Amber Archive May 2016: by subject

David A Case (Sat May 07 2016 - 06:07:00 PDT)
Fatemeh Arabi (Sat May 07 2016 - 05:42:09 PDT)
Fatemeh Arabi (Sat May 07 2016 - 00:16:15 PDT)
[AMBER] "sanderf"
- Jason Swails (Tue May 31 2016 - 10:11:36 PDT)
- Odin Zeus (Tue May 31 2016 - 06:37:23 PDT)
[AMBER] .nc trajectory format
- Neha Gandhi (Wed May 18 2016 - 18:19:30 PDT)
- David A Case (Wed May 18 2016 - 04:44:19 PDT)
- Neha Gandhi (Tue May 17 2016 - 21:35:01 PDT)
[AMBER] About AMBER Advanced Tutorial 17 on GPUs
- Ross Walker (Fri May 27 2016 - 10:50:43 PDT)
- mish (Fri May 27 2016 - 07:44:08 PDT)
[AMBER] About harmonic restraints on dihedral angle in pmemd.cuda
- Hector A. Baldoni (Thu May 12 2016 - 16:55:26 PDT)
- mish (Thu May 12 2016 - 16:16:27 PDT)
- David Cerutti (Thu May 12 2016 - 07:05:24 PDT)
- mish (Thu May 12 2016 - 06:58:21 PDT)
[AMBER] acetone as solvent for simulation
- FyD (Wed May 25 2016 - 23:11:38 PDT)
- Shilpa Gupta (Wed May 25 2016 - 22:39:22 PDT)
- Shilpa Gupta (Mon May 09 2016 - 22:53:48 PDT)
[AMBER] adaptive qm/mm NVT not reaching target temperature
- Dr. Andreas W. Goetz (Wed May 25 2016 - 16:45:50 PDT)
- Stanislav Simko (Wed May 25 2016 - 05:58:39 PDT)
[AMBER] Adaptively Biased MD: Problems with executing groupfile
- Feng Pan (Fri May 27 2016 - 13:09:26 PDT)
- Jason Imamoto (Fri May 27 2016 - 10:20:07 PDT)
[AMBER] Amber 12 and VMware workstation 12 player
- Jason Swails (Tue May 03 2016 - 17:20:56 PDT)
- Ibrahim Said (Tue May 03 2016 - 13:00:42 PDT)
[AMBER] Amber 8 on RHEL 6
- Jason Swails (Mon May 02 2016 - 18:03:59 PDT)
- Nhai (Mon May 02 2016 - 09:42:37 PDT)
- boyken.divms.uiowa.edu (Mon May 02 2016 - 09:30:41 PDT)
[AMBER] Amber compilation fail after plumed patch
- Charles Lin (Fri May 13 2016 - 13:39:42 PDT)
- Fabrício Bracht (Fri May 13 2016 - 13:36:34 PDT)
- Fabrício Bracht (Fri May 13 2016 - 13:29:41 PDT)
[AMBER] Amber coordinates to chemshell coords file (coords.c)
- Jason Swails (Tue May 24 2016 - 08:23:04 PDT)
- Jenner Bonanata (Fri May 20 2016 - 06:10:25 PDT)
[AMBER] AMBER Digest, Vol 1578, Issue 1
- Iqbal, Muhammad Sajid (Mon May 16 2016 - 22:21:12 PDT)
[AMBER] amber error - reg
- Jason Swails (Wed May 11 2016 - 05:16:57 PDT)
- David A Case (Wed May 11 2016 - 05:04:43 PDT)
- Arthi Venkat (Wed May 11 2016 - 04:50:58 PDT)
- Jason Swails (Wed May 11 2016 - 03:42:56 PDT)
- Bill Ross (Wed May 11 2016 - 03:13:16 PDT)
- Arthi Venkat (Wed May 11 2016 - 02:35:17 PDT)
[AMBER] Amber12 install error
- Hai Nguyen (Mon May 09 2016 - 09:48:26 PDT)
- Hai Nguyen (Mon May 09 2016 - 09:41:39 PDT)
- 유효정 (Mon May 09 2016 - 08:39:11 PDT)
[AMBER] Amber16: COM's in GPU version
- Feng Pan (Fri May 27 2016 - 13:29:51 PDT)
- Ilyas Yildirim (Fri May 27 2016 - 06:26:47 PDT)
- Jason Swails (Thu May 26 2016 - 11:07:16 PDT)
- Ross Walker (Thu May 26 2016 - 10:12:55 PDT)
- Ilyas Yildirim (Thu May 26 2016 - 10:01:27 PDT)
- Ross Walker (Thu May 26 2016 - 09:06:42 PDT)
- Åsmund Røhr Kjendseth (Thu May 26 2016 - 05:50:52 PDT)
[AMBER] Amino Acid Residues in QM/MM Simulation
- Gustavo Seabra (Tue May 24 2016 - 12:00:44 PDT)
- Nisler, Collin R. (Mon May 23 2016 - 19:25:23 PDT)
[AMBER] Analysis of protein-protein interaction
- Daniel Roe (Tue May 10 2016 - 07:12:14 PDT)
- James Starlight (Mon May 09 2016 - 03:10:22 PDT)
[AMBER] angle between normals to dna bases?
