Amber Archive Feb 2014: by subject

[AMBER] about MCPB : addFragment terminal/CH3
- Jason Swails (Tue Feb 25 2014 - 05:17:57 PST)
- Setyanto Md (Tue Feb 25 2014 - 04:48:17 PST)
[AMBER] about protonation state check.
- Brian Radak (Wed Feb 12 2014 - 05:37:48 PST)
- setyanto md (Tue Feb 11 2014 - 04:15:55 PST)
[AMBER] Accuracy of solvation free energy calculated by 3D-RISM
- Kayo (Sat Feb 01 2014 - 03:38:56 PST)
[AMBER] ACS COMP Division student and junior faculty awards for Fall 2014 meeting in San Francisco
- Carlos Simmerling (Tue Feb 18 2014 - 13:30:45 PST)
[AMBER] Adaptive Biasing calculations
- Geoffrey Gray (Tue Feb 25 2014 - 16:46:17 PST)
- de Waal, Parker (Tue Feb 25 2014 - 14:14:03 PST)
- Geoffrey Gray (Tue Feb 25 2014 - 13:21:06 PST)
[AMBER] alanine scanning and free energy decomposition
- Nitin Sharma (Thu Feb 27 2014 - 19:33:51 PST)
- Bill Miller III (Thu Feb 27 2014 - 12:21:30 PST)
- Nitin Sharma (Thu Feb 27 2014 - 07:40:36 PST)
[AMBER] aligning
- Jio M (Thu Feb 27 2014 - 08:14:59 PST)
- Daniel Roe (Thu Feb 27 2014 - 07:37:36 PST)
- Jio M (Thu Feb 27 2014 - 05:14:29 PST)
- Daniel Roe (Wed Feb 26 2014 - 17:23:49 PST)
- Jio M (Wed Feb 26 2014 - 08:22:27 PST)
- Daniel Roe (Wed Feb 26 2014 - 07:38:23 PST)
- Jio M (Wed Feb 26 2014 - 07:27:29 PST)
- Daniel Roe (Wed Feb 26 2014 - 07:12:36 PST)
- Jio M (Wed Feb 26 2014 - 06:09:40 PST)
[AMBER] Amber 12 bugfix 22
- ahmed.sajid.stfc.ac.uk (Thu Feb 27 2014 - 05:23:26 PST)
- Jason Swails (Thu Feb 27 2014 - 05:22:57 PST)
- ahmed.sajid.stfc.ac.uk (Thu Feb 27 2014 - 01:26:43 PST)
[AMBER] amber 14 release
- Ross Walker (Sun Feb 23 2014 - 16:34:51 PST)
- psu4.uic.edu (Sun Feb 23 2014 - 12:46:38 PST)
- Jason Swails (Mon Feb 17 2014 - 12:34:07 PST)
- Ross Walker (Mon Feb 17 2014 - 11:18:25 PST)
- psu4.uic.edu (Mon Feb 17 2014 - 10:58:59 PST)
[AMBER] AMBER Digest, Vol 759, Issue 1
- David A Case (Sat Feb 08 2014 - 19:08:33 PST)
- Arjun Sharma (Sat Feb 08 2014 - 15:15:02 PST)
[AMBER] AMBER Digest, Vol 760, Issue 1
- David A Case (Sun Feb 09 2014 - 14:08:51 PST)
- Arjun Sharma (Sun Feb 09 2014 - 12:40:16 PST)
[AMBER] Amber12 CUDA input file
- Jason Swails (Sun Feb 23 2014 - 07:30:37 PST)
- richa anand (Sat Feb 22 2014 - 21:45:13 PST)
[AMBER] AmberTools13-conformational search in MTK++
- Sun (Wed Feb 19 2014 - 05:51:22 PST)
- Jason Swails (Wed Feb 19 2014 - 05:36:57 PST)
- Sun (Wed Feb 19 2014 - 05:14:09 PST)
[AMBER] Amntechamber MOPAC and SQM
- Nitin Sharma (Sat Feb 15 2014 - 08:13:04 PST)
- David A Case (Sat Feb 15 2014 - 07:33:56 PST)
- Nitin Sharma (Fri Feb 14 2014 - 18:04:44 PST)
- Nitin Sharma (Fri Feb 14 2014 - 10:58:53 PST)
- David A Case (Fri Feb 14 2014 - 05:43:29 PST)
- hannes.loeffler.stfc.ac.uk (Fri Feb 14 2014 - 00:22:03 PST)
- Nitin Sharma (Thu Feb 13 2014 - 23:36:49 PST)
[AMBER] asking about pmemd and GTX 660 Ti compatibility
- Setyanto Md (Mon Feb 24 2014 - 23:28:24 PST)
- Jason Swails (Mon Feb 24 2014 - 05:07:49 PST)
- setyanto md (Mon Feb 24 2014 - 00:31:46 PST)
[AMBER] Atom does not have a type.
