Amber Archive Dec 2014: by subject

[AMBER] "Unit 18 Error on OPEN: logfile"
- kurisaki (Sat Dec 13 2014 - 17:20:34 PST)
- kurisaki (Sat Dec 13 2014 - 17:04:24 PST)
- kurisaki (Sat Dec 13 2014 - 16:57:28 PST)
[AMBER] 8Mureabox URE residue unknown
- Jason Swails (Sat Dec 13 2014 - 07:31:17 PST)
- CHAMI F. (Sat Dec 13 2014 - 06:13:21 PST)
[AMBER] a problem in MM-GBSA calculation
- Jason Swails (Tue Dec 23 2014 - 19:53:22 PST)
- Jinfeng Huang (Tue Dec 23 2014 - 18:33:24 PST)
- Carlos Simmerling (Tue Dec 23 2014 - 05:31:45 PST)
- 朱亚莉 (Tue Dec 23 2014 - 05:22:11 PST)
[AMBER] accelerated MD set up
- Asmita Gupta (Tue Dec 02 2014 - 07:43:19 PST)
- Vlad Cojocaru (Tue Dec 02 2014 - 04:32:16 PST)
- Asmita Gupta (Tue Dec 02 2014 - 03:15:27 PST)
[AMBER] acetate params for mtkpp
- Francesco Pietra (Mon Dec 08 2014 - 08:19:36 PST)
- Jason Swails (Sun Dec 07 2014 - 19:18:27 PST)
- Francesco Pietra (Sun Dec 07 2014 - 13:47:08 PST)
- Francesco Pietra (Sun Dec 07 2014 - 09:41:32 PST)
[AMBER] Add MgCl2 salts
- David A Case (Tue Dec 09 2014 - 18:58:50 PST)
- Jason Swails (Tue Dec 09 2014 - 18:07:33 PST)
- Haining Liu (Tue Dec 09 2014 - 13:13:58 PST)
[AMBER] Alignment before calculation?
- Daniel Roe (Fri Dec 05 2014 - 08:11:39 PST)
- Soumendranath Bhakat (Fri Dec 05 2014 - 07:12:38 PST)
[AMBER] Amber 12 on K20 GPUs -- how am I doing?
- Ross Walker (Tue Dec 16 2014 - 10:15:36 PST)
- Baker D.J. (Tue Dec 16 2014 - 04:22:22 PST)
[AMBER] Amber 14 Performance and Other Questions
- Ross Walker (Fri Dec 26 2014 - 14:13:25 PST)
- Novosielski, Ryan (Fri Dec 26 2014 - 13:16:05 PST)
[AMBER] amber force field
- Jiri Sponer (Tue Dec 30 2014 - 02:12:52 PST)
- pavel.banas.upol.cz (Mon Dec 29 2014 - 08:32:13 PST)
- 王珍 (Sun Dec 28 2014 - 03:51:25 PST)
[AMBER] Amber12 parallel installation error
- David A Case (Thu Dec 11 2014 - 04:30:51 PST)
- Jason Swails (Wed Dec 10 2014 - 07:22:50 PST)
- Kanin Wichapong (Wed Dec 10 2014 - 06:43:05 PST)
[AMBER] amber14 CUDA GPU for workstation?
- Jason Swails (Tue Dec 30 2014 - 14:55:33 PST)
- Ross Walker (Tue Dec 30 2014 - 14:03:19 PST)
- Michael Shokhen (Tue Dec 30 2014 - 13:49:24 PST)
- Adrian Roitberg (Tue Dec 30 2014 - 12:56:31 PST)
- Michael Shokhen (Tue Dec 30 2014 - 12:51:48 PST)
- Ross Walker (Tue Dec 30 2014 - 12:11:42 PST)
- Michael Shokhen (Tue Dec 30 2014 - 11:31:33 PST)
[AMBER] AmberTools suppose program
- Yu Chen (Tue Dec 09 2014 - 19:30:44 PST)
- David A Case (Tue Dec 09 2014 - 18:56:18 PST)
- Chris Moth (Tue Dec 09 2014 - 13:50:14 PST)
- Yu Chen (Tue Dec 09 2014 - 12:27:28 PST)
[AMBER] Ambertools14 Installation Appears to Reset
- Jason Swails (Mon Dec 01 2014 - 18:37:15 PST)
- Edward Kalkreuter (Mon Dec 01 2014 - 18:16:12 PST)
[AMBER] AmberTools14/Amber10
- Francesco Pietra (Fri Dec 12 2014 - 07:10:44 PST)
- Francesco Pietra (Fri Dec 12 2014 - 06:59:03 PST)
- Jason Swails (Fri Dec 12 2014 - 04:43:36 PST)
- aksbmbg_s.caluniv.ac.in (Fri Dec 12 2014 - 03:56:49 PST)
- aksbmbg_s.caluniv.ac.in (Fri Dec 12 2014 - 03:54:12 PST)
- Francesco Pietra (Fri Dec 12 2014 - 03:40:56 PST)
[AMBER] analyze.x error when dealing with the system containing ions in tinker
- Ya Gao (Mon Dec 08 2014 - 21:41:19 PST)
- Ya Gao (Mon Dec 08 2014 - 21:40:12 PST)
- David A Case (Mon Dec 08 2014 - 17:30:50 PST)
- Jason Swails (Mon Dec 08 2014 - 10:00:51 PST)
- Ya Gao (Mon Dec 08 2014 - 08:47:05 PST)
[AMBER] Analyzing multiple trajectories in cpptraj
- Daniel Roe (Tue Dec 16 2014 - 09:52:46 PST)
- Gard Nelson (Tue Dec 16 2014 - 09:50:11 PST)
- Daniel Roe (Mon Dec 15 2014 - 19:21:26 PST)
- Gard Nelson (Mon Dec 15 2014 - 17:37:32 PST)
[AMBER] another segfault with sander14 and TI/softcore
- Hannes Loeffler (Wed Dec 17 2014 - 06:46:19 PST)
- David A Case (Wed Dec 17 2014 - 05:41:32 PST)
- Hannes Loeffler (Wed Dec 10 2014 - 02:04:48 PST)
[AMBER] Antechamber problem
- Jason Swails (Tue Dec 09 2014 - 04:11:38 PST)
- hannes.loeffler.stfc.ac.uk (Mon Dec 08 2014 - 23:28:38 PST)