- Bill Ross (Sun May 01 2016 - 20:57:56 PDT)
- Hai Nguyen (Sun May 01 2016 - 20:46:41 PDT)
- Bill Ross (Sun May 01 2016 - 20:00:50 PDT)
[AMBER] ante-mmpbsa.py: general question
- Jason Swails (Fri May 27 2016 - 05:57:54 PDT)
- George Tzotzos (Thu May 26 2016 - 11:33:44 PDT)
[AMBER] autoimage and TI
- Daniel Roe (Tue May 24 2016 - 08:06:02 PDT)
- Khabiri, Morteza (Tue May 24 2016 - 07:44:34 PDT)
[AMBER] bad data error in sander run
- Mary Varughese (Wed May 04 2016 - 09:44:49 PDT)
- Bill Ross (Wed May 04 2016 - 07:57:46 PDT)
- Jason Swails (Wed May 04 2016 - 05:22:13 PDT)
- Mary Varughese (Wed May 04 2016 - 05:11:09 PDT)
- David A Case (Wed May 04 2016 - 04:46:39 PDT)
- Carlos Simmerling (Wed May 04 2016 - 04:19:40 PDT)
- Mary Varughese (Wed May 04 2016 - 04:07:47 PDT)
[AMBER] Best Linux Choice
- Robert Molt (Sat May 21 2016 - 13:28:04 PDT)
- Mark Abraham (Sat May 21 2016 - 10:48:44 PDT)
- Karl Kirschner (Fri May 20 2016 - 23:55:40 PDT)
- Ho Leung Ng (Fri May 20 2016 - 16:13:36 PDT)
- Wesley Michael Botello-Smith (Fri May 20 2016 - 15:42:49 PDT)
- Jason Swails (Fri May 20 2016 - 11:04:59 PDT)
- Vlad Cojocaru (Fri May 20 2016 - 08:38:35 PDT)
- Ross Walker (Fri May 20 2016 - 07:51:17 PDT)
- Kenneth Huang (Fri May 20 2016 - 07:02:36 PDT)
- Marcos Serrou do Amaral (Fri May 20 2016 - 06:54:47 PDT)
- Robert Molt (Fri May 20 2016 - 06:03:27 PDT)
[AMBER] Bug: Gasteiger parameters for S(-1)
- Mahmoud A. A. Ibrahim (Wed May 18 2016 - 00:42:02 PDT)
[AMBER] calculated rmsd
- Daniel Roe (Tue May 31 2016 - 07:58:19 PDT)
- Ziba Bahadori (Tue May 31 2016 - 00:12:29 PDT)
[AMBER] calculating binding free energy
- Carlos Romero (Thu May 26 2016 - 17:18:56 PDT)
[AMBER] Calculating LJ parameters in Amber format
- anu chandra (Thu May 05 2016 - 08:15:52 PDT)
- David A Case (Thu May 05 2016 - 07:28:20 PDT)
- Jason Swails (Thu May 05 2016 - 07:08:38 PDT)
- anu chandra (Thu May 05 2016 - 06:45:58 PDT)
[AMBER] Can I build parameters of hydroxyapatites?
- FyD (Wed May 25 2016 - 10:45:22 PDT)
- Mijiddorj Batsaikhan (Wed May 25 2016 - 02:34:39 PDT)
[AMBER] choice of lipid type in MD simulation
- Zhang Marc (Fri May 20 2016 - 00:51:40 PDT)
[AMBER] Choline Chloride
- Christopher Jesudason (Sun May 29 2016 - 13:06:20 PDT)
[AMBER] Clustering of MD trajectories: ptraj, cpptraj
- Daniel Roe (Fri May 27 2016 - 13:31:17 PDT)
- Francesco Gentile (Thu May 19 2016 - 11:41:16 PDT)
[AMBER] clustering with ptraj
- Nhai (Thu May 19 2016 - 17:20:13 PDT)
- Francesco Gentile (Thu May 19 2016 - 17:08:37 PDT)
[AMBER] Combining .mdvel and .nc(NetCDF) into one file
- ATUL KUMAR (Sat May 14 2016 - 06:26:59 PDT)
- Daniel Roe (Sat May 14 2016 - 05:13:16 PDT)
- ATUL KUMAR (Sat May 14 2016 - 00:12:55 PDT)
[AMBER] Constant area simulation
- Batuhan Kav (Fri May 27 2016 - 02:07:39 PDT)
[AMBER] Constant pH simulation
- Jason Swails (Tue May 10 2016 - 07:12:33 PDT)
- Tanmoy Paul (Tue May 10 2016 - 06:16:18 PDT)
[AMBER] cpptraj + nastruct
- Daniel Roe (Fri May 27 2016 - 08:03:17 PDT)
- Thomas C. Bishop (Thu May 26 2016 - 12:27:42 PDT)
- Daniel Roe (Thu May 26 2016 - 07:21:08 PDT)
- Vlad Cojocaru (Thu May 26 2016 - 07:09:51 PDT)
- Hai Nguyen (Thu May 26 2016 - 06:48:14 PDT)
- Daniel Roe (Thu May 26 2016 - 06:16:03 PDT)
- Thomas C. Bishop (Thu May 26 2016 - 05:49:38 PDT)
- Vlad Cojocaru (Thu May 26 2016 - 00:33:52 PDT)
- Thomas C. Bishop (Wed May 25 2016 - 16:31:23 PDT)
[AMBER] cpptraj - rmsd/rmsf & reference structure
- Daniel Roe (Thu May 26 2016 - 08:07:29 PDT)
- colvin chin (Thu May 26 2016 - 07:58:34 PDT)
- Daniel Roe (Thu May 26 2016 - 07:42:04 PDT)
- colvin chin (Thu May 26 2016 - 06:56:03 PDT)
- Daniel Roe (Thu May 26 2016 - 06:22:55 PDT)
- colvin (Thu May 26 2016 - 02:19:16 PDT)
[AMBER] cpptraj clustering based on ligand cavity