- Aldo Segura (Thu Feb 20 2014 - 08:47:10 PST)
- Aldo Segura (Thu Feb 20 2014 - 08:38:47 PST)
- Javier Alejandro Rendon Carrillo (Thu Feb 20 2014 - 08:23:44 PST)
- Javier Alejandro Rendon Carrillo (Thu Feb 20 2014 - 08:12:00 PST)
- Aldo Segura (Thu Feb 20 2014 - 07:35:35 PST)
- Jason Swails (Thu Feb 20 2014 - 07:26:08 PST)
- Javier Alejandro Rendon Carrillo (Thu Feb 20 2014 - 07:09:52 PST)
[AMBER] Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM
- David A Case (Wed Feb 19 2014 - 07:13:13 PST)
- Daniel Roe (Wed Feb 19 2014 - 07:12:37 PST)
- Saeed Nasiri (Wed Feb 19 2014 - 06:17:00 PST)
[AMBER] Bond continues to break in simulation even after the bond command was used.
- Daniel Roe (Tue Feb 18 2014 - 21:44:26 PST)
- Yip Yew Mun (Tue Feb 18 2014 - 20:04:33 PST)
[AMBER] broken bond in minimization
- Jason Swails (Sun Feb 23 2014 - 07:38:08 PST)
- Zahra Khatti (Sun Feb 23 2014 - 07:04:57 PST)
- Dr. Vitaly Chaban (Sun Feb 23 2014 - 05:26:59 PST)
- Zahra Khatti (Sat Feb 22 2014 - 21:35:34 PST)
[AMBER] Calculating parameters for glycosides
- FyD (Tue Feb 25 2014 - 22:42:58 PST)
- Lachele Foley (Tue Feb 25 2014 - 10:51:03 PST)
- R R S Pissurlenkar (Tue Feb 25 2014 - 09:20:49 PST)
[AMBER] calculating rotational diffusion for a portion in a lipid
- David A Case (Wed Feb 05 2014 - 04:45:29 PST)
- Vijay Manickam Achari (Wed Feb 05 2014 - 01:52:30 PST)
[AMBER] Calculating second rank Legendre polynomial C_2(t) autocorrelation function
- George M Giambasu (Thu Feb 13 2014 - 06:50:30 PST)
- Vijay Manickam Achari (Thu Feb 13 2014 - 06:15:12 PST)
[AMBER] CDC20 / temperature
- David A Case (Thu Feb 27 2014 - 19:09:08 PST)
[AMBER] Change email address
- David A Case (Wed Feb 26 2014 - 04:55:20 PST)
- Fernando Martín García (Wed Feb 26 2014 - 02:55:12 PST)
[AMBER] Charge on zinc ion bound to residues.