- Atila Petrosian (Mon Dec 08 2014 - 22:49:45 PST)
[AMBER] antechamber script
- Ahmet yıldırım (Mon Dec 22 2014 - 15:10:10 PST)
- David A Case (Mon Dec 22 2014 - 14:13:52 PST)
- Nhai (Mon Dec 22 2014 - 13:19:33 PST)
- hannes.loeffler.stfc.ac.uk (Mon Dec 22 2014 - 10:17:59 PST)
- Ahmet yıldırım (Mon Dec 22 2014 - 10:10:11 PST)
- Marc van der Kamp (Mon Dec 22 2014 - 08:45:50 PST)
- Bill Ross (Mon Dec 22 2014 - 08:39:18 PST)
- Ahmet yıldırım (Mon Dec 22 2014 - 07:05:48 PST)
[AMBER] B-factor values
- Jason Swails (Wed Dec 03 2014 - 11:18:35 PST)
- George Tzotzos (Wed Dec 03 2014 - 10:49:28 PST)
[AMBER] bug in "natural language" system to define nmropt restraints: generalized distance coordinate
- Marc van der Kamp (Tue Dec 02 2014 - 01:29:50 PST)
[AMBER] Calculating of charge
- David A Case (Mon Dec 08 2014 - 04:43:18 PST)
- MOHD HOMAIDUR RAHMAN (Mon Dec 08 2014 - 03:57:47 PST)
[AMBER] Can i combine the result given by sander and pmemd together
- David A Case (Sat Dec 06 2014 - 06:14:30 PST)
- YC Sun (Sat Dec 06 2014 - 02:22:23 PST)
- wangmt (Sat Dec 06 2014 - 01:21:54 PST)
[AMBER] CHAMBER error
- Abhishek TYAGI (Thu Dec 04 2014 - 19:25:06 PST)
[AMBER] change the mode of my AMBER mail list from digest to normal
- fjliu (Fri Dec 12 2014 - 17:51:47 PST)
- Ross Walker (Fri Dec 12 2014 - 08:39:22 PST)
- aksbmbg_s.caluniv.ac.in (Fri Dec 12 2014 - 04:02:51 PST)
- fjliu (Fri Dec 12 2014 - 03:56:56 PST)
[AMBER] charmmlipid2amber.py
- Jacopo Sgrignani (Fri Dec 26 2014 - 06:21:24 PST)
[AMBER] closeness
- David A Case (Sat Dec 06 2014 - 06:05:33 PST)
- Sylvester Tumusiime (Fri Dec 05 2014 - 18:32:55 PST)
- Daniel Roe (Fri Dec 05 2014 - 10:58:15 PST)
- Sylvester Tumusiime (Fri Dec 05 2014 - 10:44:38 PST)
- Sylvester Tumusiime (Fri Dec 05 2014 - 10:05:37 PST)
- Daniel Roe (Fri Dec 05 2014 - 08:07:51 PST)
- David A Case (Fri Dec 05 2014 - 05:41:33 PST)
- Sylvester Tumusiime (Fri Dec 05 2014 - 03:49:35 PST)
- Daniel Roe (Thu Dec 04 2014 - 21:32:26 PST)
- Sylvester Tumusiime (Thu Dec 04 2014 - 21:12:36 PST)
[AMBER] clustering problem in ambertool14
- Daniel Roe (Tue Dec 16 2014 - 12:19:51 PST)
- Mahendra B Thapa (Tue Dec 16 2014 - 10:28:13 PST)
[AMBER] convergence problem in antechamber with Ambertools14
- Rebeca García Fandiño (Tue Dec 30 2014 - 00:58:22 PST)
- David A Case (Mon Dec 29 2014 - 18:11:39 PST)
- Rebeca García Fandiño (Mon Dec 29 2014 - 05:05:12 PST)
[AMBER] conversion of amber outputs to gromacs
- Sarah Witzke (Fri Dec 26 2014 - 16:24:27 PST)
- Jason Swails (Fri Dec 26 2014 - 07:07:25 PST)
- shahab shariati (Fri Dec 26 2014 - 05:16:41 PST)
- Kshatresh Dutta Dubey (Fri Dec 26 2014 - 04:17:25 PST)
- shahab shariati (Thu Dec 25 2014 - 23:55:43 PST)
- shahab shariati (Thu Dec 25 2014 - 23:48:35 PST)
[AMBER] conversion of AMBER trajectory to Gromacs trajectory
- Daniel Roe (Sat Dec 13 2014 - 08:27:20 PST)
- Jason Swails (Sat Dec 13 2014 - 07:11:19 PST)
- aksbmbg_s.caluniv.ac.in (Fri Dec 12 2014 - 23:25:45 PST)
- Robin Jain (Fri Dec 12 2014 - 23:14:24 PST)
[AMBER] Different convergence in pmemd.cuda against CPU
- Hiromasa WATANABE (Sun Dec 21 2014 - 22:18:02 PST)
- Ross Walker (Tue Dec 16 2014 - 10:19:02 PST)
- Hiromasa WATANABE (Mon Dec 15 2014 - 22:26:37 PST)
- Ross Walker (Mon Dec 15 2014 - 21:43:42 PST)
- Hiromasa WATANABE (Mon Dec 15 2014 - 20:42:18 PST)
[AMBER] DMPC lipids are slightly charged in lipid14?
- Gould, Ian R (Tue Dec 02 2014 - 22:37:43 PST)
- Matthew Harrigan (Tue Dec 02 2014 - 22:00:41 PST)
[AMBER] Docking with Dock6
- Wong, Sook (NIH/NCATS) [V] (Thu Dec 04 2014 - 12:00:12 PST)
- David A Case (Thu Dec 04 2014 - 10:53:54 PST)
- Aldo Segura (Thu Dec 04 2014 - 10:14:22 PST)
- Wong, Sook (NIH/NCATS) [V] (Thu Dec 04 2014 - 09:28:28 PST)
[AMBER] Empirical force fields: release of R.E.D. Server Dev./PyRED Nov. 2014
- FyD (Tue Dec 09 2014 - 00:30:32 PST)
[AMBER] Enthalpy calculation of protein.