- Daniel Roe (Tue May 31 2016 - 08:00:18 PDT)
- Neha Gandhi (Sun May 29 2016 - 18:12:10 PDT)
[AMBER] cpptraj mask command
- Daniel Roe (Sun May 01 2016 - 08:40:20 PDT)
- Saman Yousuf ali (Sun May 01 2016 - 08:29:43 PDT)
[AMBER] cpptraj rms fit to rst file
- Bill Ross (Tue May 03 2016 - 23:23:02 PDT)
- Bill Ross (Tue May 03 2016 - 21:22:04 PDT)
[AMBER] CUDA MPI issues
- David A Case (Fri May 27 2016 - 04:44:24 PDT)
- Brent Krueger (Fri May 27 2016 - 04:36:55 PDT)
- Biplab Ghosh (Fri May 27 2016 - 00:12:49 PDT)
- Biplab Ghosh (Thu May 26 2016 - 11:12:18 PDT)
- Ross Walker (Thu May 26 2016 - 10:57:14 PDT)
- Biplab Ghosh (Thu May 26 2016 - 10:40:56 PDT)
- Ross Walker (Thu May 26 2016 - 09:20:10 PDT)
- Biplab Ghosh (Wed May 25 2016 - 23:00:53 PDT)
- Ross Walker (Mon May 23 2016 - 08:47:36 PDT)
- Jason Swails (Mon May 23 2016 - 06:22:20 PDT)
- Bill Ross (Mon May 23 2016 - 04:01:05 PDT)
- Biplab Ghosh (Mon May 23 2016 - 03:45:08 PDT)
[AMBER] DFTB convergence
- Marc van der Kamp (Tue May 03 2016 - 13:35:47 PDT)
- Jacopo Sgrignani (Tue May 03 2016 - 12:23:17 PDT)
[AMBER] DNA Origami
- Ramkumar B (Fri May 06 2016 - 10:26:55 PDT)
- David A Case (Wed May 04 2016 - 12:36:44 PDT)
- Ramkumar B (Wed May 04 2016 - 11:35:27 PDT)
[AMBER] Error during frames generation from production run
- Jason Swails (Thu May 12 2016 - 13:10:38 PDT)
- Daniel Roe (Thu May 12 2016 - 08:50:23 PDT)
- Sneha Rai (Thu May 12 2016 - 02:07:25 PDT)
- Bill Ross (Thu May 12 2016 - 01:37:56 PDT)
- Bill Ross (Thu May 12 2016 - 01:33:27 PDT)
- Bill Ross (Thu May 12 2016 - 01:21:27 PDT)
- Sneha Rai (Thu May 12 2016 - 01:18:34 PDT)
[AMBER] error in cluster analysis by cpptraj
- Daniel Roe (Thu May 12 2016 - 07:21:48 PDT)
- Dr. Anselm Horn (Thu May 12 2016 - 05:05:43 PDT)
- Michael Shokhen (Thu May 12 2016 - 04:12:48 PDT)
- Dr. Anselm Horn (Thu May 12 2016 - 03:28:29 PDT)
- Michael Shokhen (Thu May 12 2016 - 03:06:39 PDT)
[AMBER] Ewald force using debugf
- Zhenyu Meng (Tue May 03 2016 - 20:28:42 PDT)
- David Cerutti (Tue May 03 2016 - 12:06:56 PDT)
- David A Case (Tue May 03 2016 - 07:48:08 PDT)
- Zhenyu Meng (Tue May 03 2016 - 04:43:20 PDT)
- David A Case (Mon May 02 2016 - 04:52:05 PDT)
- Zhenyu Meng (Mon May 02 2016 - 04:07:17 PDT)
[AMBER] Fix dimension of the box throughout the MD simulations
- David A Case (Mon May 16 2016 - 11:50:49 PDT)
- Iqbal, Muhammad Sajid (Mon May 16 2016 - 08:56:15 PDT)
- Carlos Simmerling (Sat May 14 2016 - 14:59:18 PDT)
- David A Case (Sat May 14 2016 - 14:52:57 PDT)
- Carlos Simmerling (Sat May 14 2016 - 12:56:24 PDT)
- Iqbal, Muhammad Sajid (Sat May 14 2016 - 12:49:43 PDT)
[AMBER] GAFF2 setup
- David A Case (Thu May 19 2016 - 05:06:23 PDT)
- Hannes Loeffler (Thu May 19 2016 - 02:03:25 PDT)
[AMBER] help identifying dihedral parameters for paracetemol using Antechamber
- Karl Kirschner (Sat May 07 2016 - 12:16:00 PDT)
- David A Case (Thu May 05 2016 - 17:50:49 PDT)
- conor parks (Thu May 05 2016 - 16:13:28 PDT)
- Karl Kirschner (Wed May 04 2016 - 01:28:34 PDT)
- conor parks (Tue May 03 2016 - 13:13:05 PDT)
- David A Case (Tue May 03 2016 - 12:53:58 PDT)
- conor parks (Tue May 03 2016 - 08:51:06 PDT)
- David A Case (Tue May 03 2016 - 08:05:31 PDT)
- conor parks (Mon May 02 2016 - 09:11:28 PDT)
- David A Case (Sun May 01 2016 - 05:42:21 PDT)
- conor parks (Sat Apr 30 2016 - 21:13:49 PDT)
[AMBER] help: what cause Sandar crash
- David A Case (Thu May 05 2016 - 07:01:06 PDT)
- Yang, Hui (Thu May 05 2016 - 06:23:23 PDT)
[AMBER] HMR with protein-ligand system
- Niel Henriksen (Thu May 05 2016 - 10:43:03 PDT)
- Alessio Atzori (Thu May 05 2016 - 00:36:26 PDT)
[AMBER] How adding cluster to a model
- Damiano Spadoni (Tue May 10 2016 - 04:57:14 PDT)
[AMBER] How to deal with Heme?
