) [C] (Mon Aug 07 2017 - 08:53:57 PDT)
[AMBER] How many GPU card is working
- Saikat Pal (Fri Aug 18 2017 - 07:33:34 PDT)
- Daniel Roe (Fri Aug 18 2017 - 07:13:37 PDT)
- Saikat Pal (Fri Aug 18 2017 - 06:50:13 PDT)
- Daniel Roe (Fri Aug 18 2017 - 06:09:12 PDT)
- Saikat Pal (Fri Aug 18 2017 - 05:35:48 PDT)
- Daniel Roe (Fri Aug 18 2017 - 05:15:09 PDT)
- Saikat Pal (Fri Aug 18 2017 - 04:33:47 PDT)
[AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file.
- Bill Ross (Thu Aug 31 2017 - 12:50:42 PDT)
- Parviz Seifpanahi Shabane (Thu Aug 31 2017 - 10:11:49 PDT)
- Bill Ross (Thu Aug 31 2017 - 10:02:55 PDT)
- Parviz Seifpanahi Shabane (Thu Aug 31 2017 - 08:11:44 PDT)
[AMBER] How to cross-corrlation matrix betwern 3 Calpha atom
- Arpita Goswami (Tue Aug 15 2017 - 22:34:37 PDT)
[AMBER] how to implement GEN keyword in QM/MM with external program
- Goetz, Andreas (Fri Aug 18 2017 - 11:33:04 PDT)
- chemist zobia (Wed Aug 16 2017 - 22:31:16 PDT)
[AMBER] How to move the protein to the corner of the box.
- David A Case (Sun Aug 20 2017 - 06:05:52 PDT)
- Parviz Seifpanahi Shabane (Sat Aug 19 2017 - 13:49:37 PDT)
[AMBER] How to put the restrain on just part of the system.
- James Kress (Mon Aug 28 2017 - 15:33:13 PDT)
- Daniel Roe (Mon Aug 28 2017 - 05:42:13 PDT)
- Parviz Seifpanahi Shabane (Sun Aug 27 2017 - 15:57:17 PDT)
- David A Case (Sun Aug 27 2017 - 13:45:10 PDT)
- Parviz Seifpanahi Shabane (Sun Aug 27 2017 - 08:05:24 PDT)
[AMBER] Hybridization problem in Amber
- Julian Stys (Mon Aug 28 2017 - 15:11:08 PDT)
- David A Case (Sun Aug 27 2017 - 14:08:55 PDT)
- Julian Stys (Fri Aug 25 2017 - 12:14:24 PDT)
[AMBER] I have generated an AMBER trajectory with coordinates, velocities and forces. How can I place the relevant data sets in the text file?
- Jewgeni Starikow (Mon Aug 28 2017 - 06:45:45 PDT)
- Daniel Roe (Mon Aug 28 2017 - 05:39:36 PDT)
- Bill Ross (Mon Aug 28 2017 - 01:44:35 PDT)
- Jewgeni Starikow (Mon Aug 28 2017 - 00:26:42 PDT)
- Bill Ross (Sun Aug 27 2017 - 23:16:21 PDT)
- Jewgeni Starikow (Sun Aug 27 2017 - 22:24:26 PDT)
- Jewgeni Starikow (Sun Aug 27 2017 - 22:22:29 PDT)
- Hai Nguyen (Sun Aug 27 2017 - 19:01:01 PDT)
- Bill Ross (Sun Aug 27 2017 - 15:38:45 PDT)
- Jewgeni Starikow (Sun Aug 27 2017 - 14:41:29 PDT)
[AMBER] iat >= 3 in PMEMD and PMEMD.cuda
- kurisaki (Tue Aug 08 2017 - 18:09:51 PDT)
[AMBER] If I use source leaprc.gaff command for DNA and protein is it load gaff forcefield or ff14SB force field??