- Abhilash J (Sun Dec 28 2014 - 21:09:32 PST)
- aneesh cna (Sun Dec 28 2014 - 21:05:10 PST)
- David A Case (Sun Dec 28 2014 - 19:27:04 PST)
- Abhilash J (Sun Dec 28 2014 - 07:30:17 PST)
- David A Case (Sun Dec 28 2014 - 06:16:05 PST)
- Abhilash J (Sat Dec 27 2014 - 23:42:46 PST)
[AMBER] error creating mol2 files
- FyD (Sat Dec 06 2014 - 05:27:16 PST)
- Anupam Goel (Fri Dec 05 2014 - 12:51:31 PST)
- Aldo Segura (Fri Dec 05 2014 - 12:49:45 PST)
- Anupam Goel (Fri Dec 05 2014 - 12:41:10 PST)
- David A Case (Fri Dec 05 2014 - 12:08:36 PST)
- Aldo Segura (Fri Dec 05 2014 - 11:59:01 PST)
- hannes.loeffler.stfc.ac.uk (Fri Dec 05 2014 - 10:36:29 PST)
- Anupam Goel (Fri Dec 05 2014 - 10:35:13 PST)
- Anupam Goel (Fri Dec 05 2014 - 10:34:32 PST)
- Aldo Segura (Fri Dec 05 2014 - 10:05:38 PST)
- Anupam Goel (Fri Dec 05 2014 - 09:16:58 PST)
- Aldo Segura (Fri Dec 05 2014 - 08:54:04 PST)
- Anupam Goel (Fri Dec 05 2014 - 08:26:13 PST)
[AMBER] Error during Adding Fragment（about MCPB ）
- wjli (Sat Dec 27 2014 - 20:26:35 PST)
[AMBER] error in acpype
- Yaser Hosseini (Sun Dec 21 2014 - 08:34:13 PST)
[AMBER] Error in Box Dimension
- David A Case (Tue Dec 16 2014 - 05:01:19 PST)
- 杨川 (Mon Dec 15 2014 - 21:15:43 PST)
- Daniel Roe (Sun Dec 14 2014 - 20:27:17 PST)
- 杨川 (Sun Dec 14 2014 - 20:13:13 PST)
[AMBER] error in install amber
- Alan (Sun Dec 21 2014 - 13:55:02 PST)
- Jason Swails (Sun Dec 21 2014 - 11:14:47 PST)
- Yaser Hosseini (Sun Dec 21 2014 - 08:36:49 PST)
- David A Case (Fri Dec 19 2014 - 05:10:51 PST)
- Yaser Hosseini (Fri Dec 19 2014 - 02:05:24 PST)
[AMBER] error in parallel installation of Amber 12 with AmberTools13
- David A Case (Wed Dec 17 2014 - 04:32:24 PST)
- aksbmbg_s.caluniv.ac.in (Wed Dec 17 2014 - 02:53:33 PST)
- Robin Jain (Wed Dec 17 2014 - 01:47:07 PST)
[AMBER] Error in pmemd.amoeba.MPI run
- Jason Swails (Sun Dec 21 2014 - 07:35:54 PST)
- Ya Gao (Sun Dec 21 2014 - 05:17:01 PST)
[AMBER] error running equilibration (wall clock called)
- Anupam Goel (Wed Dec 17 2014 - 13:50:42 PST)
- David A Case (Wed Dec 17 2014 - 12:17:43 PST)
- Anupam Goel (Wed Dec 17 2014 - 11:41:00 PST)
[AMBER] ERROR USING tleap
- David A Case (Tue Dec 09 2014 - 04:24:01 PST)
- Jason Swails (Tue Dec 09 2014 - 04:16:16 PST)
- ROOPALI VERMA (Tue Dec 09 2014 - 00:25:07 PST)
- Hai Nguyen (Mon Dec 08 2014 - 20:12:06 PST)
- David A Case (Mon Dec 08 2014 - 04:39:09 PST)
- ROOPALI VERMA (Mon Dec 08 2014 - 03:08:15 PST)
[AMBER] error while saving prmtop and inpcrd
- David A Case (Mon Dec 15 2014 - 17:30:04 PST)
- Anupam Goel (Mon Dec 15 2014 - 14:38:07 PST)
[AMBER] Errors during Adding hydrogen atoms to the PDB file（MCPB program）
- wjli (Tue Dec 23 2014 - 20:42:50 PST)
[AMBER] excluding atom sets from MMPB/GB-SA calculations
- Hallel Freedman (Wed Dec 17 2014 - 21:04:36 PST)
- Jason Swails (Wed Dec 17 2014 - 19:35:48 PST)
- Hallel Freedman (Wed Dec 17 2014 - 12:33:50 PST)
- Jason Swails (Wed Dec 17 2014 - 11:30:08 PST)
- Hallel Freedman (Wed Dec 17 2014 - 11:20:52 PST)
- Jason Swails (Wed Dec 17 2014 - 11:06:31 PST)
- Hallel Freedman (Wed Dec 17 2014 - 10:06:40 PST)
- Ray Luo, Ph.D. (Wed Dec 17 2014 - 09:58:28 PST)
- Hallel Freedman (Tue Dec 16 2014 - 16:50:34 PST)
- Hallel Freedman (Tue Dec 16 2014 - 16:49:18 PST)
[AMBER] Failure to restart H-REMD
- Carlo Guardiani (Wed Dec 10 2014 - 07:27:41 PST)
- Jason Swails (Wed Dec 10 2014 - 04:11:09 PST)
- Carlo Guardiani (Wed Dec 10 2014 - 01:57:03 PST)
[AMBER] Forcefield for DNA
- Nihal Korkmaz (Wed Dec 24 2014 - 19:44:59 PST)
[AMBER] Free energy landscape
- Carlos Simmerling (Thu Dec 11 2014 - 06:08:55 PST)
[AMBER] Free Energy Workshop, Münster, March 9-11, 2015
- Vlad Cojocaru (Fri Dec 19 2014 - 04:58:42 PST)
[AMBER] Fwd: leap crashes and set: Improper number of arguments!