- Anna Cebrian Prats (Wed May 18 2016 - 09:15:14 PDT)
- David A Case (Wed May 18 2016 - 09:06:11 PDT)
- Anna Cebrian Prats (Wed May 18 2016 - 07:32:59 PDT)
- Abelak, Kavin (Wed May 18 2016 - 05:16:32 PDT)
- David A Case (Sat May 14 2016 - 06:16:45 PDT)
- Morteza Chehel Amirani (Fri May 13 2016 - 15:44:20 PDT)
- David A Case (Fri May 13 2016 - 05:21:04 PDT)
- Morteza Chehel Amirani (Thu May 12 2016 - 10:53:44 PDT)
[AMBER] How to do QHA with outputs after considering every n-frames of trajectory?
- Daniel Roe (Tue May 24 2016 - 12:18:21 PDT)
- SHAILESH KUMAR (Tue May 24 2016 - 11:16:56 PDT)
[AMBER] How to modify the LENNARD_JONES_BCOEF in amber topology
- Jason Swails (Mon May 09 2016 - 09:23:10 PDT)
- Pengfei Li (Mon May 09 2016 - 07:23:33 PDT)
- anu chandra (Mon May 09 2016 - 03:51:57 PDT)
- Pengfei Li (Sat May 07 2016 - 19:55:58 PDT)
- anu chandra (Sat May 07 2016 - 08:52:25 PDT)
[AMBER] How to modify the LENNARD_JONES_BCOEF in amber topologyer
- JAIME RUBIO MARTINEZ (Sun May 08 2016 - 06:12:28 PDT)
[AMBER] Hydroxyapatites force field
- Pengfei Li (Sat May 07 2016 - 19:45:53 PDT)
- Mijiddorj Batsaikhan (Sat May 07 2016 - 00:03:57 PDT)
- Mijiddorj Batsaikhan (Sat May 07 2016 - 00:00:40 PDT)
[AMBER] Installing AmberTools16 on OSX 10.11
- Adams, John E. (Tue May 10 2016 - 10:42:36 PDT)
- Hai Nguyen (Tue May 10 2016 - 09:48:31 PDT)
- Jason Swails (Tue May 10 2016 - 08:57:31 PDT)
- Adams, John E. (Tue May 10 2016 - 07:48:54 PDT)
[AMBER] issues with NONBOND LIST?
- David A Case (Wed May 18 2016 - 04:51:02 PDT)
- Thomas Pochapsky (Tue May 17 2016 - 13:05:20 PDT)
- Carlos Simmerling (Tue May 17 2016 - 12:37:51 PDT)
- Thomas Pochapsky (Tue May 17 2016 - 12:27:40 PDT)
- Carlos Simmerling (Tue May 17 2016 - 12:01:31 PDT)
- Thomas Pochapsky (Tue May 17 2016 - 11:45:32 PDT)
[AMBER] iwrap=1 issue
- Kenneth McGuinness (Mon May 02 2016 - 08:26:43 PDT)
- Daniel Roe (Mon May 02 2016 - 07:40:28 PDT)
- Kenneth McGuinness (Mon May 02 2016 - 06:53:16 PDT)
- Carlos Simmerling (Mon May 02 2016 - 05:11:02 PDT)
- Hirdesh Kumar (Mon May 02 2016 - 04:57:07 PDT)
[AMBER] Licence
- Jacopo Sgrignani (Wed May 18 2016 - 08:46:36 PDT)
[AMBER] live dCAT simulation
- Bill Ross (Wed May 11 2016 - 21:39:27 PDT)
- Bill Ross (Wed May 11 2016 - 21:25:29 PDT)
- Bill Ross (Wed May 11 2016 - 03:05:32 PDT)
- Bill Ross (Tue May 10 2016 - 22:39:49 PDT)
- Charles Lin (Tue May 10 2016 - 20:55:54 PDT)
- Bill Ross (Tue May 10 2016 - 20:09:04 PDT)
- Charles Lin (Tue May 10 2016 - 19:59:28 PDT)
- Bill Ross (Tue May 10 2016 - 19:42:22 PDT)
- Bill Ross (Thu May 05 2016 - 16:52:40 PDT)
[AMBER] Magnesium ion in AMBER
- Pengfei Li (Tue May 31 2016 - 07:36:15 PDT)
- David A Case (Mon May 30 2016 - 06:19:36 PDT)
- Shreeramesh (Mon May 30 2016 - 05:03:46 PDT)
[AMBER] MD Output File
- Wong Li Zhe (Tue May 17 2016 - 00:56:59 PDT)
[AMBER] mdl file for 1d-rism
- David A Case (Fri May 27 2016 - 18:22:06 PDT)
- Jingyi Yan (Fri May 27 2016 - 15:39:41 PDT)
[AMBER] metal ion models for Zn+2
- Fabian gmail (Wed May 04 2016 - 06:10:33 PDT)