- David A Case (Tue Aug 01 2017 - 05:21:25 PDT)
- Daniel Roe (Tue Aug 01 2017 - 05:13:12 PDT)
- Saikat Pal (Tue Aug 01 2017 - 03:54:10 PDT)
[AMBER] Impose bond lengths
- Bill Ross (Fri Aug 18 2017 - 10:18:30 PDT)
- RYDER WHITTAKER HAWKINS (Fri Aug 18 2017 - 08:35:58 PDT)
[AMBER] Install amber 14 in nvidia gpu tesla k40
- David A Case (Sat Aug 19 2017 - 09:04:59 PDT)
- Saikat Pal (Sat Aug 19 2017 - 00:24:36 PDT)
[AMBER] Install in gpu AMBER14 for high performance computer
- Saikat Pal (Thu Aug 17 2017 - 23:57:46 PDT)
- David A Case (Thu Aug 17 2017 - 11:57:18 PDT)
- Saikat Pal (Thu Aug 17 2017 - 08:46:02 PDT)
[AMBER] Is this necessary HOH=SPC command
- David A Case (Thu Aug 10 2017 - 10:24:21 PDT)
- Saikat Pal (Thu Aug 10 2017 - 05:32:52 PDT)
[AMBER] LINMIN Error while minimizing
- David A Case (Fri Aug 25 2017 - 13:07:09 PDT)
- James Kress (Fri Aug 25 2017 - 10:36:32 PDT)
- Bill Ross (Fri Aug 25 2017 - 09:58:51 PDT)
- Chayya Bhargac (Fri Aug 25 2017 - 08:19:38 PDT)
- Bill Ross (Thu Aug 24 2017 - 23:10:23 PDT)
- Chayya Bhargac (Thu Aug 24 2017 - 23:05:10 PDT)
[AMBER] Manual parameterization of the TIP4P/2005 water model
- Hannes Konegger (Wed Aug 02 2017 - 01:27:32 PDT)
[AMBER] mpirun -np 1 and mpirun -np 2 Peer to Peer support problem
- Saikat Pal (Mon Aug 21 2017 - 03:22:17 PDT)
[AMBER] Number of triangulated 3-point waters found: 0
- David A Case (Thu Aug 03 2017 - 05:09:32 PDT)
- Shilpa Gupta (Thu Aug 03 2017 - 03:50:59 PDT)
[AMBER] Pairwise Decomposition-Mask not wroking?
- Jag Silwal (Tue Aug 15 2017 - 09:09:21 PDT)
[AMBER] Pairwise-Decomposition Energy
- Jag Silwal (Mon Aug 14 2017 - 07:45:08 PDT)
[AMBER] Parameters for HEME-CYS covalent bond
- Pengfei Li (Sat Aug 05 2017 - 20:16:24 PDT)
- Thomas Charles Pochapsky (Sat Aug 05 2017 - 05:25:31 PDT)
- Avijit Rakshit (Sat Aug 05 2017 - 00:56:42 PDT)
- Andrew Schaub (Sat Aug 05 2017 - 00:43:18 PDT)
- Avijit Rakshit (Sat Aug 05 2017 - 00:29:21 PDT)
[AMBER] parametrization of an RNA base
- David A Case (Sun Aug 06 2017 - 11:33:40 PDT)
- Andrew Schaub (Sat Aug 05 2017 - 00:47:50 PDT)
- Bill Ross (Fri Aug 04 2017 - 15:29:03 PDT)
- giulia palermo (Fri Aug 04 2017 - 14:48:01 PDT)
[AMBER] pbc box information missing
- David A Case (Thu Aug 03 2017 - 04:59:00 PDT)
- Albert (Wed Aug 02 2017 - 13:13:44 PDT)
[AMBER] Performed MMPBSA.py.MPI failed in Amber16 with Ambertools 17
- Jiyuan Liu (Mon Aug 21 2017 - 07:22:48 PDT)
- Jiyuan Liu (Sun Aug 20 2017 - 07:35:09 PDT)
- Jiyuan Liu (Sat Aug 19 2017 - 05:48:07 PDT)
- David A Case (Fri Aug 18 2017 - 13:59:41 PDT)
- JiYuan Liu (Fri Aug 18 2017 - 10:28:05 PDT)
[AMBER] Periodicity of metal bond
- Pengfei Li (Tue Aug 15 2017 - 07:50:00 PDT)
- Lizelle Lubbe (Tue Aug 15 2017 - 06:28:22 PDT)
[AMBER] polarization force field
- sangita kachhap (Tue Aug 08 2017 - 05:50:46 PDT)
- David A Case (Tue Aug 08 2017 - 04:19:40 PDT)
- sangita kachhap (Tue Aug 08 2017 - 03:25:12 PDT)
[AMBER] problem in minimization and heating
- David A Case (Tue Aug 29 2017 - 04:53:28 PDT)
- Bill Ross (Tue Aug 29 2017 - 00:50:46 PDT)
- Saikat Pal (Tue Aug 29 2017 - 00:42:37 PDT)
[AMBER] Problem with leaprc.ff14SB
- George Tzotzos (Wed Aug 09 2017 - 08:20:53 PDT)
- David A Case (Tue Aug 08 2017 - 12:55:00 PDT)
- George Tzotzos (Tue Aug 08 2017 - 10:50:59 PDT)