- Bill Ross (Wed Dec 17 2014 - 18:16:03 PST)
- Francesco Pietra (Wed Dec 17 2014 - 14:15:49 PST)
[AMBER] Fwd: pmemd.MPI fails to run
- Ross Walker (Mon Dec 29 2014 - 08:05:21 PST)
- Fabian Glaser (Mon Dec 29 2014 - 05:28:09 PST)
[AMBER] Fwd: RED-III.52-Tools stopped to work suddenly.
- Zeinab Emami (Wed Dec 17 2014 - 02:45:59 PST)
- FyD (Tue Dec 16 2014 - 10:15:07 PST)
- Zeinab Emami (Tue Dec 16 2014 - 03:05:19 PST)
[AMBER] Fwd: unclear leap crashing
- David A Case (Mon Dec 22 2014 - 05:30:56 PST)
- Francesco Pietra (Sat Dec 20 2014 - 08:23:22 PST)
[AMBER] gas phase, nonperiodic system with AMOEBA ff in AMBER
- Lawrenz, Morgan (Mon Dec 15 2014 - 14:52:13 PST)
- Jason Swails (Mon Dec 15 2014 - 14:42:06 PST)
- Lawrenz, Morgan (Mon Dec 15 2014 - 12:17:51 PST)
[AMBER] Generate pmf of small molecule membrane insertion
- wmsmith (Thu Dec 11 2014 - 14:34:02 PST)
[AMBER] Generation of 3D structure of polypeptides with modified amino acids
- Jason Swails (Sat Dec 13 2014 - 07:24:56 PST)
- Suman Chakrabarty (Sat Dec 13 2014 - 02:01:47 PST)
[AMBER] getting the input files for antechamber
- Ahmet yıldırım (Tue Dec 09 2014 - 11:49:05 PST)
[AMBER] Glycan-protein h-bond ptraj
- Daniel Roe (Mon Dec 15 2014 - 00:37:14 PST)
- maryam azimzadehirani (Sun Dec 14 2014 - 23:05:57 PST)
- Daniel Roe (Sun Dec 14 2014 - 20:23:15 PST)
- maryam azimzadehirani (Sun Dec 14 2014 - 19:40:05 PST)
[AMBER] help in calculating diffusion coefficient
- David A Case (Mon Dec 08 2014 - 07:00:58 PST)
- Robin Jain (Mon Dec 08 2014 - 06:40:52 PST)
[AMBER] help in calculation of diffusion coefficient
- Daniel Roe (Thu Dec 18 2014 - 08:01:39 PST)
- Robin Jain (Thu Dec 18 2014 - 07:28:33 PST)
[AMBER] help on the AMBER Tutorial B0
- Daniel Roe (Thu Dec 18 2014 - 08:40:14 PST)
- Dabing Chen (Thu Dec 18 2014 - 08:37:52 PST)
[AMBER] Help regarding error in top n crd generation
- David A Case (Thu Dec 04 2014 - 04:38:30 PST)
- Ruchika Bhat (Thu Dec 04 2014 - 04:32:17 PST)
- Ayesha Fatima (Thu Dec 04 2014 - 03:37:05 PST)
- Ruchika Bhat (Wed Dec 03 2014 - 23:14:29 PST)
[AMBER] how can i use acpype
- Jason Swails (Fri Dec 19 2014 - 06:03:59 PST)
- Yaser Hosseini (Fri Dec 19 2014 - 00:04:11 PST)
- Jason Swails (Thu Dec 18 2014 - 11:13:53 PST)
- Yaser Hosseini (Thu Dec 18 2014 - 10:39:06 PST)
- David A Case (Thu Dec 18 2014 - 09:50:27 PST)
- yaser (Thu Dec 18 2014 - 08:55:18 PST)
[AMBER] How to analyze REMD results
- Carlos Simmerling (Sun Dec 21 2014 - 19:10:59 PST)
- Wang Moye (Sun Dec 21 2014 - 16:13:15 PST)
- Wang Moye (Mon Dec 15 2014 - 22:42:04 PST)
[AMBER] How to calculate energy change between two conformations
- Kshatresh Dutta Dubey (Thu Dec 04 2014 - 13:43:58 PST)
- Jason Swails (Thu Dec 04 2014 - 13:33:38 PST)
- Kshatresh Dutta Dubey (Thu Dec 04 2014 - 13:18:16 PST)
- Jason Swails (Thu Dec 04 2014 - 12:20:03 PST)
- Kshatresh Dutta Dubey (Thu Dec 04 2014 - 07:28:57 PST)
[AMBER] how to retain the MG++ coordination geometry during simulation
- BERGY (Tue Dec 02 2014 - 13:42:17 PST)
- Marc van der Kamp (Tue Dec 02 2014 - 12:33:51 PST)
- Ken Merz (Tue Dec 02 2014 - 12:31:55 PST)
- BERGY (Tue Dec 02 2014 - 11:59:57 PST)
[AMBER] hydophobicity
- Mary Varughese (Sun Nov 30 2014 - 17:38:19 PST)
[AMBER] Hydrogen charge site and Oxygen V-site displacement
- Sylvester Tumusiime (Mon Dec 22 2014 - 19:12:19 PST)
- David A Case (Mon Dec 22 2014 - 05:29:07 PST)
- Sylvester Tumusiime (Sun Dec 21 2014 - 04:29:18 PST)
[AMBER] ifqnt
- Jason Swails (Wed Dec 24 2014 - 08:00:51 PST)