[AMBER] MM-PBSA result
- asdda asa (Wed May 25 2016 - 04:36:28 PDT)
- David A Case (Wed May 25 2016 - 04:34:10 PDT)
- asdda asa (Tue May 24 2016 - 15:20:43 PDT)
[AMBER] mmpbsa
- Ziba Bahadori (Tue May 24 2016 - 11:14:24 PDT)
- Jason Swails (Tue May 24 2016 - 08:57:04 PDT)
- Lara rajam (Tue May 24 2016 - 06:15:41 PDT)
- Jason Swails (Wed May 18 2016 - 10:53:54 PDT)
- Ziba Bahadori (Wed May 18 2016 - 10:37:26 PDT)
[AMBER] MMPBSA doubt
- Mary Varughese (Thu May 12 2016 - 21:07:54 PDT)
- Jason Swails (Thu May 12 2016 - 10:50:40 PDT)
- Mary Varughese (Wed May 11 2016 - 21:26:46 PDT)
- Jason Swails (Wed May 11 2016 - 05:25:34 PDT)
- Kenneth Huang (Wed May 11 2016 - 04:43:38 PDT)
- Mary Varughese (Wed May 11 2016 - 04:28:03 PDT)
- Jason Swails (Wed May 11 2016 - 03:25:37 PDT)
- Mary Varughese (Tue May 10 2016 - 21:01:03 PDT)
[AMBER] MMPBSA final results of MMPBSA.py different from tutorial
- David A Case (Sat May 21 2016 - 05:25:53 PDT)
- LI An-Bang (Fri May 20 2016 - 19:38:17 PDT)
[AMBER] MMPBSA final results of MMPBSA.py different fromtutorial
- Ray Luo (Sun May 22 2016 - 08:47:15 PDT)
- David A Case (Sat May 21 2016 - 10:01:08 PDT)
- LI An-Bang (Sat May 21 2016 - 06:29:04 PDT)
[AMBER] MMPBSA for homo-dimer system with ligands
- Kat G (Sun May 15 2016 - 22:03:35 PDT)
[AMBER] MMPBSA Results
- asdda asa (Thu May 19 2016 - 15:02:33 PDT)
- Jason Swails (Thu May 19 2016 - 05:22:13 PDT)
- asdda asa (Thu May 19 2016 - 02:19:45 PDT)
[AMBER] MMPBSA- topology files preparation
- Jason Swails (Mon May 23 2016 - 05:57:44 PDT)
- Kat G (Sat May 21 2016 - 19:44:56 PDT)
[AMBER] MMPBSA.py issue with complex prmtop file
- Kalenkiewicz, Andrew (NIH/NICHD) [F] (Mon May 23 2016 - 14:33:59 PDT)
- Jason Swails (Mon May 23 2016 - 05:53:50 PDT)
- Kalenkiewicz, Andrew (NIH/NICHD) [F] (Fri May 20 2016 - 15:23:16 PDT)
[AMBER] MMPBSA: question of pairwise per residue decomposition
- Jason Swails (Thu May 05 2016 - 06:09:26 PDT)
- George Tzotzos (Thu May 05 2016 - 03:23:12 PDT)
- Jason Swails (Wed May 04 2016 - 18:03:28 PDT)
- George Tzotzos (Wed May 04 2016 - 12:42:39 PDT)
- Bill Ross (Wed May 04 2016 - 12:36:11 PDT)
- George Tzotzos (Wed May 04 2016 - 12:27:21 PDT)
[AMBER] Modified ARG LYS parameters
- Vlad Cojocaru (Wed May 25 2016 - 04:51:35 PDT)
[AMBER] nativecontacts
- Abelak, Kavin (Mon May 23 2016 - 02:40:02 PDT)
- Neha Gandhi (Mon May 23 2016 - 00:25:36 PDT)
[AMBER] nativecontacts resout command change with AmberTools16 [cpptraj]
- Daniel Roe (Tue May 31 2016 - 07:53:33 PDT)
- Daniel Roe (Fri May 27 2016 - 13:22:22 PDT)
- Daniel Roe (Fri May 27 2016 - 07:54:06 PDT)
- Eiros Zamora, Juan (Fri May 27 2016 - 02:25:23 PDT)
[AMBER] Nickel parameters in Amber
- Pengfei Li (Fri May 13 2016 - 13:56:00 PDT)
- Marcelo Andrade Chagas (Fri May 13 2016 - 08:40:22 PDT)
- Rebeca García Fandiño (Fri May 13 2016 - 08:14:44 PDT)
[AMBER] NMR restraints violation limit
- Duggan, Brendan (Tue May 31 2016 - 12:04:56 PDT)
- Vasantha Kumar (Mon May 30 2016 - 07:38:10 PDT)
[AMBER] No leaprc.ff14SB anymore in AmberTools16 - reason?