- FyD (Sun Feb 16 2014 - 03:30:13 PST)
- tongzhu9110 (Sat Feb 15 2014 - 23:08:17 PST)
- nalini chauhan (Sat Feb 15 2014 - 22:56:49 PST)
[AMBER] Charged Ions Sticking Together
- Jio M (Thu Feb 27 2014 - 06:57:33 PST)
- Thomas Cheatham (Wed Feb 26 2014 - 19:28:47 PST)
- Alexander Chiu (Wed Feb 26 2014 - 17:11:16 PST)
[AMBER] combine results
- Saeed Nasiri (Sun Feb 02 2014 - 00:57:05 PST)
[AMBER] Compiling amber12 with openmp
- Eugene Yedvabny (Mon Feb 17 2014 - 22:12:04 PST)
- Quentin Kaas (Mon Feb 17 2014 - 21:09:34 PST)
[AMBER] Convergence failure
- Gustavo Seabra (Wed Feb 05 2014 - 06:18:13 PST)
- Tanmoy Paul (Tue Feb 04 2014 - 23:30:22 PST)
[AMBER] Converting Amoeba .xyz for use with Amber
- Jason Swails (Fri Feb 07 2014 - 11:57:57 PST)
[AMBER] Correlation times
- psu4.uic.edu (Mon Feb 17 2014 - 10:44:10 PST)
- Mutangana Dieudonne (Mon Feb 17 2014 - 00:45:29 PST)
[AMBER] corrplane in cpptraj and ptraj
- Michael F. Bruist (Fri Feb 28 2014 - 11:59:57 PST)
- Daniel Roe (Thu Feb 27 2014 - 15:18:26 PST)
- Michael F. Bruist (Thu Feb 27 2014 - 11:52:26 PST)
[AMBER] Could not find target 281.850000 in any of the replica trajectories
- sunita.tifrh.res.in (Mon Feb 10 2014 - 04:01:33 PST)
- Daniel Roe (Sat Feb 08 2014 - 09:34:09 PST)
- sunita.tifrh.res.in (Sat Feb 08 2014 - 03:39:30 PST)
[AMBER] Cpptraj bridge
- Alessandra Lacetera (Fri Feb 28 2014 - 07:05:01 PST)
- Daniel Roe (Thu Feb 27 2014 - 09:48:16 PST)
- Alessandra Lacetera (Thu Feb 27 2014 - 09:33:03 PST)
[AMBER] cpptraj: linear interaction energy - lie
- Jason Swails (Wed Feb 05 2014 - 05:45:38 PST)
- Anselm Horn (Wed Feb 05 2014 - 01:09:37 PST)
- Jason Swails (Tue Feb 04 2014 - 05:45:53 PST)
- Anselm Horn (Tue Feb 04 2014 - 05:01:19 PST)
[AMBER] CUDA 4 support in future Amber
- Ross Walker (Mon Feb 17 2014 - 23:04:41 PST)
- Eugene Yedvabny (Mon Feb 17 2014 - 22:44:23 PST)
[AMBER] defects in modified parameter with parmed.py
- Jason Swails (Fri Feb 21 2014 - 06:04:49 PST)
- Daniel Roe (Fri Feb 21 2014 - 05:34:54 PST)
- Saeed Nasiri (Fri Feb 21 2014 - 01:49:39 PST)
[AMBER] Desmond vs Amber vs Analysis vs VMD
- filip fratev (Thu Feb 27 2014 - 07:10:44 PST)
- Jason Swails (Thu Feb 27 2014 - 06:28:54 PST)
- Soumendranath Bhakat (Thu Feb 27 2014 - 06:05:51 PST)
[AMBER] differences in PBSA energies (INP=1 verses INP=2)
- Ray Luo, Ph.D. (Sat Feb 15 2014 - 10:47:48 PST)
- Divi/GMAIL (Sat Feb 15 2014 - 09:29:21 PST)
[AMBER] distance and angle rst to zinc atoms
- David A Case (Sat Feb 15 2014 - 07:31:24 PST)
- Jorgen Simonsen (Fri Feb 14 2014 - 14:17:40 PST)
- David A Case (Fri Feb 14 2014 - 12:45:17 PST)
- Jorgen Simonsen (Fri Feb 14 2014 - 12:10:21 PST)
[AMBER] Does chain type matter?
