Amber Archive Apr 2015: by subject

[AMBER] a question for hydrocarbons simulation using amber FF
- Nahid Khiabani (Sun Apr 12 2015 - 06:22:16 PDT)
- David A Case (Sun Apr 12 2015 - 06:18:19 PDT)
- David A Case (Sun Apr 12 2015 - 06:04:14 PDT)
- Nahid Khiabani (Sun Apr 12 2015 - 04:50:51 PDT)
- Marc van der Kamp (Sun Apr 12 2015 - 04:12:14 PDT)
- Nahid Khiabani (Sun Apr 12 2015 - 03:53:54 PDT)
- hannes.loeffler.stfc.ac.uk (Sun Apr 12 2015 - 03:50:24 PDT)
- Nahid Khiabani (Sun Apr 12 2015 - 03:33:15 PDT)
- Nahid Khiabani (Sat Apr 11 2015 - 00:09:14 PDT)
- Nahid Khiabani (Thu Apr 09 2015 - 13:33:43 PDT)
[AMBER] AHTECHAMBER - G09
- Ayesha Fatima (Wed Apr 08 2015 - 07:33:47 PDT)
- Sanja Zivanovic (Wed Apr 08 2015 - 06:33:10 PDT)
[AMBER] Alanin scanning MMGBSA.py error: TypeError: not all arguments converted during string formatting
- Jason Swails (Fri Apr 17 2015 - 04:56:36 PDT)
- maryam azimzadehirani (Fri Apr 17 2015 - 01:38:21 PDT)
- Jason Swails (Thu Apr 16 2015 - 06:33:00 PDT)
- maryam azimzadehirani (Thu Apr 16 2015 - 00:06:05 PDT)
[AMBER] all in one pc for MD simulation calculations
- Jason Swails (Thu Apr 16 2015 - 07:57:55 PDT)
- Atila Petrosian (Thu Apr 16 2015 - 07:50:45 PDT)
[AMBER] AMBER 14 installation problem
- Sanjib Paul (Thu Apr 23 2015 - 06:27:33 PDT)
- Jason Swails (Thu Apr 23 2015 - 03:50:59 PDT)
- Sanjib Paul (Wed Apr 22 2015 - 22:49:14 PDT)
[AMBER] Amber GPU Segmentation fault
- AJ Venkatakrishnan (Fri Apr 24 2015 - 19:02:05 PDT)
- Ross Walker (Tue Apr 21 2015 - 16:06:21 PDT)
- AJ Venkatakrishnan (Tue Apr 21 2015 - 15:29:31 PDT)
[AMBER] AMBER parametrization questions
- Carlos Simmerling (Mon Apr 13 2015 - 06:36:12 PDT)
- Jeffrey Teillet (Mon Apr 13 2015 - 06:20:11 PDT)
[AMBER] amber14 errors
- Novosielski, Ryan (Thu Apr 02 2015 - 12:10:29 PDT)
[AMBER] AMBER14 pmemd.cuda.MPI : *** in mdout files
- Ross Walker (Fri Apr 03 2015 - 22:18:58 PDT)
- Himanshu Joshi (Tue Mar 31 2015 - 21:13:02 PDT)
- Himanshu Joshi (Tue Mar 31 2015 - 20:32:38 PDT)
[AMBER] Amino acid as ligand
- Jason Swails (Sat Apr 11 2015 - 21:01:58 PDT)
- Dhiraj Srivastava (Sat Apr 11 2015 - 20:06:20 PDT)
[AMBER] Antechamber Algorithm for Atom Type
- Robert Molt (Tue Apr 28 2015 - 17:42:08 PDT)
- Jason Swails (Tue Apr 28 2015 - 07:14:41 PDT)
- Hannes Loeffler (Tue Apr 28 2015 - 07:08:23 PDT)
- Hannes Loeffler (Tue Apr 28 2015 - 07:06:14 PDT)
- Jason Swails (Tue Apr 28 2015 - 06:56:02 PDT)
- Robert Molt (Tue Apr 28 2015 - 06:51:08 PDT)
- Hannes Loeffler (Tue Apr 28 2015 - 06:29:57 PDT)
- Robert Molt (Tue Apr 28 2015 - 06:03:24 PDT)
- hannes.loeffler.stfc.ac.uk (Mon Apr 27 2015 - 23:21:32 PDT)
- Robert Molt (Mon Apr 27 2015 - 18:19:57 PDT)
[AMBER] Any timeline for TI on GPU's?
- Ross Walker (Wed Apr 22 2015 - 23:10:42 PDT)
- filip fratev (Wed Apr 22 2015 - 11:01:45 PDT)
- Ucisik, Melek Nihan (Wed Apr 22 2015 - 09:39:56 PDT)
[AMBER] Arrangement of molecules in 3D packed state
- jacob wick (Thu Apr 23 2015 - 10:46:39 PDT)
- jacob wick (Thu Apr 23 2015 - 10:43:11 PDT)
- Pawel Janowski (Thu Apr 23 2015 - 07:57:12 PDT)
- David A Case (Thu Apr 23 2015 - 07:31:08 PDT)
- jacob wick (Thu Apr 23 2015 - 01:59:59 PDT)
- David A Case (Wed Apr 22 2015 - 08:13:29 PDT)
- jacob wick (Tue Apr 21 2015 - 01:16:25 PDT)
- David A Case (Sun Apr 12 2015 - 19:50:34 PDT)
- Bill Ross (Sun Apr 12 2015 - 17:04:50 PDT)
- jacob wick (Sun Apr 12 2015 - 11:30:25 PDT)
[AMBER] ATTN needs revision
- David A Case (Wed Apr 22 2015 - 08:08:52 PDT)
- Sanja Zivanovic (Tue Apr 21 2015 - 08:13:35 PDT)
[AMBER] Bad atom Type in MMPBSA.py
- Kenneth Huang (Sun Apr 12 2015 - 12:15:48 PDT)
- wjli (Sun Apr 12 2015 - 00:19:24 PDT)
- Kenneth Huang (Sat Apr 11 2015 - 11:17:42 PDT)
- wjli (Fri Apr 10 2015 - 19:35:15 PDT)
[AMBER] barosts command in amber 12
- Jason Swails (Sun Apr 05 2015 - 17:33:52 PDT)
- Chris Gaughan (Sun Apr 05 2015 - 11:04:52 PDT)
[AMBER] Batch leap error!