- Hannes Loeffler (Mon May 16 2016 - 08:42:55 PDT)
- Marc van der Kamp (Mon May 16 2016 - 08:37:11 PDT)
- Hannes Loeffler (Mon May 16 2016 - 08:33:04 PDT)
- Nhai (Mon May 16 2016 - 08:30:49 PDT)
- Marc van der Kamp (Mon May 16 2016 - 08:27:38 PDT)
[AMBER] non zero net charge on molecule from AM1-BCC charge parameter fit
- Jason Swails (Wed May 04 2016 - 18:01:47 PDT)
- Thomas Cheatham (Wed May 04 2016 - 13:49:29 PDT)
- Bill Ross (Wed May 04 2016 - 13:06:33 PDT)
- conor parks (Wed May 04 2016 - 12:54:29 PDT)
- Thomas Cheatham (Tue May 03 2016 - 22:22:09 PDT)
- conor parks (Tue May 03 2016 - 20:25:44 PDT)
[AMBER] obtain or build parameters for non-natural residues
- FyD (Wed May 25 2016 - 00:09:19 PDT)
- David Cerutti (Mon May 23 2016 - 07:12:23 PDT)
- Karl Kirschner (Mon May 23 2016 - 00:31:24 PDT)
- ALINE THOMAS (Fri May 20 2016 - 00:45:10 PDT)
[AMBER] on antechamber
- David A Case (Mon May 02 2016 - 04:56:57 PDT)
- Brett (Sat Apr 30 2016 - 20:51:58 PDT)
[AMBER] on antechamber of AMBER
- Brett (Mon May 02 2016 - 08:01:13 PDT)
- David A Case (Mon May 02 2016 - 07:25:30 PDT)
- Brett (Mon May 02 2016 - 06:02:48 PDT)
[AMBER] on GAFF
- Carlos Simmerling (Mon May 09 2016 - 07:18:41 PDT)
- Brett (Mon May 09 2016 - 06:55:45 PDT)
[AMBER] Opening mol2 file in xleap
- FyD (Wed May 25 2016 - 00:04:29 PDT)
- Yves Boulard (Fri May 20 2016 - 06:51:23 PDT)
- Nikolay N. Kuzmich (Fri May 20 2016 - 06:36:19 PDT)
[AMBER] optimised corrections to ff03
- David Cerutti (Sun May 22 2016 - 19:21:07 PDT)
- Neha Gandhi (Sun May 22 2016 - 18:09:04 PDT)
[AMBER] Organic solvent box - Amber do not see the molecule but its atoms
- David A Case (Tue May 24 2016 - 06:03:37 PDT)
- Stregone (Tue May 24 2016 - 04:27:40 PDT)
[AMBER] Parametrisation of ligand with ions
- julian.zachmann selvita.home.pl (Fri May 13 2016 - 02:30:27 PDT)
[AMBER] Paramfit trajectory read error
- David Poole (Sun May 01 2016 - 21:28:56 PDT)
[AMBER] Paramfit'ing forces
- Robin Betz (Sat May 07 2016 - 10:45:43 PDT)
- David Poole (Thu May 05 2016 - 17:53:53 PDT)
[AMBER] parmed units and version numbers
- Jason Swails (Sat May 14 2016 - 19:50:15 PDT)
- Hai Nguyen (Sat May 14 2016 - 09:01:56 PDT)
- hannes.loeffler.stfc.ac.uk (Sat May 14 2016 - 06:49:24 PDT)
[AMBER] pdb2pqr PDB processing for Amber force field
- James Starlight (Thu May 05 2016 - 06:46:41 PDT)
- Abelak, Kavin (Thu May 05 2016 - 05:14:16 PDT)
- James Starlight (Thu May 05 2016 - 03:39:49 PDT)
[AMBER] Phosphorylated-RNA
- Thomas Cheatham (Mon May 09 2016 - 19:11:30 PDT)
- yhzahsc (Mon May 09 2016 - 17:48:38 PDT)
[AMBER] problem in calculating velocity autocorrelation
- Hai Nguyen (Sun May 15 2016 - 09:22:15 PDT)
- ATUL KUMAR (Sun May 15 2016 - 06:34:09 PDT)
[AMBER] Problem in Restarting production run
- David A Case (Thu May 12 2016 - 03:57:29 PDT)
- Bill Ross (Thu May 12 2016 - 01:00:13 PDT)
- ATUL KUMAR (Thu May 12 2016 - 00:46:52 PDT)
- Bill Ross (Thu May 12 2016 - 00:23:08 PDT)
- ATUL KUMAR (Thu May 12 2016 - 00:19:04 PDT)
[AMBER] problem installing AmberTools16 pytraj on Mac
- Marc van der Kamp (Mon May 16 2016 - 08:39:32 PDT)
- Hannes Loeffler (Mon May 16 2016 - 08:37:14 PDT)
- Marc van der Kamp (Mon May 16 2016 - 08:23:11 PDT)
[AMBER] Problem interpreting cpptraj hbond output file
- Daniel Roe (Tue May 03 2016 - 06:44:08 PDT)
- maryam azimzadehirani (Tue May 03 2016 - 05:00:03 PDT)
[AMBER] Problem with closest command in cpptraj
- Indrajit Deb (Wed May 11 2016 - 10:17:33 PDT)
- Daniel Roe (Wed May 11 2016 - 09:49:30 PDT)
- Indrajit Deb (Wed May 11 2016 - 08:38:54 PDT)
- Daniel Roe (Wed May 11 2016 - 08:03:40 PDT)
- Indrajit Deb (Wed May 11 2016 - 07:16:14 PDT)
[AMBER] Problem with MCPB.py
- Surya Prakash Tiwari (Thu May 05 2016 - 10:37:59 PDT)
[AMBER] problem with new residu in Xleap
- Muriel Jourdan (Tue May 17 2016 - 08:06:07 PDT)
- Muriel Jourdan (Tue May 17 2016 - 07:15:10 PDT)
[AMBER] Problems with cpinutil.py in CpHMD as adding a new titratable ligand