- Bill Ross (Tue Feb 11 2014 - 21:42:26 PST)
- David A Case (Tue Feb 11 2014 - 03:34:30 PST)
- David Winogradoff (Mon Feb 10 2014 - 19:44:55 PST)
- David A Case (Mon Feb 10 2014 - 19:00:28 PST)
- David Winogradoff (Mon Feb 10 2014 - 14:33:30 PST)
[AMBER] enquiry regarding latest Amber
- Ross Walker (Wed Feb 12 2014 - 09:37:23 PST)
- Francesco Pietra (Wed Feb 12 2014 - 00:36:36 PST)
- Ross Walker (Tue Feb 11 2014 - 12:11:52 PST)
- Francesco Pietra (Tue Feb 11 2014 - 06:42:29 PST)
- Ved Prakash (Tue Feb 11 2014 - 04:35:02 PST)
- Ross Walker (Mon Feb 10 2014 - 10:10:10 PST)
- Jason Swails (Mon Feb 10 2014 - 04:43:19 PST)
- Ved Prakash (Mon Feb 10 2014 - 03:36:12 PST)
[AMBER] error in amber installation
- Kshatresh Dutta Dubey (Tue Feb 25 2014 - 22:25:45 PST)
- Arunima Shilpi (Tue Feb 25 2014 - 22:07:26 PST)
- Ross Walker (Mon Feb 24 2014 - 21:10:58 PST)
- Arunima Shilpi (Mon Feb 24 2014 - 21:03:27 PST)
[AMBER] error in creating topology file
- Jason Swails (Fri Feb 28 2014 - 05:07:36 PST)
- Arunima Shilpi (Thu Feb 27 2014 - 23:19:16 PST)
[AMBER] error in editing Ligand file
- Jason Swails (Fri Feb 28 2014 - 07:36:29 PST)
- Arunima Shilpi (Fri Feb 28 2014 - 07:13:29 PST)
[AMBER] error in extending simulation from .rst file
- Jason Swails (Tue Feb 04 2014 - 10:20:57 PST)
- Nitin Sharma (Tue Feb 04 2014 - 10:07:11 PST)
- Jason Swails (Tue Feb 04 2014 - 05:02:07 PST)
- David A Case (Tue Feb 04 2014 - 05:00:56 PST)
- Nitin Sharma (Mon Feb 03 2014 - 21:18:54 PST)
[AMBER] ERROR in sidechain.bcl file in MCPB
- Jason Swails (Mon Feb 24 2014 - 18:09:44 PST)
- nalini chauhan (Mon Feb 24 2014 - 09:23:47 PST)
[AMBER] error with md simulation
- David A Case (Sun Feb 16 2014 - 14:46:47 PST)
- Zahra Khatti (Sun Feb 16 2014 - 13:22:40 PST)
[AMBER] Falling apart of membrane
- Ross Walker (Tue Feb 25 2014 - 09:48:58 PST)
- Gözde YALÇIN (Tue Feb 25 2014 - 09:45:11 PST)
- Gözde YALÇIN (Tue Feb 25 2014 - 09:43:10 PST)
- Gözde YALÇIN (Thu Feb 13 2014 - 02:51:10 PST)
- Ross Walker (Wed Feb 12 2014 - 09:42:07 PST)
- Dickson, Callum J (Wed Feb 12 2014 - 06:14:00 PST)
- Gözde YALÇIN (Wed Feb 12 2014 - 05:24:57 PST)
[AMBER] FapydG parameters
- Christina Bergonzo (Tue Feb 11 2014 - 06:56:43 PST)
- Norbert GARNIER (Tue Feb 11 2014 - 05:34:42 PST)
[AMBER] Force field generation