[AMBER] Problem with tleap (non atom type)
- Bill Ross (Fri Aug 18 2017 - 13:48:09 PDT)
- David A Case (Fri Aug 18 2017 - 13:44:33 PDT)
- Bill Ross (Fri Aug 18 2017 - 10:20:39 PDT)
- Parviz Seifpanahi Shabane (Fri Aug 18 2017 - 07:51:06 PDT)
[AMBER] problems with the HAP tutorial
- Kris Feher (Thu Aug 10 2017 - 03:25:06 PDT)
[AMBER] QM/MM calculation Amber16/DFTB
- Amani Eshtiwi (Thu Aug 10 2017 - 17:38:48 PDT)
[AMBER] QM/MM calculation in Amber
- David A Case (Sun Aug 06 2017 - 11:37:38 PDT)
- Albert (Fri Aug 04 2017 - 23:39:52 PDT)
[AMBER] QMMM error: "| Flags: getting box info from netcdf restart file"
- Goetz, Andreas (Thu Aug 10 2017 - 09:52:58 PDT)
- Charles Mariasoosai (Thu Aug 10 2017 - 09:20:24 PDT)
[AMBER] Query about SPC and SPCE water model
- David A Case (Thu Aug 10 2017 - 04:18:12 PDT)
- Saikat Pal (Thu Aug 10 2017 - 04:03:35 PDT)
[AMBER] Query regarding water-water interaction potential in GIST output
- Rakesh Srivastava (Tue Aug 29 2017 - 21:22:07 PDT)
- Steven Ramsey (Tue Aug 29 2017 - 07:03:40 PDT)
- Rakesh Srivastava (Tue Aug 29 2017 - 04:56:54 PDT)
[AMBER] RDF for dendrimer
- Daniel Roe (Mon Aug 07 2017 - 08:56:16 PDT)
- Hai Nguyen (Fri Aug 04 2017 - 14:34:55 PDT)
- Christopher Gorman (Fri Aug 04 2017 - 14:18:33 PDT)
[AMBER] Regarding GPU card
- Scott Le Grand (Thu Aug 24 2017 - 11:25:17 PDT)
- Ross Walker (Thu Aug 24 2017 - 09:58:30 PDT)
- Alessandro Contini (Thu Aug 24 2017 - 07:41:11 PDT)
- MOHD HOMAIDUR RAHMAN (Thu Aug 24 2017 - 07:32:10 PDT)
[AMBER] RESP calculation in MCPBpy
- Lizelle Lubbe (Fri Aug 25 2017 - 03:39:18 PDT)
[AMBER] results for string methods
- Chunli Yan (Tue Aug 08 2017 - 10:33:36 PDT)
- Feng Pan (Tue Aug 08 2017 - 10:27:38 PDT)
- Chunli Yan (Mon Aug 07 2017 - 18:49:45 PDT)
[AMBER] RMSD colvar
- Feng Pan (Sun Aug 27 2017 - 21:09:03 PDT)
- Chunli Yan (Thu Aug 24 2017 - 12:57:01 PDT)
[AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files
- Bill Ross (Tue Aug 01 2017 - 11:23:02 PDT)
- Szymon Żaczek (Tue Aug 01 2017 - 11:17:17 PDT)
- Alonso Martinez, Diego (Tue Aug 01 2017 - 09:49:42 PDT)
- Carlos Simmerling (Tue Aug 01 2017 - 07:54:17 PDT)
- Alonso Martinez, Diego (Tue Aug 01 2017 - 07:48:34 PDT)
[AMBER] SASA energy
- Daniel Roe (Wed Aug 16 2017 - 11:51:02 PDT)
- Mohammad Zahidul Hossain Khan (Wed Aug 16 2017 - 11:41:12 PDT)
- Daniel Roe (Wed Aug 16 2017 - 11:39:26 PDT)
- Mohammad Zahidul Hossain Khan (Wed Aug 16 2017 - 11:09:14 PDT)
- David A Case (Sat Aug 12 2017 - 06:32:57 PDT)
- Elvis Martis (Fri Aug 11 2017 - 20:13:53 PDT)
- Mohammad Zahidul Hossain Khan (Fri Aug 11 2017 - 12:17:08 PDT)
- Elvis Martis (Fri Aug 11 2017 - 12:06:40 PDT)
- Mohammad Zahidul Hossain Khan (Fri Aug 11 2017 - 10:17:57 PDT)
[AMBER] Segmentation error in minimization
- David A Case (Mon Aug 28 2017 - 08:03:23 PDT)
- Lizelle Lubbe (Mon Aug 28 2017 - 05:49:06 PDT)
[AMBER] string methods in AMBER16
- Chunli Yan (Tue Aug 01 2017 - 17:32:58 PDT)
- Chunli Yan (Tue Aug 01 2017 - 13:58:10 PDT)
- Feng Pan (Tue Aug 01 2017 - 13:37:33 PDT)
- Chunli Yan (Tue Aug 01 2017 - 13:07:35 PDT)
- Feng Pan (Tue Aug 01 2017 - 12:59:28 PDT)
- Scott Brozell (Tue Aug 01 2017 - 12:59:07 PDT)
- Chunli Yan (Tue Aug 01 2017 - 12:00:33 PDT)
[AMBER] The Amber web site is down....