- Jason Swails (Fri May 06 2016 - 15:27:41 PDT)
- Yong Wang (Fri May 06 2016 - 13:43:20 PDT)
[AMBER] Problems with GTX titan-X GPU
- Ross Walker (Tue May 24 2016 - 07:40:30 PDT)
- Elvis Martis (Tue May 24 2016 - 05:20:13 PDT)
- Elvis Martis (Mon May 23 2016 - 17:27:08 PDT)
- Ross Walker (Mon May 23 2016 - 08:35:23 PDT)
- Elvis Martis (Sat May 21 2016 - 03:19:54 PDT)
[AMBER] Problems with pairwise command in cpptraj
- Osman, Roman (Thu May 19 2016 - 07:17:36 PDT)
- Daniel Roe (Wed May 18 2016 - 11:43:49 PDT)
- Osman, Roman (Wed May 18 2016 - 11:14:38 PDT)
- Daniel Roe (Wed May 18 2016 - 11:01:36 PDT)
- Osman, Roman (Wed May 18 2016 - 10:47:13 PDT)
- Osman, Roman (Tue May 17 2016 - 13:24:41 PDT)
[AMBER] process_mdout.perl script
- Ruth Helena Tichauer (Tue May 03 2016 - 06:35:47 PDT)
[AMBER] Protein moving out of the water box
- David A Case (Sat May 21 2016 - 09:58:05 PDT)
- Arati Paudyal (Sat May 21 2016 - 06:32:51 PDT)
- David A Case (Sat May 21 2016 - 05:21:18 PDT)
- Arati Paudyal (Fri May 20 2016 - 17:21:33 PDT)
- Hai Nguyen (Fri May 20 2016 - 13:37:18 PDT)
- Arati Paudyal (Fri May 20 2016 - 12:58:31 PDT)
- Nhai (Thu May 19 2016 - 19:26:38 PDT)
- Arati Paudyal (Thu May 19 2016 - 19:11:17 PDT)
[AMBER] QM/MM energy minimization
- Stanislav Simko (Fri May 20 2016 - 03:34:28 PDT)
[AMBER] QM/MM Interface
- Dr. Andreas W. Goetz (Mon May 23 2016 - 19:44:41 PDT)
- Nisler, Collin R. (Sun May 22 2016 - 23:27:13 PDT)
- Nisler, Collin R. (Sun May 22 2016 - 16:46:39 PDT)
- Stanislav Simko (Sun May 22 2016 - 02:31:58 PDT)
- Nisler, Collin R. (Sat May 21 2016 - 17:19:13 PDT)
- Stanislav Simko (Sat May 21 2016 - 16:44:40 PDT)
- Nisler, Collin R. (Sat May 21 2016 - 16:00:52 PDT)
- Stanislav Simko (Sat May 21 2016 - 00:37:58 PDT)
- Nisler, Collin R. (Fri May 20 2016 - 22:37:11 PDT)
[AMBER] query
- Vasantha Kumar (Thu May 26 2016 - 05:27:30 PDT)
- David A Case (Thu May 26 2016 - 04:46:29 PDT)
- Vasantha Kumar (Thu May 26 2016 - 02:24:33 PDT)
- ankita mehta (Wed May 25 2016 - 23:30:28 PDT)
- Daniel Roe (Wed May 25 2016 - 13:55:36 PDT)
- ankita mehta (Tue May 24 2016 - 22:57:07 PDT)
[AMBER] Query about amber 16, external electric field support
- Kshatresh Dutta Dubey (Sun May 01 2016 - 07:25:03 PDT)
- Charles Lin (Sun May 01 2016 - 07:15:46 PDT)
- Kshatresh Dutta Dubey (Sun May 01 2016 - 06:54:50 PDT)
[AMBER] rdf cpptraj.
- Daniel Roe (Tue May 03 2016 - 06:41:25 PDT)
- Saman Yousuf ali (Tue May 03 2016 - 02:37:48 PDT)
[AMBER] RE_POSITION
- Nisler, Collin R. (Mon May 23 2016 - 18:15:24 PDT)
- Wong Li Zhe (Mon May 23 2016 - 18:07:15 PDT)
[AMBER] Regarding Force Field Inquiry
- Kevin Hauser (Wed May 25 2016 - 06:31:30 PDT)
- Vishal Nemaysh (Wed May 25 2016 - 05:41:01 PDT)
- Dr. Anselm Horn (Wed May 25 2016 - 04:51:05 PDT)
- David A Case (Wed May 25 2016 - 04:41:40 PDT)
- Carlos Simmerling (Wed May 25 2016 - 04:34:20 PDT)
- Vishal Nemaysh (Wed May 25 2016 - 04:22:48 PDT)
[AMBER] Regarding joining of two pdb file
- MOHD HOMAIDUR RAHMAN (Wed May 11 2016 - 07:12:12 PDT)
- David A Case (Wed May 11 2016 - 05:08:13 PDT)
- Bill Ross (Tue May 10 2016 - 23:14:34 PDT)
- MOHD HOMAIDUR RAHMAN (Tue May 10 2016 - 22:53:14 PDT)
[AMBER] Regarding parameter file not saved
- Daniel Roe (Tue May 24 2016 - 10:10:31 PDT)
- Vishal Nemaysh (Tue May 24 2016 - 10:02:07 PDT)
- Hai Nguyen (Tue May 24 2016 - 09:38:36 PDT)
- Vishal Nemaysh (Tue May 24 2016 - 09:21:10 PDT)
[AMBER] Regarding RMSF calculation of protein using AMBER
- David A Case (Thu May 05 2016 - 06:54:53 PDT)
- Sivanandam M (Thu May 05 2016 - 05:46:34 PDT)
[AMBER] Release of FESetup 1.2
- Hannes Loeffler (Tue May 24 2016 - 12:55:19 PDT)
[AMBER] Replacing water with a H2O2 and restart the simulation
- David A Case (Fri May 27 2016 - 04:51:17 PDT)
- Morteza Chehel Amirani (Thu May 26 2016 - 15:21:16 PDT)
[AMBER] RESP charges
- Chi Jin (Thu May 05 2016 - 15:11:16 PDT)