- David A Case (Thu Feb 27 2014 - 04:59:24 PST)
- hannes.loeffler.stfc.ac.uk (Thu Feb 27 2014 - 00:30:39 PST)
- Gargi Borgohai (Wed Feb 26 2014 - 22:13:14 PST)
[AMBER] Forcefield for transition metals
- Kshatresh Dutta Dubey (Wed Feb 26 2014 - 21:32:30 PST)
- Thomas Cheatham (Wed Feb 26 2014 - 19:57:39 PST)
- de Waal, Parker (Wed Feb 26 2014 - 14:50:33 PST)
- Kshatresh Dutta Dubey (Wed Feb 26 2014 - 14:17:57 PST)
- de Waal, Parker (Wed Feb 26 2014 - 14:05:09 PST)
- Kshatresh Dutta Dubey (Wed Feb 26 2014 - 13:39:46 PST)
[AMBER] Fwd:
- James Luginsland (Thu Feb 27 2014 - 18:15:21 PST)
- James Luginsland (Thu Feb 27 2014 - 17:49:25 PST)
[AMBER] Fwd: amber
- Daniel Roe (Sat Feb 01 2014 - 08:47:49 PST)
- David A Case (Sat Feb 01 2014 - 08:33:28 PST)
- Daniel Roe (Sat Feb 01 2014 - 07:54:25 PST)
- Daniel Roe (Sat Feb 01 2014 - 07:42:46 PST)
[AMBER] Fwd: Contact angle simulation of brine drop onto halite NaCl surface -different results between Amber11 and Amber12
- David A Case (Wed Feb 19 2014 - 18:09:58 PST)
- Vu Truong (Wed Feb 19 2014 - 12:52:12 PST)
[AMBER] Generating RST file using Cpptraj
- Nitin Sharma (Tue Feb 04 2014 - 23:24:51 PST)
- Yip Yew Mun (Tue Feb 04 2014 - 21:12:52 PST)
[AMBER] GLYCAM parameters for cis double conformation
- ABEL Stephane 175950 (Fri Feb 21 2014 - 02:34:12 PST)
- Karl Kirschner (Fri Feb 21 2014 - 01:22:22 PST)
- ABEL Stephane 175950 (Mon Feb 17 2014 - 08:00:20 PST)
- Lachele Foley (Mon Feb 17 2014 - 07:33:59 PST)
- Karl Kirschner (Mon Feb 17 2014 - 07:26:34 PST)
- Lachele Foley (Mon Feb 17 2014 - 07:08:52 PST)
- ABEL Stephane 175950 (Mon Feb 17 2014 - 05:35:54 PST)
[AMBER] GTX-Titan Black Edition Timings
- filip fratev (Fri Feb 21 2014 - 14:19:41 PST)
- Ross Walker (Fri Feb 21 2014 - 13:17:26 PST)
[AMBER] GTX670
- Deák Robert (Thu Feb 27 2014 - 02:22:57 PST)
- Ross Walker (Mon Feb 24 2014 - 09:26:52 PST)
- Carlos Simmerling (Mon Feb 24 2014 - 09:03:48 PST)
- Deák Robert (Mon Feb 24 2014 - 08:48:52 PST)
- Gould, Ian R (Mon Feb 24 2014 - 08:33:59 PST)
- Deák Robert (Mon Feb 24 2014 - 08:30:15 PST)
- Ross Walker (Mon Feb 24 2014 - 08:12:43 PST)
- Scott Le Grand (Mon Feb 24 2014 - 08:03:08 PST)
- Deák Robert (Mon Feb 24 2014 - 03:01:26 PST)
[AMBER] How to prepare the leap files for protein residues covalently bonded to ligand?