- Hector A. Baldoni (Fri Apr 17 2015 - 09:16:25 PDT)
- Hannes Loeffler (Fri Apr 17 2015 - 08:52:22 PDT)
- Pallavi Mohanty (Fri Apr 17 2015 - 08:45:57 PDT)
- Jason Swails (Fri Apr 17 2015 - 06:42:29 PDT)
- Hannes Loeffler (Fri Apr 17 2015 - 06:31:29 PDT)
- hannes.loeffler.stfc.ac.uk (Fri Apr 17 2015 - 05:07:47 PDT)
- Jason Swails (Fri Apr 17 2015 - 05:12:29 PDT)
- Jason Swails (Fri Apr 17 2015 - 05:07:17 PDT)
- Pallavi Mohanty (Fri Apr 17 2015 - 04:59:43 PDT)
- Hannes Loeffler (Fri Apr 17 2015 - 04:17:59 PDT)
- Pallavi Mohanty (Fri Apr 17 2015 - 04:02:00 PDT)
[AMBER] Boltzman Weights from MD trajectory
- Emilio Angelina (Tue Apr 07 2015 - 13:22:24 PDT)
- Jason Swails (Tue Apr 07 2015 - 11:41:36 PDT)
- Emilio Angelina (Tue Apr 07 2015 - 11:33:33 PDT)
[AMBER] Build long polymer from the monomer using Xleap
- James Starlight (Fri Apr 10 2015 - 04:40:12 PDT)
- FyD (Mon Apr 06 2015 - 22:52:51 PDT)
- Karl Kirschner (Thu Apr 02 2015 - 07:39:46 PDT)
- James Starlight (Thu Apr 02 2015 - 07:08:54 PDT)
- Karl Kirschner (Thu Apr 02 2015 - 06:23:42 PDT)
- James Starlight (Thu Apr 02 2015 - 05:41:24 PDT)
[AMBER] Bursary deadline, May 15, 2015: Drug Discovery Workshops Canada
- Thomas Exner (Thu Apr 30 2015 - 13:01:24 PDT)
[AMBER] Bursary deadline, May 15, 2015: Drug Discovery Workshops Milan
- Thomas Exner (Thu Apr 30 2015 - 12:59:52 PDT)
[AMBER] Calculating Cp values from NPT simulations using ptraj
- Daniel Roe (Tue Apr 21 2015 - 11:01:18 PDT)
- Vivek Shankar Bharadwaj (Tue Apr 14 2015 - 14:42:13 PDT)
[AMBER] Calculating protein center of mass (COM) using vector command
- George Green (Tue Apr 07 2015 - 08:39:38 PDT)
- Daniel Roe (Tue Apr 07 2015 - 08:30:53 PDT)
- George Green (Tue Apr 07 2015 - 07:51:11 PDT)
[AMBER] Carbon nanotube simulation
- Pierre Bertin (Fri Apr 17 2015 - 08:32:06 PDT)
- Daniel Roe (Fri Apr 17 2015 - 07:00:46 PDT)
- Karl Kirschner (Fri Apr 17 2015 - 00:32:56 PDT)
- Pierre Bertin (Thu Apr 16 2015 - 23:51:08 PDT)
[AMBER] CENTOS 6.6 :ERROR - INSTALLATION OF AMBERTOOLS14/AMBER14
- Jason Swails (Thu Apr 23 2015 - 03:42:56 PDT)
- vitonoja.yahoo.com (Wed Apr 22 2015 - 20:06:11 PDT)
[AMBER] Charmm force field parameters in Amber
- Jason Swails (Mon Apr 13 2015 - 06:47:47 PDT)
- anu chandra (Mon Apr 13 2015 - 06:33:30 PDT)
[AMBER] charmmlipid2amber.py error
- Gözde YALÇIN (Wed Apr 29 2015 - 00:03:40 PDT)
- Jason Swails (Sat Apr 25 2015 - 13:48:03 PDT)
- Gözde YALÇIN (Sat Apr 25 2015 - 11:39:33 PDT)
[AMBER] charmmlipid2amber2.py error
- Michele Bonus (Sat Apr 25 2015 - 06:10:25 PDT)
- Gözde YALÇIN (Sat Apr 25 2015 - 04:35:51 PDT)
[AMBER] close contacts in equilibrated structure
- Asmita Gupta (Sat Apr 25 2015 - 14:59:35 PDT)
- Jason Swails (Sat Apr 25 2015 - 13:40:35 PDT)
- Asmita Gupta (Sat Apr 25 2015 - 08:37:25 PDT)
[AMBER] COM distance restraints and pmemd.cuda
- Ilyas Yildirim (Tue Apr 07 2015 - 15:30:26 PDT)
- David A Case (Tue Apr 07 2015 - 10:39:24 PDT)
- Ilyas Yildirim (Tue Apr 07 2015 - 10:12:51 PDT)
[AMBER] Community network analysis for the Amber trajectories
- James Starlight (Wed Apr 15 2015 - 05:39:03 PDT)
- Vlad Cojocaru (Tue Apr 14 2015 - 12:19:13 PDT)
- Vlad Cojocaru (Tue Apr 14 2015 - 12:11:56 PDT)
- James Starlight (Tue Apr 14 2015 - 11:32:04 PDT)
- Daniel Roe (Tue Apr 14 2015 - 08:59:51 PDT)
- James Starlight (Tue Apr 14 2015 - 07:25:27 PDT)
[AMBER] Could anyone tell me how to run targeted MD correctly
- 肖立 (Fri Apr 17 2015 - 11:04:29 PDT)
- 肖立 (Fri Apr 17 2015 - 11:03:23 PDT)
- Carlos Simmerling (Fri Apr 17 2015 - 10:17:19 PDT)
- 肖立 (Fri Apr 17 2015 - 10:10:10 PDT)
- Carlos Simmerling (Fri Apr 17 2015 - 05:24:37 PDT)
- 肖立 (Thu Apr 16 2015 - 23:45:08 PDT)
[AMBER] cpptraj V14.25 issues with old Amber topology files (Amber 11)
- Daniel Roe (Mon Apr 27 2015 - 10:35:54 PDT)
- CHAMI F. (Mon Apr 27 2015 - 10:31:53 PDT)
- Daniel Roe (Mon Apr 27 2015 - 08:36:43 PDT)
- Jason Swails (Mon Apr 27 2015 - 08:22:29 PDT)
- CHAMI F. (Mon Apr 27 2015 - 07:11:32 PDT)
[AMBER] cpptraj write data from runanalysis
- Gard Nelson (Fri Apr 10 2015 - 15:25:08 PDT)
- Daniel Roe (Fri Apr 10 2015 - 13:29:14 PDT)
- Gard Nelson (Fri Apr 10 2015 - 11:29:45 PDT)
[AMBER] cpptraj writting box coordinates issue
- CHAMI F. (Mon Apr 20 2015 - 08:24:43 PDT)
- Daniel Roe (Mon Apr 20 2015 - 08:04:46 PDT)
- CHAMI F. (Mon Apr 20 2015 - 08:00:09 PDT)
[AMBER] defining residues in steered molecular dynamics
- Sourav Purohit (Wed Apr 08 2015 - 09:08:25 PDT)
- Ayesha Fatima (Wed Apr 08 2015 - 07:57:53 PDT)
[AMBER] deletion of H atoms for pdb file
- Daniel Roe (Thu Apr 16 2015 - 12:38:54 PDT)
- hannes.loeffler.stfc.ac.uk (Thu Apr 16 2015 - 12:16:34 PDT)
[AMBER] Deletion of H atoms from pdb file used for MD simulations
- Daniel Roe (Wed Apr 15 2015 - 08:02:22 PDT)
- Jason Swails (Wed Apr 15 2015 - 06:05:11 PDT)
- Sofia Vasilakaki (Wed Apr 15 2015 - 05:46:22 PDT)
- Hannes Loeffler (Wed Apr 15 2015 - 03:49:09 PDT)
- suma jayakrishnan (Wed Apr 15 2015 - 03:21:20 PDT)
- Ashutosh Shandilya (Wed Apr 15 2015 - 02:19:03 PDT)
- muhammad tahir ayub (Tue Apr 14 2015 - 23:35:51 PDT)
[AMBER] Diffusion constant calculation
- Daniel Roe (Thu Apr 16 2015 - 07:44:41 PDT)
- pooja chahal (Wed Apr 15 2015 - 20:42:21 PDT)
- Daniel Roe (Wed Apr 15 2015 - 10:13:01 PDT)
- pooja chahal (Wed Apr 15 2015 - 05:25:58 PDT)
- Daniel Roe (Tue Apr 14 2015 - 07:06:05 PDT)
- pooja chahal (Mon Apr 13 2015 - 21:42:24 PDT)
- Daniel Roe (Mon Apr 13 2015 - 08:42:35 PDT)
- pooja chahal (Thu Apr 09 2015 - 23:20:24 PDT)
[AMBER] dispersion for QM/MM missing parameters
- Jorgen Simonsen (Wed Apr 29 2015 - 00:17:16 PDT)
[AMBER] DNA partial charges in Amber library
- Thomas Cheatham (Thu Apr 23 2015 - 22:54:28 PDT)
- jacob wick (Thu Apr 23 2015 - 22:23:08 PDT)
[AMBER] Does atomicflut byres report the fluctuations of the residue CM?