[AMBER] Restrain a single atom in the residue during minimization, instead of all the atoms in a residue with RES option
- Carlos Simmerling (Tue May 10 2016 - 02:47:02 PDT)
- Vasantha Kumar (Tue May 10 2016 - 02:28:55 PDT)
- Vasantha Kumar (Tue May 10 2016 - 01:32:54 PDT)
- Carlos Simmerling (Mon May 09 2016 - 13:34:31 PDT)
- Vasantha Kumar (Mon May 09 2016 - 13:32:39 PDT)
[AMBER] rms to pdb for a subset of atoms [cpptraj]
- Bill Ross (Thu May 19 2016 - 12:13:18 PDT)
- Daniel Roe (Thu May 19 2016 - 07:37:31 PDT)
- Eiros Zamora, Juan (Thu May 19 2016 - 06:55:25 PDT)
[AMBER] Rotating the protein along x-axis
- Bill Ross (Mon May 02 2016 - 16:55:13 PDT)
- Hai Nguyen (Mon May 02 2016 - 16:13:18 PDT)
- Aishani Prem (Mon May 02 2016 - 16:04:09 PDT)
- Hai Nguyen (Mon May 02 2016 - 16:02:23 PDT)
- Aishani Prem (Mon May 02 2016 - 14:53:27 PDT)
[AMBER] Scripts to gradually remove NMR restraints during MD simulation
- ankita mehta (Fri May 13 2016 - 03:02:48 PDT)
- Vasantha Kumar (Fri May 13 2016 - 02:46:10 PDT)
[AMBER] Simulation of DNA structure with a three-phosphate at 5'
- FyD (Sun May 29 2016 - 23:55:38 PDT)
- Vlad Cojocaru (Sun May 29 2016 - 05:44:52 PDT)
- M. Reza Ganjalikhany (Sun May 29 2016 - 05:23:50 PDT)
- M. Reza Ganjalikhany (Fri May 27 2016 - 02:32:06 PDT)
- Vlad Cojocaru (Fri May 27 2016 - 01:25:30 PDT)
- M. Reza Ganjalikhany (Fri May 27 2016 - 01:11:30 PDT)
[AMBER] slinky on a hot tin roof
- Bill Ross (Fri May 13 2016 - 01:25:12 PDT)
[AMBER] Solvation free energy in rism1d
- David A Case (Wed May 25 2016 - 04:38:48 PDT)
- Jingyi Yan (Tue May 24 2016 - 15:51:39 PDT)
[AMBER] standard parameter for sialic acid
- Bisignano, Paola (Thu May 26 2016 - 12:02:22 PDT)
- Lachele Foley (Wed May 25 2016 - 22:08:28 PDT)
- David A Case (Wed May 25 2016 - 17:02:39 PDT)
- Bisignano, Paola (Wed May 25 2016 - 16:43:53 PDT)
[AMBER] Thermodynamic Integration introduce charge
- Ignacio J. General (Wed May 04 2016 - 04:15:35 PDT)
- hannes.loeffler.stfc.ac.uk (Tue May 03 2016 - 23:10:23 PDT)
- Johannes Loeffler (Tue May 03 2016 - 22:36:39 PDT)
[AMBER] tleap - protein + ligand + heme group
- Bill Ross (Fri May 06 2016 - 05:48:39 PDT)
- Anna Cebrian Prats (Fri May 06 2016 - 04:23:50 PDT)
- Anna Cebrian Prats (Tue May 03 2016 - 03:16:18 PDT)
- Anna Cebrian Prats (Tue May 03 2016 - 02:47:55 PDT)
[AMBER] tleap: opls-ua parm for an arbitrary molecule
- Nhai (Tue May 17 2016 - 09:05:32 PDT)
- David A Case (Tue May 17 2016 - 08:47:57 PDT)
- Ekaterina Ratkova (Tue May 17 2016 - 07:02:33 PDT)
[AMBER] Unable to run Antechamber
- David A Case (Fri May 13 2016 - 07:55:36 PDT)
- Shreeramesh (Fri May 13 2016 - 05:12:48 PDT)
[AMBER] Units in dist_vs_t file from SMD simulation
- Adrian Roitberg (Sat May 07 2016 - 16:33:03 PDT)
- Nisler, Collin R. (Fri May 06 2016 - 14:08:34 PDT)
[AMBER] Visualization of all-in-one mdcrd file in VMD
- Trang Nguyen (Tue May 10 2016 - 12:46:54 PDT)
- Hai Nguyen (Tue May 10 2016 - 12:24:11 PDT)
- Hai Nguyen (Tue May 10 2016 - 12:21:57 PDT)
- Trang Nguyen (Tue May 10 2016 - 11:53:08 PDT)
- Nhai (Tue May 10 2016 - 11:33:25 PDT)
- Trang Nguyen (Tue May 10 2016 - 11:26:02 PDT)
[AMBER] VMD visualization of netcdf trajectories through the terminal
- James Starlight (Tue May 10 2016 - 04:28:03 PDT)
- Karolina Markowska (Tue May 10 2016 - 02:36:29 PDT)
- James Starlight (Tue May 10 2016 - 02:24:57 PDT)
[AMBER] water residence time calculation
- Daniel Roe (Mon May 02 2016 - 07:44:59 PDT)
- maryam azimzadehirani (Sun May 01 2016 - 20:55:18 PDT)
- Daniel Roe (Sun May 01 2016 - 08:42:20 PDT)
- maryam azimzadehirani (Sun May 01 2016 - 05:59:57 PDT)
[AMBER] Working with pytraj
- Hai Nguyen (Mon May 16 2016 - 12:28:05 PDT)
- MOHD HOMAIDUR RAHMAN (Mon May 16 2016 - 12:05:00 PDT)
[AMBER] xLeap
- Ramkumar B (Thu May 05 2016 - 04:33:29 PDT)
- hannes.loeffler.stfc.ac.uk (Thu May 05 2016 - 00:46:54 PDT)
- Ramkumar B (Thu May 05 2016 - 00:20:55 PDT)

Amber Archive May 2016 by subject