- Jason Swails (Wed Dec 24 2014 - 07:59:09 PST)
- Kshatresh Dutta Dubey (Wed Dec 24 2014 - 03:06:45 PST)
- chemjxn.126.com (Tue Dec 23 2014 - 22:06:20 PST)
- Jason Swails (Tue Dec 23 2014 - 21:26:18 PST)
- chemjxn.126.com (Tue Dec 23 2014 - 20:12:54 PST)
- Jason Swails (Tue Dec 23 2014 - 19:57:23 PST)
- chemjxn (Tue Dec 23 2014 - 18:24:56 PST)
[AMBER] Imaging membrane proteins
- David A Case (Mon Dec 29 2014 - 18:29:58 PST)
- Parker de Waal (Mon Dec 29 2014 - 16:37:26 PST)
[AMBER] Improper torsions in NMA
- David A Case (Sat Dec 20 2014 - 06:43:45 PST)
- Ganesh Kamath (Fri Dec 19 2014 - 12:08:57 PST)
- David A Case (Fri Dec 19 2014 - 05:07:10 PST)
- Ganesh Kamath (Thu Dec 18 2014 - 14:13:17 PST)
[AMBER] Information on ff12polA and ff12polL
- David A Case (Thu Dec 11 2014 - 04:22:14 PST)
- Manikanthan Bhavaraju (Wed Dec 10 2014 - 10:55:18 PST)
[AMBER] installing amber12 in GPU
- Ross Walker (Mon Dec 01 2014 - 06:31:54 PST)
- Vijay Achari (Sun Nov 30 2014 - 23:30:21 PST)
[AMBER] installing error Amber 12 Error
- Daniel Roe (Thu Dec 18 2014 - 07:56:43 PST)
- Houcemeddine Othman (Thu Dec 18 2014 - 07:37:54 PST)
[AMBER] Instructions on How to install Amber on Suse Linux
- Aldo Segura (Mon Dec 08 2014 - 12:54:39 PST)
- Daniel Roe (Mon Dec 08 2014 - 09:56:51 PST)
- Jin Zhang (Mon Dec 08 2014 - 07:55:55 PST)
[AMBER] Is BUG in cpptraj of version 14??
- Daniel Roe (Thu Dec 11 2014 - 07:01:25 PST)
- Chris Gao (Wed Dec 10 2014 - 22:51:43 PST)
[AMBER] Laccase studies of 2013
- mmaestre.gate.sinica.edu.tw (Sun Dec 21 2014 - 22:24:12 PST)
[AMBER] leap crashes and set: Improper number of arguments!
- Francesco Pietra (Wed Dec 17 2014 - 13:52:57 PST)
[AMBER] LEaP Error
- Daniel Roe (Mon Dec 01 2014 - 15:01:12 PST)
- Daniel Roe (Mon Dec 01 2014 - 14:24:43 PST)
- Aronica, Pietro (Mon Dec 01 2014 - 14:21:12 PST)
- Aronica, Pietro (Mon Dec 01 2014 - 14:00:17 PST)
- David A Case (Mon Dec 01 2014 - 04:36:23 PST)
- Aronica, Pietro (Mon Dec 01 2014 - 03:23:28 PST)
[AMBER] Linker Attached to DNA
- FyD (Tue Dec 02 2014 - 23:13:30 PST)
- chandan patel (Tue Dec 02 2014 - 16:24:58 PST)
- Brittany Boykin (Tue Dec 02 2014 - 13:58:41 PST)
[AMBER] Lipid 14 PDB format
- Romero, Raquel (Mon Dec 08 2014 - 10:56:58 PST)
[AMBER] lipid conversion
- Jonathan Gough (Sat Dec 27 2014 - 16:57:07 PST)
- Jacopo Sgrignani (Sat Dec 27 2014 - 10:07:12 PST)
- Sarah Witzke (Sat Dec 27 2014 - 10:00:01 PST)
- Jacopo Sgrignani (Sat Dec 27 2014 - 08:17:37 PST)
[AMBER] Looking for AMBER FF12SB for CHARMM
- Zhang, Sixue (Sun Dec 14 2014 - 14:52:03 PST)
[AMBER] Missing psi dihedral at cationic N-terminus of protein/peptide?
- Carlos Simmerling (Mon Dec 22 2014 - 15:38:48 PST)
- David A Case (Mon Dec 22 2014 - 05:36:27 PST)
- nealec (Mon Dec 15 2014 - 13:32:42 PST)
[AMBER] MM-PBSA (addions)
- Atila Petrosian (Fri Dec 12 2014 - 04:54:15 PST)
- Jason Swails (Fri Dec 12 2014 - 04:45:16 PST)
- Atila Petrosian (Fri Dec 12 2014 - 03:20:02 PST)
[AMBER] MMGBSA.py - issues with molsurf
- Marcus Arieno (Fri Dec 05 2014 - 08:50:31 PST)
- Daniel Roe (Fri Dec 05 2014 - 07:58:48 PST)
- de Manzanos Guinot, Angela (Fri Dec 05 2014 - 02:29:41 PST)
[AMBER] MMGBSA.py cpptraj - autoimaging issue
- Daniel Roe (Wed Dec 03 2014 - 06:57:56 PST)
- Jason Swails (Wed Dec 03 2014 - 04:19:58 PST)
- de Manzanos Guinot, Angela (Wed Dec 03 2014 - 03:22:46 PST)
- de Manzanos Guinot, Angela (Wed Dec 03 2014 - 02:54:09 PST)
[AMBER] MMPBSA-ERROR for firstmolecule-dna
- Abhishek TYAGI (Sat Dec 20 2014 - 22:57:52 PST)