- David A Case (Fri Aug 11 2017 - 09:54:54 PDT)
[AMBER] Thermodynamic Integration question
- Lin Song (Tue Aug 22 2017 - 16:33:43 PDT)
- David Cerutti (Tue Aug 22 2017 - 16:01:29 PDT)
- Lin Song (Tue Aug 22 2017 - 15:51:08 PDT)
[AMBER] Thermodynamic Integration using PMEMD
- Hannes Loeffler (Fri Aug 18 2017 - 09:36:24 PDT)
- Roma Mukhopadhyay (Fri Aug 18 2017 - 09:13:46 PDT)
- Hannes Loeffler (Fri Aug 18 2017 - 07:20:10 PDT)
- Roma Mukhopadhyay (Fri Aug 18 2017 - 06:34:32 PDT)
- Hannes Loeffler (Fri Aug 18 2017 - 00:09:45 PDT)
- Roma Mukhopadhyay (Thu Aug 17 2017 - 11:24:00 PDT)
[AMBER] TIP3p lennard jones parameters
- Lizelle Lubbe (Thu Aug 31 2017 - 01:45:57 PDT)
- David A Case (Fri Aug 25 2017 - 13:17:08 PDT)
- Lizelle Lubbe (Fri Aug 25 2017 - 08:19:10 PDT)
[AMBER] TIP3PBOX for membrane system
- James Starlight (Wed Aug 30 2017 - 02:54:33 PDT)
- Bill Ross (Wed Aug 30 2017 - 02:43:17 PDT)
- James Starlight (Wed Aug 30 2017 - 02:42:57 PDT)
- Bill Ross (Wed Aug 30 2017 - 02:41:50 PDT)
- James Starlight (Wed Aug 30 2017 - 02:39:21 PDT)
- Bill Ross (Wed Aug 30 2017 - 02:30:58 PDT)
- James Starlight (Wed Aug 30 2017 - 02:25:00 PDT)
[AMBER] Tleap parametrisation of NA+ bound proteins
- James Starlight (Wed Aug 02 2017 - 06:29:45 PDT)
- James Starlight (Wed Aug 02 2017 - 03:47:22 PDT)
- David A Case (Tue Aug 01 2017 - 10:23:42 PDT)
- James Starlight (Tue Aug 01 2017 - 06:56:25 PDT)
[AMBER] Tleap processing of membrane protein in amber-16
- James Starlight (Wed Aug 02 2017 - 06:56:45 PDT)
- David A Case (Wed Aug 02 2017 - 06:42:27 PDT)
- James Starlight (Wed Aug 02 2017 - 03:52:14 PDT)
[AMBER] Units in dist_vs_t file from SMD simulation
- Xing (Tue Aug 15 2017 - 17:10:51 PDT)
- Adrian Roitberg (Tue Aug 15 2017 - 08:22:52 PDT)
- Xing (Mon Aug 14 2017 - 21:08:24 PDT)
[AMBER] Use of param.Frosst parameters to prepare a ligand in Ambertools?
- David A Case (Thu Aug 10 2017 - 10:47:54 PDT)
- Anne Nierobisch (Wed Aug 09 2017 - 06:57:57 PDT)
[AMBER] Using polarizable force field ff02 in AMBER 14
- David A Case (Mon Aug 07 2017 - 12:54:42 PDT)
- Anthony Cruz-Balberdy (Mon Aug 07 2017 - 12:41:04 PDT)
- Aishwarya Venkatramani (Mon Aug 07 2017 - 11:41:23 PDT)
- David A Case (Fri Aug 04 2017 - 08:18:42 PDT)
- Aishwarya Venkatramani (Fri Aug 04 2017 - 05:47:34 PDT)
- Carlos Simmerling (Fri Aug 04 2017 - 05:40:05 PDT)
- Aishwarya Venkatramani (Thu Aug 03 2017 - 20:15:17 PDT)
- Aishwarya Venkatramani (Thu Aug 03 2017 - 17:00:00 PDT)
[AMBER] Webinar: “An AI Quantum Breakthrough: ANAKIN-ME”
- Mark Berger (Thu Aug 31 2017 - 13:33:34 PDT)
[AMBER] wrong ligand geometry
- David A Case (Sun Aug 27 2017 - 05:40:51 PDT)
- Thomas Evangelidis (Sat Aug 26 2017 - 12:41:33 PDT)
Ambermd Error: an illegal memory access was encountered launching kernel kClearForces
- David A Case (Sun Aug 27 2017 - 13:49:16 PDT)
- Silvana Valdebenito Silva (Sat Aug 26 2017 - 10:13:16 PDT)

Amber Archive Aug 2017 by subject