- Jose Borreguero (Mon Apr 13 2015 - 09:01:59 PDT)
- Daniel Roe (Mon Apr 13 2015 - 08:49:11 PDT)
- Jose Borreguero (Fri Apr 10 2015 - 15:44:38 PDT)
[AMBER] EGB and EEL Values in MM-GBSA -reg
- Jason Swails (Tue Apr 28 2015 - 11:54:37 PDT)
- Muthukumaran R (Tue Apr 28 2015 - 11:03:58 PDT)
[AMBER] EGB and ESCF might not be converged if the net charge not equal to 0 in the QM/MM-GBSA
- Ross Walker (Mon Apr 06 2015 - 09:21:03 PDT)
- psu4.uic.edu (Sun Apr 05 2015 - 17:35:39 PDT)
- Ross Walker (Fri Apr 03 2015 - 15:57:23 PDT)
- psu4.uic.edu (Fri Apr 03 2015 - 15:48:37 PDT)
- Gerald Monard (Thu Apr 02 2015 - 01:42:11 PDT)
- psu4.uic.edu (Thu Apr 02 2015 - 00:27:31 PDT)
[AMBER] Energy drift issue
- Jason Swails (Tue Apr 07 2015 - 13:09:14 PDT)
- Steven Ramsey (Tue Apr 07 2015 - 12:52:55 PDT)
[AMBER] Error
- David A Case (Sun Apr 12 2015 - 06:14:12 PDT)
- Adnan Gulzar (Sat Apr 11 2015 - 15:18:53 PDT)
[AMBER] error **** in output file with wrapping first molecule on GPU
- Gerald Monard (Fri Apr 03 2015 - 14:50:15 PDT)
- Gerald Monard (Fri Apr 03 2015 - 05:15:53 PDT)
- Jason Swails (Thu Apr 02 2015 - 11:35:14 PDT)
- Jason Swails (Thu Apr 02 2015 - 10:27:21 PDT)
- Quynh Vo (Thu Apr 02 2015 - 09:41:23 PDT)
- Gerald Monard (Thu Apr 02 2015 - 00:13:44 PDT)
- Quynh Vo (Wed Apr 01 2015 - 23:00:08 PDT)
[AMBER] error generating P450 prmtop incrd file
- Vaibhav Dixit (Thu Apr 09 2015 - 02:22:29 PDT)
- Jason Swails (Wed Apr 08 2015 - 10:08:58 PDT)
- Jason Swails (Wed Apr 08 2015 - 10:06:43 PDT)
- Vaibhav Dixit (Wed Apr 08 2015 - 08:33:48 PDT)
- Mark Williamson (Tue Apr 07 2015 - 07:29:00 PDT)
- Daniel Roe (Tue Apr 07 2015 - 07:27:11 PDT)
- Jason Swails (Tue Apr 07 2015 - 06:01:29 PDT)
- Vaibhav Dixit (Tue Apr 07 2015 - 05:54:02 PDT)
- David A Case (Tue Apr 07 2015 - 05:10:39 PDT)
- Vaibhav Dixit (Tue Apr 07 2015 - 04:54:14 PDT)
[AMBER] error in amber installation
- David A Case (Tue Apr 28 2015 - 05:14:30 PDT)
- Atila Petrosian (Tue Apr 28 2015 - 04:14:55 PDT)
[AMBER] error in minimization
- Jason Swails (Tue Apr 14 2015 - 10:03:01 PDT)
- Carlos Romero (Tue Apr 14 2015 - 09:52:28 PDT)
- Jason Swails (Tue Apr 14 2015 - 09:01:14 PDT)
- Carlos Romero (Tue Apr 14 2015 - 08:55:38 PDT)
- Carlos Romero (Mon Apr 13 2015 - 10:29:09 PDT)
- Jason Swails (Mon Apr 13 2015 - 10:26:09 PDT)
- Carlos Romero (Mon Apr 13 2015 - 10:23:07 PDT)
- Jason Swails (Mon Apr 13 2015 - 10:11:01 PDT)
- Carlos Romero (Mon Apr 13 2015 - 10:00:28 PDT)
- Jason Swails (Mon Apr 13 2015 - 06:43:21 PDT)
- Carlos Romero (Mon Apr 13 2015 - 06:30:20 PDT)
- David A Case (Mon Apr 13 2015 - 04:25:04 PDT)
- Vaibhav Dixit (Mon Apr 13 2015 - 03:18:02 PDT)
- Bill Ross (Sun Apr 12 2015 - 21:20:41 PDT)
- Carlos Romero (Sun Apr 12 2015 - 20:18:37 PDT)
- David A Case (Sun Apr 12 2015 - 19:52:55 PDT)
- Carlos Romero (Sun Apr 12 2015 - 16:45:38 PDT)
- Bill Ross (Sun Apr 12 2015 - 16:06:22 PDT)
- Carlos Romero (Sun Apr 12 2015 - 12:05:08 PDT)
- Bill Ross (Sun Apr 12 2015 - 09:53:30 PDT)
- Carlos Romero (Sun Apr 12 2015 - 08:37:00 PDT)
- David A Case (Sun Apr 12 2015 - 06:06:58 PDT)
- Carlos Romero (Sat Apr 11 2015 - 22:25:53 PDT)
- Bill Ross (Sat Apr 11 2015 - 21:03:58 PDT)
- Carlos Romero (Sat Apr 11 2015 - 13:55:32 PDT)
[AMBER] Error in tutorial A16, Amber 14
- Benjamin D Madej (Thu Apr 09 2015 - 13:28:19 PDT)
- Michael Shokhen (Thu Apr 09 2015 - 03:14:54 PDT)
- Benjamin D Madej (Wed Apr 08 2015 - 20:15:08 PDT)
- Michael Shokhen (Tue Apr 07 2015 - 23:16:48 PDT)
[AMBER] Error message in Amber14 tutorial A16
- Michael Shokhen (Tue Apr 07 2015 - 12:57:12 PDT)
[AMBER] Error while running MMPBSA
- Kenneth Huang (Fri Apr 03 2015 - 08:01:26 PDT)
- Shreeramesh (Fri Apr 03 2015 - 02:24:10 PDT)
- Bill Ross (Thu Apr 02 2015 - 08:31:25 PDT)
- Kenneth Huang (Thu Apr 02 2015 - 08:25:34 PDT)
- Shreeramesh (Thu Apr 02 2015 - 08:15:21 PDT)
- Kenneth Huang (Thu Apr 02 2015 - 07:57:33 PDT)
- Shreeramesh (Thu Apr 02 2015 - 07:47:42 PDT)
- Jason Swails (Thu Apr 02 2015 - 05:40:32 PDT)