- #YIP YEW MUN# (Sun Feb 23 2014 - 17:40:51 PST)
- Nitin Sharma (Sun Feb 23 2014 - 10:31:54 PST)
- Jason Swails (Sun Feb 23 2014 - 07:39:57 PST)
- Yip Yew Mun (Sun Feb 23 2014 - 04:53:10 PST)
[AMBER] Illegal CONECT record in pdb file after mutations
- Jason Swails (Mon Feb 10 2014 - 09:22:31 PST)
- Xu Zhou (Mon Feb 10 2014 - 09:07:09 PST)
[AMBER] Including amino acid backbone into QM part during QM/MM
- Dmitry Nilov (Wed Feb 26 2014 - 23:59:50 PST)
- Andreas Goetz (Wed Feb 26 2014 - 14:44:16 PST)
- Dmitry Nilov (Wed Feb 26 2014 - 06:17:34 PST)
[AMBER] internal energy in TI decomposition
- Jason Swails (Wed Feb 05 2014 - 05:54:32 PST)
- Schackert Nico (Wed Feb 05 2014 - 05:22:14 PST)
- Jason Swails (Mon Feb 03 2014 - 04:21:29 PST)
- Schackert Nico (Mon Feb 03 2014 - 03:55:11 PST)
[AMBER] LEAP-CHARMM
- Jason Swails (Wed Feb 05 2014 - 08:05:43 PST)
- Hannes Loeffler (Wed Feb 05 2014 - 07:15:06 PST)
- Gözde YALÇIN (Wed Feb 05 2014 - 06:14:10 PST)
[AMBER] LIPID 14
- Jason Swails (Wed Feb 26 2014 - 10:17:04 PST)
- Jason Swails (Wed Feb 26 2014 - 10:16:43 PST)
- Ghulam Mustafa (Wed Feb 26 2014 - 10:12:04 PST)
[AMBER] mass
- Zahra Khatti (Sun Feb 23 2014 - 12:47:18 PST)
[AMBER] membrane
- Gözde YALÇIN (Wed Feb 12 2014 - 06:21:30 PST)
[AMBER] MM-PBSA problem
- almarques (Sat Feb 15 2014 - 03:37:36 PST)
- almarques (Sat Feb 15 2014 - 01:45:38 PST)
- Ray Luo, Ph.D. (Fri Feb 14 2014 - 12:05:18 PST)
- almarques (Fri Feb 14 2014 - 11:28:18 PST)
- almarques (Fri Feb 14 2014 - 11:26:10 PST)
[AMBER] MMGBSA decomposition for a ligand molecule
- Jason Swails (Thu Feb 13 2014 - 07:33:33 PST)
- Rajeswari A. (Thu Feb 13 2014 - 05:27:19 PST)
[AMBER] MMGBSA problem
- Jason Swails (Tue Feb 25 2014 - 09:32:12 PST)
- Maryam Azimzadeh Irani (Thu Feb 06 2014 - 00:11:41 PST)
[AMBER] MMGBSA/BSA electrostatic energy values very high
- Jason Swails (Sat Feb 15 2014 - 08:10:41 PST)
- Rajesh Kumar (Sat Feb 15 2014 - 04:01:35 PST)
[AMBER] MMPBSA binding energy for all frames
- Vlad Cojocaru (Mon Feb 24 2014 - 05:34:25 PST)
- Arun Kumar Somavarapu (Mon Feb 24 2014 - 05:21:27 PST)
- Vlad Cojocaru (Fri Feb 21 2014 - 04:41:34 PST)
- Arun Kumar Somavarapu (Fri Feb 21 2014 - 03:56:52 PST)
- Vlad Cojocaru (Thu Feb 20 2014 - 10:42:44 PST)
- Vlad Cojocaru (Thu Feb 20 2014 - 09:51:52 PST)
- Jason Swails (Thu Feb 20 2014 - 09:29:44 PST)
- Arun Kumar Somavarapu (Thu Feb 20 2014 - 08:55:25 PST)
- Vlad Cojocaru (Thu Feb 20 2014 - 04:39:13 PST)
- Arun Kumar Somavarapu (Thu Feb 20 2014 - 03:45:19 PST)
- Vlad Cojocaru (Thu Feb 20 2014 - 03:18:29 PST)
- Arun Kumar Somavarapu (Thu Feb 20 2014 - 03:12:56 PST)
[AMBER] MMPBSA on Protein/DNA complex
- Ray Luo, Ph.D. (Sun Feb 02 2014 - 09:07:09 PST)
- Yip Yew Mun (Fri Jan 31 2014 - 23:12:34 PST)
[AMBER] MMPBSA.py and entropy
- Aldo Segura (Thu Feb 27 2014 - 06:03:54 PST)
- hannes.loeffler.stfc.ac.uk (Wed Feb 26 2014 - 23:05:02 PST)
- Javier Alejandro Rendon Carrillo (Wed Feb 26 2014 - 22:05:46 PST)
- Hannes Loeffler (Fri Feb 21 2014 - 08:04:55 PST)
- Fernando Martín García (Fri Feb 21 2014 - 07:38:55 PST)
[AMBER] MMPBSA.py error
- Jason Swails (Fri Feb 28 2014 - 08:02:53 PST)
- almarques (Fri Feb 28 2014 - 07:35:22 PST)
- Jason Swails (Thu Feb 27 2014 - 09:37:21 PST)
- almarques (Wed Feb 26 2014 - 14:13:38 PST)
- Jason Swails (Mon Feb 24 2014 - 06:57:57 PST)
- almarques (Mon Feb 24 2014 - 06:28:09 PST)
- Jason Swails (Mon Feb 24 2014 - 05:13:31 PST)
- almarques (Mon Feb 24 2014 - 03:31:18 PST)
[AMBER] MMPBSA.py positive delta G?