- Ray Luo, Ph.D. (Fri Dec 19 2014 - 15:48:03 PST)
- Daniel Roe (Fri Dec 19 2014 - 11:00:01 PST)
- Ray Luo, Ph.D. (Fri Dec 19 2014 - 10:25:23 PST)
- Jason Swails (Fri Dec 19 2014 - 10:15:35 PST)
- Ray Luo, Ph.D. (Fri Dec 19 2014 - 09:47:39 PST)
- Abhishek TYAGI (Fri Dec 19 2014 - 01:14:49 PST)
- Ray Luo, Ph.D. (Wed Dec 17 2014 - 09:53:58 PST)
- Jason Swails (Tue Dec 16 2014 - 20:44:04 PST)
- Abhishek TYAGI (Tue Dec 16 2014 - 19:56:30 PST)
- Abhishek TYAGI (Mon Dec 15 2014 - 03:03:41 PST)
- Abhishek TYAGI (Fri Dec 12 2014 - 23:48:14 PST)
- Jason Swails (Thu Dec 11 2014 - 05:50:10 PST)
- Abhishek TYAGI (Wed Dec 10 2014 - 19:05:46 PST)
[AMBER] MMPBSA.py bad atom type
- Jason Swails (Mon Dec 08 2014 - 07:10:22 PST)
[AMBER] Monitoring GPU voltage
- Tru Huynh (Tue Dec 09 2014 - 15:46:43 PST)
- Kenneth Lam (Fri Dec 05 2014 - 13:08:16 PST)
- Ross Walker (Thu Dec 04 2014 - 19:06:31 PST)
- Kenneth Lam (Thu Dec 04 2014 - 15:00:52 PST)
- Ross Walker (Thu Dec 04 2014 - 14:16:32 PST)
- Kenneth Lam (Thu Dec 04 2014 - 13:24:17 PST)
- Jason Swails (Thu Dec 04 2014 - 13:14:59 PST)
- Kenneth Lam (Thu Dec 04 2014 - 13:02:41 PST)
- Tru Huynh (Thu Dec 04 2014 - 12:30:26 PST)
- Kenneth Lam (Thu Dec 04 2014 - 12:08:32 PST)
[AMBER] Monitoring pi-cationic interaction
- asdda asa (Sun Nov 30 2014 - 19:37:03 PST)
[AMBER] Need help in SMD
- Kshatresh Dutta Dubey (Wed Dec 31 2014 - 04:20:37 PST)
- Jason Swails (Tue Dec 30 2014 - 15:03:53 PST)
- Kshatresh Dutta Dubey (Tue Dec 30 2014 - 09:32:34 PST)
[AMBER] Need help in Targeted MD
- Carlos Simmerling (Wed Dec 31 2014 - 06:55:15 PST)
- David A Case (Wed Dec 31 2014 - 06:35:08 PST)
- Pallavi Mohanty (Wed Dec 31 2014 - 03:57:14 PST)
[AMBER] NVE simulation
- George M Giambasu (Mon Dec 22 2014 - 08:30:37 PST)
- Daniel Roe (Sun Dec 21 2014 - 22:04:13 PST)
- Robin Jain (Sun Dec 21 2014 - 21:48:07 PST)
[AMBER] On the significant dG error in the MMGBSA results.dat
- James Starlight (Mon Dec 08 2014 - 23:36:35 PST)
- James Starlight (Mon Dec 08 2014 - 00:35:06 PST)
- Aron Broom (Fri Dec 05 2014 - 07:19:34 PST)
- Jason Swails (Fri Dec 05 2014 - 05:59:56 PST)
- James Starlight (Fri Dec 05 2014 - 03:33:58 PST)
- Aron Broom (Wed Dec 03 2014 - 06:50:20 PST)
- James Starlight (Wed Dec 03 2014 - 00:15:18 PST)
- Aron Broom (Tue Dec 02 2014 - 15:35:47 PST)
- James Starlight (Tue Dec 02 2014 - 13:29:27 PST)
[AMBER] Optimization under restraint atoms using ibelly option
- Akihiro Yamane (Thu Dec 18 2014 - 04:09:11 PST)
- David A Case (Mon Dec 15 2014 - 17:33:59 PST)
- Akihiro Yamane (Mon Dec 15 2014 - 04:12:08 PST)
[AMBER] Parameter could not be saved
- Kshatresh Dutta Dubey (Tue Dec 23 2014 - 06:39:30 PST)
- Jason Swails (Tue Dec 23 2014 - 06:06:40 PST)
- Soumendranath Bhakat (Tue Dec 23 2014 - 03:11:04 PST)
- Harmeet Kaur (Tue Dec 23 2014 - 03:00:25 PST)
[AMBER] PCA 2dprojection with xtal data and energy information
- BERGY (Tue Dec 16 2014 - 21:47:42 PST)
- Daniel Roe (Tue Dec 16 2014 - 14:53:44 PST)
- BERGY (Tue Dec 16 2014 - 13:23:52 PST)
- Daniel Roe (Sat Dec 13 2014 - 20:26:54 PST)
- BERGY (Sat Dec 13 2014 - 18:45:17 PST)
- Daniel Roe (Sat Dec 13 2014 - 15:48:58 PST)
- BERGY (Sat Dec 13 2014 - 14:39:58 PST)
[AMBER] Peter Kollman lectureship, Jan 8
- David A Case (Tue Dec 30 2014 - 14:29:33 PST)
- Gustavo Seabra (Tue Dec 30 2014 - 06:04:01 PST)
- David A Case (Mon Dec 29 2014 - 14:11:49 PST)
[AMBER] phosphoserine parameters
- David A Case (Tue Dec 16 2014 - 08:27:34 PST)