- Shreeramesh (Thu Apr 02 2015 - 00:00:59 PDT)
[AMBER] Error with quasi-harmonic MMPBSA.py calculations
- Jason Swails (Thu Apr 23 2015 - 03:55:19 PDT)
- Abhishek TYAGI (Thu Apr 23 2015 - 00:56:00 PDT)
- Jason Swails (Fri Apr 17 2015 - 08:43:03 PDT)
- Abhishek TYAGI (Fri Apr 17 2015 - 08:30:04 PDT)
- Jason Swails (Thu Apr 16 2015 - 06:40:26 PDT)
- Abhishek TYAGI (Wed Apr 15 2015 - 21:26:20 PDT)
[AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program
- vijay kumar narsapuram (Fri Apr 24 2015 - 07:52:10 PDT)
- Jason Swails (Fri Apr 24 2015 - 04:59:14 PDT)
- vijay kumar narsapuram (Thu Apr 23 2015 - 12:56:43 PDT)
- Jason Swails (Thu Apr 23 2015 - 12:19:45 PDT)
- Jason Swails (Thu Apr 23 2015 - 11:26:29 PDT)
- vijay kumar narsapuram (Thu Apr 23 2015 - 09:50:14 PDT)
- Jason Swails (Thu Apr 23 2015 - 05:06:05 PDT)
- vijay kumar narsapuram (Thu Apr 23 2015 - 04:48:19 PDT)
- vijay kumar narsapuram (Thu Apr 23 2015 - 04:02:01 PDT)
- Jason Swails (Thu Apr 23 2015 - 03:59:32 PDT)
- vijay kumar narsapuram (Thu Apr 23 2015 - 03:15:09 PDT)
[AMBER] Evaluating hydrogen boding lifetime
- Vijay Achari (Fri Apr 17 2015 - 20:40:52 PDT)
- Daniel Roe (Fri Apr 17 2015 - 07:12:07 PDT)
- Vijay Achari (Thu Apr 16 2015 - 22:47:05 PDT)
- Daniel Roe (Thu Apr 16 2015 - 07:41:21 PDT)
- Vijay Achari (Wed Apr 15 2015 - 23:41:54 PDT)
[AMBER] Force Field Parameters for Monoamino Acids at acidic and basic conditions?
- Jason Swails (Fri Apr 10 2015 - 03:12:25 PDT)
- Gerald Monard (Fri Apr 10 2015 - 00:25:31 PDT)
- Alain Chaumont (Fri Apr 10 2015 - 00:08:21 PDT)
[AMBER] Free energy calculation of ligand binding energy: Thermodynamic integration - long range dispersion correction - recalculate trajectory with different potential
- Hannes Loeffler (Thu Apr 02 2015 - 04:31:11 PDT)
- vladimir.palivec.marge.uochb.cas.cz (Thu Apr 02 2015 - 03:57:35 PDT)
[AMBER] Free energy calculation of ligand binding energy: Thermodynamic integration - pmemd - single topology - vdw
- hannes.loeffler.stfc.ac.uk (Sat Apr 25 2015 - 07:46:20 PDT)
- vladimir.palivec.marge.uochb.cas.cz (Sat Apr 25 2015 - 04:58:53 PDT)
- hannes.loeffler.stfc.ac.uk (Thu Apr 23 2015 - 09:04:34 PDT)
- vladimir.palivec.marge.uochb.cas.cz (Thu Apr 23 2015 - 08:26:11 PDT)
[AMBER] Fwd: Tleap atom type - template not found
- David A Case (Tue Apr 28 2015 - 04:59:24 PDT)
- Balaji Selvam (Mon Apr 27 2015 - 23:02:29 PDT)
[AMBER] Help regarding appropriate analysis for correlated motion using cpptraj
- Kshatresh Dutta Dubey (Wed Apr 01 2015 - 07:59:14 PDT)
- Jason Swails (Wed Apr 01 2015 - 07:49:17 PDT)
- Kshatresh Dutta Dubey (Wed Apr 01 2015 - 07:42:50 PDT)
- Jason Swails (Wed Apr 01 2015 - 06:04:26 PDT)
[AMBER] How to obtain potential energy using mdcrd trajectories in AMBER12
- Gerald Monard (Fri Apr 03 2015 - 08:44:24 PDT)
- Jason Swails (Fri Apr 03 2015 - 07:07:47 PDT)
- Brian Radak (Thu Apr 02 2015 - 13:49:14 PDT)
- Jason Swails (Thu Apr 02 2015 - 13:12:09 PDT)
- Brian Radak (Thu Apr 02 2015 - 12:06:23 PDT)
[AMBER] How to resolve the problem when amber14 configured with cuda 6.5
- Jason Swails (Sun Apr 19 2015 - 12:29:51 PDT)
- 金毅 (Sat Apr 18 2015 - 06:35:29 PDT)
- 金毅 (Sat Apr 18 2015 - 04:50:02 PDT)
- Jason Swails (Sat Apr 18 2015 - 04:48:50 PDT)
- Ross Walker (Sat Apr 18 2015 - 01:53:07 PDT)
- 金毅 (Fri Apr 17 2015 - 23:28:41 PDT)
[AMBER] how to run non standard simulation
- David A Case (Mon Apr 27 2015 - 14:51:35 PDT)
- muhammad tahir ayub (Mon Apr 27 2015 - 11:39:46 PDT)
[AMBER] How to use the mmpbsa.py to calcualte the free energy of a modified protein ?
- Jason Swails (Tue Apr 14 2015 - 07:31:28 PDT)
- windy (Fri Apr 10 2015 - 21:35:39 PDT)
- Jason Swails (Fri Apr 10 2015 - 03:09:31 PDT)
- windy (Thu Apr 09 2015 - 19:29:59 PDT)
[AMBER] hydrogen bond analysis using cpptraj in amber tools 14
- Daniel Roe (Tue Apr 14 2015 - 06:56:04 PDT)
- Atila Petrosian (Tue Apr 14 2015 - 01:25:27 PDT)
[AMBER] In MMPBSY.py , how to set interval value when large conformation change ?
- windy (Wed Apr 22 2015 - 21:05:50 PDT)
- Jason Swails (Wed Apr 22 2015 - 03:59:58 PDT)
- windy (Tue Apr 21 2015 - 18:58:22 PDT)
- Jason Swails (Mon Apr 20 2015 - 11:47:27 PDT)
- George Tzotzos (Mon Apr 20 2015 - 11:20:36 PDT)
- Jason Swails (Mon Apr 20 2015 - 06:09:45 PDT)
- windy (Mon Apr 20 2015 - 01:41:27 PDT)
[AMBER] install Amber 11 and AmberTools 1.5 on CentoS 6.3
- Jason Swails (Wed Apr 22 2015 - 11:08:15 PDT)
- Hai Nguyen (Wed Apr 22 2015 - 10:49:57 PDT)
- Atila Petrosian (Wed Apr 22 2015 - 10:47:31 PDT)
- Jason Swails (Wed Apr 22 2015 - 04:05:50 PDT)
- Atila Petrosian (Tue Apr 21 2015 - 21:18:05 PDT)
- Jason Swails (Tue Apr 21 2015 - 12:23:12 PDT)
- Atila Petrosian (Tue Apr 21 2015 - 12:02:46 PDT)
[AMBER] intercalations
- Bill Ross (Sun Apr 12 2015 - 09:50:02 PDT)
- David A Case (Sun Apr 12 2015 - 05:57:54 PDT)
- Arjun Sharma (Fri Apr 10 2015 - 16:36:30 PDT)
[AMBER] Invitation to Computational Chemical Biology Conference (Aug 6th to 9th 2015), Cairns, Australia (http://tinyurl.com/nyblv7o)
- Ross Walker (Fri Apr 10 2015 - 15:25:23 PDT)
[AMBER] is it possible to output the trajectory of the center of mass of the residues?
- Jose Borreguero (Mon Apr 13 2015 - 10:22:29 PDT)
- Daniel Roe (Mon Apr 13 2015 - 09:22:58 PDT)
- Jose Borreguero (Mon Apr 13 2015 - 07:05:51 PDT)
[AMBER] Is there NHE cap in the ff02 library files?
- David A Case (Tue Apr 28 2015 - 04:56:20 PDT)
- Yip Yew Mun (Mon Apr 27 2015 - 21:06:06 PDT)
[AMBER] larger bonds between protein atoms
- Vaibhav Dixit (Thu Apr 09 2015 - 07:19:25 PDT)
- David A Case (Thu Apr 09 2015 - 05:00:56 PDT)
- Jason Swails (Thu Apr 09 2015 - 04:24:30 PDT)
- Vaibhav Dixit (Thu Apr 09 2015 - 04:15:09 PDT)
[AMBER] ligand-solvent interaction energy
- Jason Swails (Fri Apr 17 2015 - 05:34:15 PDT)
- Hannes Loeffler (Fri Apr 17 2015 - 02:23:41 PDT)
[AMBER] Lipid Conversion from Charmm PDB to Lipid14 PDB
- Wong, Sook (NIH/NCATS) [V] (Thu Apr 02 2015 - 12:59:40 PDT)
- Wong, Sook (NIH/NCATS) [V] (Thu Apr 02 2015 - 12:51:33 PDT)
- Daniel Roe (Thu Apr 02 2015 - 12:39:35 PDT)
- Wong, Sook (NIH/NCATS) [V] (Thu Apr 02 2015 - 12:35:27 PDT)
[AMBER] lipid simulation queries
- Bala subramanian (Wed Apr 29 2015 - 10:03:33 PDT)
[AMBER] mcpb problem
- Jia Xu (Sat Apr 25 2015 - 08:40:30 PDT)
- chemjxn (Sat Apr 25 2015 - 01:17:20 PDT)
- Pengfei Li (Thu Apr 23 2015 - 07:28:01 PDT)
- chemjxn (Wed Apr 22 2015 - 21:12:08 PDT)
[AMBER] MCPB subprogram problem
- Pengfei Li (Wed Apr 01 2015 - 12:43:11 PDT)
- chemjxn (Tue Mar 31 2015 - 23:41:50 PDT)
[AMBER] MMBP(GB)SA free energy decomposition error: sander failed with prmtop
- Jason Swails (Thu Apr 23 2015 - 03:58:09 PDT)
- maryam azimzadehirani (Thu Apr 23 2015 - 00:22:27 PDT)
- Kenneth Huang (Wed Apr 08 2015 - 21:59:13 PDT)
- maryam azimzadehirani (Wed Apr 08 2015 - 20:40:05 PDT)
[AMBER] mmbsa.py issue with the complex.parmtop
- James Starlight (Tue Apr 07 2015 - 05:19:17 PDT)
- Kenneth Huang (Mon Apr 06 2015 - 08:25:55 PDT)
- James Starlight (Mon Apr 06 2015 - 07:58:23 PDT)
- Kenneth Huang (Mon Apr 06 2015 - 07:23:25 PDT)
- Kenneth Huang (Mon Apr 06 2015 - 07:19:00 PDT)
- James Starlight (Mon Apr 06 2015 - 07:13:47 PDT)
- James Starlight (Mon Apr 06 2015 - 06:12:17 PDT)
- Kenneth Huang (Fri Apr 03 2015 - 08:22:25 PDT)
- James Starlight (Fri Apr 03 2015 - 05:28:48 PDT)
- James Starlight (Fri Apr 03 2015 - 04:53:46 PDT)
- Kenneth Huang (Thu Apr 02 2015 - 08:38:20 PDT)
- James Starlight (Thu Apr 02 2015 - 08:27:39 PDT)
- James Starlight (Thu Apr 02 2015 - 08:08:27 PDT)
- Kenneth Huang (Thu Apr 02 2015 - 07:50:54 PDT)
- James Starlight (Thu Apr 02 2015 - 06:17:05 PDT)
[AMBER] Mmgbsa decomposition
- James Starlight (Mon Apr 13 2015 - 01:19:01 PDT)
[AMBER] MMPBSA error
- Abhishek TYAGI (Tue Apr 14 2015 - 17:43:19 PDT)
- Jason Swails (Fri Apr 10 2015 - 03:14:26 PDT)