- Christina Bergonzo (Tue Dec 16 2014 - 07:24:36 PST)
- Jacopo Sgrignani (Tue Dec 16 2014 - 07:17:06 PST)
[AMBER] PM6-DH+ simulation problem
- Marcos Serrou do Amaral (Fri Dec 12 2014 - 06:16:27 PST)
- Andreas Goetz (Thu Dec 11 2014 - 15:51:14 PST)
- Marcos Serrou do Amaral (Wed Dec 10 2014 - 09:05:57 PST)
[AMBER] pmemd.MPI fails
- Fabian Glaser (Sun Dec 21 2014 - 07:39:31 PST)
[AMBER] pmemd.MPI fails to run
- Jason Swails (Mon Dec 29 2014 - 03:53:18 PST)
- Fabian Glaser (Mon Dec 29 2014 - 02:33:18 PST)
- Bill Ross (Sun Dec 28 2014 - 20:19:14 PST)
- Fabian Gmail (Sun Dec 28 2014 - 11:20:03 PST)
- Thomas Cheatham (Sun Dec 28 2014 - 11:07:56 PST)
- Fabian (Sun Dec 28 2014 - 10:42:25 PST)
- Ross Walker (Sun Dec 28 2014 - 09:35:59 PST)
- Ryan Novosielski (Sun Dec 28 2014 - 09:06:48 PST)
- Fabian Glaser (Sun Dec 28 2014 - 08:31:25 PST)
- Jason Swails (Sun Dec 21 2014 - 07:39:21 PST)
- Fabian Glaser (Sun Dec 21 2014 - 06:02:10 PST)
[AMBER] Problem with AMBER mail list
- Jason Swails (Mon Dec 08 2014 - 07:56:31 PST)
- David A Case (Mon Dec 08 2014 - 06:57:03 PST)
- wangmt (Mon Dec 08 2014 - 06:26:47 PST)
[AMBER] Problem with simulation of protein-DNA complex
- Daniel Roe (Mon Dec 15 2014 - 07:22:05 PST)
- Aditya Sarkar (Mon Dec 15 2014 - 03:10:59 PST)
- Jason Swails (Sat Dec 13 2014 - 07:10:04 PST)
- Aditya Sarkar (Fri Dec 12 2014 - 22:12:52 PST)
- Daniel Roe (Fri Dec 12 2014 - 06:50:39 PST)
- Aditya Sarkar (Fri Dec 12 2014 - 00:49:20 PST)
[AMBER] Problem with triangular point in parameter file
- David A Case (Tue Dec 02 2014 - 05:06:13 PST)
- Jorgen Simonsen (Mon Dec 01 2014 - 15:20:59 PST)
- David A Case (Mon Dec 01 2014 - 04:24:52 PST)
[AMBER] problem with unknown compiler: gnu
- Narendar Kolimi (Fri Dec 05 2014 - 08:29:50 PST)
- Jason Swails (Fri Dec 05 2014 - 08:22:32 PST)
- Narendar Kolimi (Fri Dec 05 2014 - 08:20:56 PST)
- David A Case (Fri Dec 05 2014 - 05:48:52 PST)
- Narendar Kolimi (Fri Dec 05 2014 - 04:20:40 PST)
[AMBER] Problems with amber14 intallation in parallel
- Jason Swails (Mon Dec 08 2014 - 06:47:26 PST)
- Jason Swails (Sun Dec 07 2014 - 19:17:34 PST)
- Dailin Li (Sat Dec 06 2014 - 17:42:10 PST)
- Daniel Roe (Mon Dec 01 2014 - 19:54:21 PST)
- Dailin Li (Mon Dec 01 2014 - 17:39:58 PST)
[AMBER] Problems with implicit solvent
- Carlos Simmerling (Fri Dec 05 2014 - 03:53:08 PST)
- Carlo Guardiani (Fri Dec 05 2014 - 03:11:56 PST)
[AMBER] production run for diffusion constant
- Daniel Roe (Sun Dec 14 2014 - 08:45:51 PST)
- Robin Jain (Sun Dec 14 2014 - 07:39:17 PST)
[AMBER] pseudo F-statistic (pSF)
- Jonathan Gough (Mon Dec 22 2014 - 18:59:12 PST)
- Daniel Roe (Mon Dec 22 2014 - 18:30:55 PST)
- Jonathan Gough (Mon Dec 22 2014 - 16:36:09 PST)
- Daniel Roe (Fri Dec 19 2014 - 08:52:55 PST)
- Jonathan Gough (Thu Dec 18 2014 - 14:54:39 PST)
[AMBER] Query about MMPBSA.py
- Jason Swails (Wed Dec 10 2014 - 04:04:28 PST)
- de Manzanos Guinot, Angela (Wed Dec 10 2014 - 02:28:37 PST)
- Jason Swails (Tue Dec 09 2014 - 09:12:07 PST)
- de Manzanos Guinot, Angela (Tue Dec 09 2014 - 08:49:04 PST)
[AMBER] questions about bcc charge
- hannes.loeffler.stfc.ac.uk (Mon Dec 08 2014 - 23:53:26 PST)
- 徐晓庶 (Mon Dec 08 2014 - 22:07:11 PST)
[AMBER] rms fit
- Sylvester Tumusiime (Tue Dec 30 2014 - 12:33:44 PST)
- David A Case (Mon Dec 29 2014 - 18:22:51 PST)
- Sylvester Tumusiime (Mon Dec 29 2014 - 12:47:16 PST)
[AMBER] sander.PUPIL compile error
- 汪盛 (Mon Dec 08 2014 - 19:12:49 PST)
[AMBER] script to convert the Gromacs topology to Amber topology?