- Abhishek TYAGI (Thu Apr 09 2015 - 21:12:06 PDT)
- Daniel Roe (Thu Apr 09 2015 - 07:16:41 PDT)
- Jason Swails (Thu Apr 09 2015 - 04:32:40 PDT)
- Abhishek TYAGI (Wed Apr 08 2015 - 20:50:51 PDT)
- Daniel Roe (Mon Apr 06 2015 - 20:51:00 PDT)
- Jason Swails (Mon Apr 06 2015 - 20:30:39 PDT)
- Abhishek TYAGI (Mon Apr 06 2015 - 20:28:08 PDT)
- Abhishek TYAGI (Mon Apr 06 2015 - 20:05:55 PDT)
- Daniel Roe (Wed Apr 01 2015 - 07:13:29 PDT)
- Abhishek TYAGI (Wed Apr 01 2015 - 06:35:10 PDT)
[AMBER] MMPBSA issues with ff12SB
- Ray Luo, Ph.D. (Fri Apr 03 2015 - 22:00:53 PDT)
- Neha Gandhi (Fri Apr 03 2015 - 19:43:50 PDT)
- Ray Luo, Ph.D. (Fri Apr 03 2015 - 10:28:20 PDT)
- Neha Gandhi (Fri Apr 03 2015 - 08:34:21 PDT)
[AMBER] MMPBSA on NAMD DCD Trajectories
- Ahmed Ezat (Fri Apr 10 2015 - 05:37:36 PDT)
- Jason Swails (Fri Apr 10 2015 - 04:42:35 PDT)
- Ahmed Ezat (Fri Apr 10 2015 - 03:55:25 PDT)
[AMBER] MMPBSA problem with calcium
- Jason Swails (Thu Apr 30 2015 - 15:38:29 PDT)
- Francesco Gentile (Thu Apr 30 2015 - 14:56:18 PDT)
- Jason Swails (Thu Apr 30 2015 - 09:38:47 PDT)
- Francesco Gentile (Wed Apr 29 2015 - 11:15:36 PDT)
[AMBER] MMPBSA.py error:length mismatch in energy vectors
- Jason Swails (Tue Apr 14 2015 - 07:10:32 PDT)
- wjli (Tue Apr 14 2015 - 01:38:26 PDT)
[AMBER] MMPBSA.py.MPI Installation Failure
- Laura Tociu (Wed Apr 08 2015 - 22:22:52 PDT)
- Jason Swails (Tue Apr 07 2015 - 08:36:40 PDT)
- Laura Tociu (Sat Apr 04 2015 - 11:34:04 PDT)
[AMBER] mpirun error
- Jason Swails (Sun Apr 26 2015 - 16:19:05 PDT)
- shahab shariati (Sun Apr 26 2015 - 09:23:40 PDT)
[AMBER] Multiple MEPs option in R.E.D tools
- FyD (Thu Apr 02 2015 - 00:46:58 PDT)
- FyD (Thu Apr 02 2015 - 00:30:47 PDT)
- Hannes Loeffler (Wed Apr 01 2015 - 01:58:34 PDT)
- Yip Yew Mun (Tue Mar 31 2015 - 20:08:17 PDT)
[AMBER] New Force Field
- sribone.fcq.unc.edu.ar (Wed Apr 01 2015 - 07:47:38 PDT)
- James Maier (Wed Apr 01 2015 - 07:43:55 PDT)
- Carlos Simmerling (Wed Apr 01 2015 - 07:36:35 PDT)
- Daniel Roe (Wed Apr 01 2015 - 07:10:22 PDT)
- Alessandro Contini (Wed Apr 01 2015 - 07:08:13 PDT)
- abdennour braka (Wed Apr 01 2015 - 07:06:42 PDT)
- Carlos Simmerling (Wed Apr 01 2015 - 06:41:26 PDT)
- Peter Kekenes-Huskey (Wed Apr 01 2015 - 06:20:00 PDT)
- Alessandro Contini (Wed Apr 01 2015 - 06:18:58 PDT)
- Jiri Sponer (Wed Apr 01 2015 - 05:58:18 PDT)
- Jason Swails (Wed Apr 01 2015 - 05:36:25 PDT)
- Adrian Roitberg (Wed Apr 01 2015 - 05:25:31 PDT)
- Jason Swails (Wed Apr 01 2015 - 04:12:07 PDT)
[AMBER] Nmode analysis calculation problem for Implicit simulation.
- David A Case (Tue Apr 28 2015 - 05:09:51 PDT)
- Bajarang Kumbhar (Tue Apr 28 2015 - 04:06:53 PDT)
[AMBER] NMode Analysis Using Truncated Trajectory
- Laura Tociu (Fri Apr 17 2015 - 05:47:40 PDT)
- Jason Swails (Fri Apr 17 2015 - 05:00:39 PDT)
- Laura Tociu (Thu Apr 16 2015 - 20:52:06 PDT)
- Jason Swails (Thu Apr 16 2015 - 13:10:07 PDT)
- Laura Tociu (Thu Apr 16 2015 - 11:53:19 PDT)
[AMBER] One chain of protein going out of box
- Jason Swails (Mon Apr 20 2015 - 05:37:02 PDT)
- Shukla, Saurabh (Sun Apr 19 2015 - 18:27:55 PDT)
[AMBER] Organic solvent from imported molecule (e.g. : nitric acid)
- Karl Kirschner (Fri Apr 10 2015 - 00:13:02 PDT)
- Pierre Bertin (Thu Apr 09 2015 - 18:51:52 PDT)
[AMBER] parameterization Zn2+ with MCPB
- Pengfei Li (Mon Apr 27 2015 - 06:54:21 PDT)
- chemjxn (Mon Apr 27 2015 - 00:42:48 PDT)
[AMBER] PCA analysis
- Muthukumaran R (Mon Apr 20 2015 - 06:24:01 PDT)
- Jason Swails (Mon Apr 20 2015 - 05:54:29 PDT)
- Muthukumaran R (Mon Apr 20 2015 - 04:44:46 PDT)
[AMBER] pdbamb gives wrong resnumber
- David A Case (Tue Apr 28 2015 - 11:49:16 PDT)
- Jason Swails (Tue Apr 28 2015 - 10:39:46 PDT)
- Miguel Ángel Mompeán García (Tue Apr 28 2015 - 10:32:59 PDT)
[AMBER] Possible bug in nativecontacts command of cpptraj (v14)?
- Samuel Bowerman (Tue Apr 07 2015 - 13:28:37 PDT)
- Daniel Roe (Tue Apr 07 2015 - 11:52:45 PDT)
- Samuel Bowerman (Tue Apr 07 2015 - 10:52:57 PDT)
[AMBER] potential issue with energy drift
- Steven Ramsey (Tue Apr 07 2015 - 06:30:25 PDT)
[AMBER] Problem in running with steered MD
- Jason Swails (Mon Apr 20 2015 - 05:34:13 PDT)
- 肖立 (Sun Apr 19 2015 - 18:29:42 PDT)
[AMBER] Problem regarding PMF curve
- Brian Radak (Thu Apr 23 2015 - 06:12:19 PDT)
- Shubhadip Das (Sun Apr 19 2015 - 08:49:15 PDT)
[AMBER] problem with CHAMBER
- Jason Swails (Sat Apr 25 2015 - 13:52:48 PDT)
- sudipta (Sat Apr 25 2015 - 11:21:19 PDT)
[AMBER] Problem with MMPBSA.py.MPI for nmode
- Jason Swails (Sat Apr 11 2015 - 20:59:12 PDT)
- Kenneth Huang (Sat Apr 11 2015 - 15:35:04 PDT)
- Sofia Vasilakaki (Fri Apr 10 2015 - 15:23:03 PDT)
- Kenneth Huang (Fri Apr 10 2015 - 09:36:04 PDT)
- Sofia Vasilakaki (Thu Apr 09 2015 - 09:07:56 PDT)
- Kenneth Huang (Thu Apr 09 2015 - 08:19:19 PDT)
- Sofia Vasilakaki (Thu Apr 09 2015 - 07:39:15 PDT)
[AMBER] Quasi-harmonic Approximation Using a Trajectory Stripped of Hydrogens
- Hannes Loeffler (Thu Apr 30 2015 - 03:15:19 PDT)
- Laura Tociu (Tue Apr 28 2015 - 21:44:57 PDT)
- Jason Swails (Tue Apr 28 2015 - 18:40:03 PDT)
- Laura Tociu (Tue Apr 28 2015 - 12:40:06 PDT)
- Hannes Loeffler (Tue Apr 28 2015 - 04:19:54 PDT)
- Josh Berryman (Tue Apr 28 2015 - 03:51:46 PDT)
- Laura Tociu (Sun Apr 26 2015 - 20:35:08 PDT)
[AMBER] Quasi-harmonic Entropy Calculated using MMPBSA.py
- Jason Swails (Sat Apr 11 2015 - 21:10:22 PDT)
- Laura Tociu (Fri Apr 10 2015 - 19:56:48 PDT)
[AMBER] query
- sanjaykumar.imtech.res.in (Tue Apr 07 2015 - 03:31:16 PDT)
- FyD (Mon Apr 06 2015 - 23:09:21 PDT)
- sanjaykumar.imtech.res.in (Mon Apr 06 2015 - 01:46:29 PDT)
[AMBER] Query about microsecond long simulation
- Jason Swails (Thu Apr 30 2015 - 11:19:07 PDT)
- Jonathan Gough (Thu Apr 30 2015 - 11:05:03 PDT)
- Jason Swails (Thu Apr 30 2015 - 11:00:00 PDT)
- Jonathan Gough (Thu Apr 30 2015 - 10:55:38 PDT)
- Jason Swails (Thu Apr 30 2015 - 10:45:04 PDT)
- Jason Swails (Thu Apr 30 2015 - 10:40:15 PDT)
- anu chandra (Thu Apr 30 2015 - 05:06:54 PDT)
- David A Case (Thu Apr 30 2015 - 05:04:13 PDT)
- David A Case (Thu Apr 30 2015 - 04:48:00 PDT)
- Ross Walker (Thu Apr 30 2015 - 04:21:42 PDT)
- Gustavo Seabra (Thu Apr 30 2015 - 03:51:00 PDT)
- Andrew Schaub (Wed Apr 29 2015 - 15:30:33 PDT)
- Dr. Robert Molt Jr. (Wed Apr 29 2015 - 15:05:41 PDT)
- Thomas C. Bishop (Wed Apr 29 2015 - 13:03:17 PDT)
- David A Case (Wed Apr 29 2015 - 12:55:18 PDT)
- Bill Ross (Wed Apr 29 2015 - 10:47:15 PDT)
- Robert Molt (Wed Apr 29 2015 - 09:13:15 PDT)
- anu chandra (Wed Apr 29 2015 - 08:46:01 PDT)
- David A Case (Wed Apr 29 2015 - 08:31:23 PDT)
- Jason Swails (Wed Apr 29 2015 - 07:48:31 PDT)
- anu chandra (Wed Apr 29 2015 - 07:34:04 PDT)
- Ahmed Ezat (Wed Apr 29 2015 - 07:00:50 PDT)
- Jason Swails (Wed Apr 29 2015 - 06:57:16 PDT)
- Ahmed Ezat (Wed Apr 29 2015 - 06:53:15 PDT)
- Ross Walker (Wed Apr 29 2015 - 06:37:04 PDT)
- anu chandra (Wed Apr 29 2015 - 06:20:22 PDT)
[AMBER] Question Regarding reduce function of Antechamber
- David A Case (Sun Apr 05 2015 - 18:13:14 PDT)
- Ziheng Wang (Sun Apr 05 2015 - 12:07:47 PDT)
- David A Case (Sun Apr 05 2015 - 04:22:40 PDT)
- Ziheng Wang (Sat Apr 04 2015 - 12:34:22 PDT)
[AMBER] Questions about T-REMD
- Jason Swails (Mon Apr 27 2015 - 06:38:52 PDT)
- lipengfei (Mon Apr 27 2015 - 05:30:45 PDT)
[AMBER] Radial distribution function (RDF) for sugars in disaccharides
- Daniel Roe (Tue Apr 07 2015 - 07:19:08 PDT)
- Vijay Achari (Mon Apr 06 2015 - 19:51:19 PDT)
[AMBER] regarding .prmtop file generation
- David A Case (Mon Apr 27 2015 - 04:58:54 PDT)
- neha chaudhary (Sun Apr 26 2015 - 21:46:10 PDT)
- Jason Swails (Sat Apr 25 2015 - 13:33:10 PDT)
- neha chaudhary (Sat Apr 25 2015 - 01:46:32 PDT)
- Jason Swails (Mon Apr 20 2015 - 06:01:06 PDT)
- neha chaudhary (Mon Apr 20 2015 - 03:58:06 PDT)
[AMBER] REGARDING ATOM TYPE ERROR
- Jason Swails (Tue Apr 07 2015 - 05:01:56 PDT)
- Swithin Hanosh (Mon Apr 06 2015 - 22:17:24 PDT)
[AMBER] REGARDING ENERGY MINIMISATION
- David A Case (Wed Apr 15 2015 - 06:15:54 PDT)
- Jason Swails (Wed Apr 15 2015 - 06:03:49 PDT)
- Swithin Hanosh (Wed Apr 15 2015 - 05:32:32 PDT)
- Jason Swails (Tue Apr 14 2015 - 07:16:10 PDT)
- Swithin Hanosh (Tue Apr 14 2015 - 04:42:26 PDT)
[AMBER] Regarding running to independent simulations
- Soumendranath Bhakat (Sun Apr 26 2015 - 07:51:23 PDT)
- David A Case (Sat Apr 25 2015 - 07:05:30 PDT)
- Kenneth Huang (Sat Apr 25 2015 - 05:12:27 PDT)
- Soumendranath Bhakat (Sat Apr 25 2015 - 03:10:36 PDT)
[AMBER] Restart file with velocity
- David A Case (Tue Apr 14 2015 - 04:13:29 PDT)
- loic etheve (Tue Apr 14 2015 - 03:40:34 PDT)
[AMBER] Restrained MD
- James Starlight (Tue Apr 07 2015 - 07:44:45 PDT)
- Daniel Roe (Tue Apr 07 2015 - 07:23:25 PDT)
- James Starlight (Tue Apr 07 2015 - 05:16:39 PDT)
- James Starlight (Thu Apr 02 2015 - 05:38:02 PDT)