- Jason Swails (Fri Dec 12 2014 - 05:00:41 PST)
- Ravi Tripathi (Fri Dec 12 2014 - 01:19:47 PST)
[AMBER] selecting the best docking pose with MM/PBSA
- Ray Luo, Ph.D. (Tue Dec 09 2014 - 15:55:14 PST)
- Thomas Evangelidis (Tue Dec 09 2014 - 13:32:15 PST)
- Ray Luo, Ph.D. (Tue Dec 09 2014 - 10:54:53 PST)
- Thomas Evangelidis (Mon Dec 08 2014 - 15:22:39 PST)
[AMBER] Singe point QM/MM energy using Gaussian interface
- Jason Swails (Sun Dec 21 2014 - 11:19:08 PST)
- Bence Hégely (Sun Dec 21 2014 - 10:37:43 PST)
[AMBER] single strand DNA
- Carlos Simmerling (Mon Dec 08 2014 - 06:09:57 PST)
- Urszula Uciechowska (Mon Dec 08 2014 - 05:45:34 PST)
[AMBER] Software announcement: Release of PUPIL 3.0
- Torras, Joan (Tue Dec 09 2014 - 01:17:12 PST)
- Marc van der Kamp (Tue Dec 09 2014 - 00:52:04 PST)
- Torras, Joan (Tue Dec 09 2014 - 00:50:15 PST)
- hannes.loeffler.stfc.ac.uk (Mon Dec 08 2014 - 23:42:56 PST)
- Joan Torras (Mon Dec 08 2014 - 15:36:14 PST)
[AMBER] Solvation free energy using soft core potential
- Teerapong Pirojsirikul (Wed Dec 31 2014 - 17:08:02 PST)
[AMBER] steered MD based on PCA
- Guillaume Roellinger (Thu Dec 11 2014 - 00:34:12 PST)
[AMBER] subscribe amber
- Jason Swails (Wed Dec 17 2014 - 07:29:00 PST)
- wliu (Tue Dec 16 2014 - 23:53:07 PST)
[AMBER] switch digest model to normal
- fjliu (Tue Dec 09 2014 - 19:17:07 PST)
[AMBER] target dynamics problem
- Carlos Simmerling (Mon Dec 22 2014 - 09:51:41 PST)
- Jason Swails (Mon Dec 22 2014 - 09:43:33 PST)
- antonio.coluccia.uniroma1.it (Mon Dec 22 2014 - 06:37:44 PST)
- Carlos Simmerling (Mon Dec 22 2014 - 06:05:49 PST)
- antonio.coluccia.uniroma1.it (Mon Dec 22 2014 - 05:52:57 PST)
- Carlos Simmerling (Mon Dec 22 2014 - 05:42:09 PST)
- antonio.coluccia.uniroma1.it (Mon Dec 22 2014 - 05:31:20 PST)
[AMBER] TI and FEW
- Nadine Homeyer (Mon Dec 01 2014 - 23:34:40 PST)
[AMBER] TI calculation using pmemd
- hannes.loeffler.stfc.ac.uk (Mon Dec 29 2014 - 09:22:57 PST)
- wangmt (Mon Dec 29 2014 - 06:21:51 PST)
[AMBER] TiMergeError
- Hannes Loeffler (Wed Dec 17 2014 - 03:34:47 PST)
- fjliu (Wed Dec 17 2014 - 03:09:53 PST)
- Hannes Loeffler (Wed Dec 17 2014 - 01:24:20 PST)
- hannes.loeffler.stfc.ac.uk (Wed Dec 17 2014 - 00:27:25 PST)
- fjliu (Tue Dec 16 2014 - 23:51:54 PST)
- hannes.loeffler.stfc.ac.uk (Tue Dec 16 2014 - 23:20:29 PST)
- fjliu (Tue Dec 16 2014 - 22:18:15 PST)
[AMBER] TINKER and SANDER minimization (AMOEBA force field)
- David A Case (Thu Dec 04 2014 - 18:55:45 PST)
- 양지현 (Thu Dec 04 2014 - 18:17:11 PST)
[AMBER] TLEAP issues
- Aldo Segura (Wed Dec 10 2014 - 07:23:52 PST)
- David A Case (Tue Dec 09 2014 - 19:03:17 PST)
- Jason Swails (Tue Dec 09 2014 - 18:06:38 PST)
- Wong, Sook (NIH/NCATS) [V] (Tue Dec 09 2014 - 13:59:01 PST)
[AMBER] tleap segmentation fault
- Daniel Roe (Mon Dec 01 2014 - 12:32:07 PST)
- George Tzotzos (Mon Dec 01 2014 - 12:17:20 PST)
- Jason Swails (Mon Dec 01 2014 - 12:15:45 PST)
- George Tzotzos (Mon Dec 01 2014 - 12:06:01 PST)
- Daniel Roe (Mon Dec 01 2014 - 12:00:40 PST)
- George Tzotzos (Mon Dec 01 2014 - 11:44:32 PST)
[AMBER] Total energy of system is positive
- Jason Swails (Mon Dec 29 2014 - 22:05:01 PST)
- MOHD HOMAIDUR RAHMAN (Mon Dec 29 2014 - 21:46:26 PST)
- Jason Swails (Mon Dec 29 2014 - 15:23:49 PST)
- Adrian Roitberg (Mon Dec 29 2014 - 14:29:33 PST)
- MOHD HOMAIDUR RAHMAN (Mon Dec 29 2014 - 11:51:53 PST)
- Jason Swails (Mon Dec 29 2014 - 08:31:53 PST)
- MOHD HOMAIDUR RAHMAN (Sun Dec 28 2014 - 21:40:26 PST)
[AMBER] Umbrella sampling for molecules moving
- Carlos Simmerling (Mon Dec 22 2014 - 15:36:42 PST)
- Helen Lvy (Mon Dec 22 2014 - 13:22:38 PST)
[AMBER] unclear leap crashing
- Francesco Pietra (Sat Dec 20 2014 - 11:40:40 PST)
- Francesco Pietra (Fri Dec 19 2014 - 12:55:51 PST)
- David A Case (Fri Dec 19 2014 - 05:05:43 PST)
- FyD (Fri Dec 19 2014 - 02:33:31 PST)
- Francesco Pietra (Thu Dec 18 2014 - 10:53:21 PST)
[AMBER] Use of special characters * and ? in ambermask
- Emilio Lence (Sat Dec 06 2014 - 11:31:27 PST)
[AMBER] WHAM tolerance
- Jason Swails (Tue Dec 30 2014 - 15:11:08 PST)
- Sun (Thu Dec 25 2014 - 19:46:20 PST)
[AMBER] Wrong bond types in Antechamber MOL2
- Hannes Loeffler (Tue Dec 09 2014 - 02:43:07 PST)
- Denis Schmidt (Tue Dec 09 2014 - 02:08:22 PST)
- Hannes Loeffler (Tue Dec 09 2014 - 01:30:11 PST)
- Denis Schmidt (Mon Dec 08 2014 - 07:21:11 PST)
[AMBER] xleap segmentation fault when removing residues
- Mickey Richards (Thu Dec 04 2014 - 15:03:42 PST)
[AMBER] 回复： Errors during Adding hydrogen atoms to the PDB file（MCPB program）
- wjli (Tue Dec 23 2014 - 21:01:27 PST)

Amber Archive Dec 2014 by subject