[AMBER] restraining in xz coordinates only
- Jason Swails (Thu Apr 30 2015 - 11:12:51 PDT)
- Samaneh Mesbahi (Thu Apr 30 2015 - 06:33:32 PDT)
- Samaneh Mesbahi (Wed Apr 29 2015 - 20:33:25 PDT)
[AMBER] re： Bad atom Type in MMPBSA.py
- Kenneth Huang (Mon Apr 13 2015 - 10:40:01 PDT)
- wjli (Mon Apr 13 2015 - 05:42:10 PDT)
[AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE"
- Vaibhav Dixit (Thu Apr 23 2015 - 12:29:14 PDT)
- Jason Swails (Tue Apr 21 2015 - 10:33:21 PDT)
- Vaibhav Dixit (Tue Apr 21 2015 - 10:04:35 PDT)
- Kenneth Huang (Tue Apr 21 2015 - 09:54:03 PDT)
- Vaibhav Dixit (Tue Apr 21 2015 - 09:16:19 PDT)
- David A Case (Tue Apr 21 2015 - 08:07:02 PDT)
- Jason Swails (Tue Apr 21 2015 - 08:04:10 PDT)
- Hector A. Baldoni (Tue Apr 21 2015 - 07:24:10 PDT)
- Sajeewa Pemasinghe (Tue Apr 21 2015 - 07:55:29 PDT)
- Vaibhav Dixit (Tue Apr 21 2015 - 07:45:02 PDT)
- Sajeewa Pemasinghe (Tue Apr 21 2015 - 07:39:48 PDT)
- Vaibhav Dixit (Tue Apr 21 2015 - 07:05:28 PDT)
- Vaibhav Dixit (Tue Apr 21 2015 - 07:04:32 PDT)
- Daniel Roe (Tue Apr 21 2015 - 06:54:19 PDT)
- Vaibhav Dixit (Tue Apr 21 2015 - 06:12:13 PDT)
- Kenneth Huang (Tue Apr 21 2015 - 05:57:32 PDT)
- Vaibhav Dixit (Tue Apr 21 2015 - 02:29:07 PDT)
[AMBER] Sander QMMM Bomb Problem
- Gulsevin,Alican (Thu Apr 02 2015 - 08:52:30 PDT)
[AMBER] Segmentation fault in AmberTool 14.25
- David A Case (Tue Apr 28 2015 - 05:05:30 PDT)
- MOHD HOMAIDUR RAHMAN (Mon Apr 27 2015 - 23:28:59 PDT)
- David A Case (Mon Apr 27 2015 - 05:11:33 PDT)
- MOHD HOMAIDUR RAHMAN (Sun Apr 26 2015 - 23:20:15 PDT)
- Bill Ross (Sat Apr 25 2015 - 13:49:16 PDT)
- Jason Swails (Sat Apr 25 2015 - 13:36:10 PDT)
- MOHD HOMAIDUR RAHMAN (Sat Apr 25 2015 - 07:56:44 PDT)
[AMBER] Simulations at High temperature (425K)
- David A Case (Fri Apr 24 2015 - 08:14:42 PDT)
- Carlos Simmerling (Fri Apr 24 2015 - 07:21:50 PDT)
- Biswa Ranjan Meher (Fri Apr 24 2015 - 07:17:17 PDT)
[AMBER] STRUCTURAL CHANGE AFTER HEATING
- David A Case (Thu Apr 30 2015 - 07:32:10 PDT)
- Swithin Hanosh (Thu Apr 30 2015 - 05:06:44 PDT)
[AMBER] The error occurs when I set radiopt =1 in MMPBSA.py
- wliu (Thu Apr 23 2015 - 05:38:28 PDT)
- Jason Swails (Tue Apr 21 2015 - 10:39:17 PDT)
- Kenneth Huang (Tue Apr 21 2015 - 10:22:25 PDT)
- wliu (Tue Apr 21 2015 - 08:28:07 PDT)
[AMBER] The force field used in MCPB
- Pengfei Li (Tue Apr 07 2015 - 09:42:45 PDT)
- Carlos Simmerling (Tue Apr 07 2015 - 09:01:08 PDT)
- Pengfei Li (Tue Apr 07 2015 - 08:14:20 PDT)
- wjli (Mon Apr 06 2015 - 23:28:41 PDT)
[AMBER] The influence of parameters in md.in when restart a MD (from rst file)
- windy (Fri Apr 17 2015 - 02:51:53 PDT)
- Daniel Roe (Wed Apr 15 2015 - 07:30:46 PDT)
- windy (Wed Apr 15 2015 - 07:05:31 PDT)
[AMBER] The Meaning of Some Parameters
- Carlos Simmerling (Sun Apr 05 2015 - 05:19:17 PDT)
- wjli (Sun Apr 05 2015 - 05:14:27 PDT)
[AMBER] The question about how to restart REMD simulation in AMBER12 and Langavin dynamics
- Jason Swails (Wed Apr 29 2015 - 05:28:06 PDT)
- Wang Moye (Wed Apr 29 2015 - 00:46:23 PDT)
[AMBER] The Stand Model in MCPB
- Pengfei Li (Tue Apr 07 2015 - 08:24:26 PDT)
- wjli (Tue Apr 07 2015 - 02:00:29 PDT)
[AMBER] the vectors of the moment of inertia protein
- CHAMI F. (Sat Apr 25 2015 - 09:07:07 PDT)
[AMBER] Trouble recomputing aMD boost from amdlog/mdout
- Brian Radak (Fri Apr 03 2015 - 12:42:02 PDT)
[AMBER] typo error in the amber14 manual
- David A Case (Tue Apr 07 2015 - 04:56:14 PDT)
- Vijay Achari (Tue Apr 07 2015 - 00:41:04 PDT)
[AMBER] Unsupported CUDA version 7.0 detected.
- Ross Walker (Fri Apr 10 2015 - 14:39:09 PDT)
- Emilio Angelina (Fri Apr 10 2015 - 14:33:44 PDT)
- Jason Swails (Fri Apr 10 2015 - 14:29:54 PDT)
- Emilio Angelina (Fri Apr 10 2015 - 13:38:09 PDT)
[AMBER] Visualization of the MMGBSA per-residue decomposition
- James Starlight (Wed Apr 08 2015 - 09:43:02 PDT)
[AMBER] water box for steered md amber14
- Asmita Gupta (Thu Apr 23 2015 - 10:50:54 PDT)
[AMBER] Writing out restart files
- Jason Swails (Thu Apr 16 2015 - 07:20:43 PDT)
- Daniel Roe (Thu Apr 16 2015 - 07:30:47 PDT)
- Christina Bergonzo (Thu Apr 16 2015 - 07:27:33 PDT)
- gepaula.web.de (Thu Apr 16 2015 - 07:14:21 PDT)
[AMBER] xleap Menu bar problems
- Pierre Bertin (Thu Apr 09 2015 - 09:16:08 PDT)
- Jason Swails (Thu Apr 09 2015 - 04:18:33 PDT)
- Pierre Bertin (Wed Apr 08 2015 - 18:21:20 PDT)
[AMBER] 发送给你的文件
- chemjxn (Tue Mar 31 2015 - 23:29:00 PDT)
amber14 errors
- Jason Swails (Thu Apr 02 2015 - 13:08:49 PDT)
- IBRAHIM M ABDELRADY (Thu Apr 02 2015 - 12:42:22 PDT)
- Jason Swails (Thu Apr 02 2015 - 11:59:19 PDT)
- IBRAHIM M ABDELRADY (Thu Apr 02 2015 - 11:16:28 PDT)
Bad atom Type in MMPBSA.py
- wjli (Sat Apr 11 2015 - 23:09:04 PDT)
TLEAP Fatal Error
- FyD (Thu Apr 09 2015 - 00:00:32 PDT)
- Wong, Sook (NIH/NCATS) [V] (Tue Apr 07 2015 - 09:23:51 PDT)
- Jason Swails (Tue Apr 07 2015 - 08:40:44 PDT)
- Wong, Sook (NIH/NCATS) [V] (Tue Apr 07 2015 - 08:15:15 PDT)

Amber Archive Apr 2015 by subject