- Jason Swails (Fri Feb 28 2014 - 05:00:06 PST)
- de Waal, Parker (Thu Feb 27 2014 - 21:49:02 PST)
- de Waal, Parker (Thu Feb 27 2014 - 21:11:22 PST)
[AMBER] MMPBSA.py.MPI hangs
- Jason Swails (Thu Feb 27 2014 - 12:19:41 PST)
- George Tzotzos (Thu Feb 27 2014 - 12:08:18 PST)
- Jason Swails (Thu Feb 27 2014 - 11:44:17 PST)
- George Tzotzos (Thu Feb 27 2014 - 11:27:18 PST)
- Jason Swails (Thu Feb 27 2014 - 11:08:36 PST)
- George Tzotzos (Thu Feb 27 2014 - 09:49:51 PST)
- Jason Swails (Thu Feb 27 2014 - 09:27:51 PST)
- George Tzotzos (Thu Feb 27 2014 - 09:16:25 PST)
- George Tzotzos (Wed Feb 26 2014 - 16:31:27 PST)
- George Tzotzos (Wed Feb 26 2014 - 14:37:53 PST)
- Jason Swails (Wed Feb 26 2014 - 14:13:44 PST)
- George Tzotzos (Wed Feb 26 2014 - 12:18:38 PST)
- George Tzotzos (Tue Feb 25 2014 - 16:56:48 PST)
- Jason Swails (Tue Feb 25 2014 - 15:58:37 PST)
- George Tzotzos (Tue Feb 25 2014 - 14:16:30 PST)
- Jason Swails (Tue Feb 25 2014 - 12:23:37 PST)
- Jason Swails (Tue Feb 25 2014 - 12:21:31 PST)
- Bill Miller III (Tue Feb 25 2014 - 12:10:39 PST)
- George Tzotzos (Tue Feb 25 2014 - 08:52:51 PST)
[AMBER] MMPBSA/MMGBSA issues
- Jason Swails (Fri Feb 14 2014 - 05:36:05 PST)
- Soumendranath Bhakat (Fri Feb 14 2014 - 05:22:12 PST)
- Jason Swails (Fri Feb 14 2014 - 05:13:39 PST)
- Soumendranath Bhakat (Thu Feb 13 2014 - 22:07:49 PST)
[AMBER] Modifying Gaussian input files for the RED Server
- FyD (Fri Feb 07 2014 - 22:42:11 PST)
- Kamali Sripathi (Fri Feb 07 2014 - 05:55:14 PST)
[AMBER] mopac.sh error
- Jason Swails (Thu Feb 06 2014 - 05:46:15 PST)
- sammia khatak (Thu Feb 06 2014 - 04:43:23 PST)
[AMBER] nastruct
- Daniel Roe (Wed Feb 12 2014 - 07:58:01 PST)
[AMBER] New bonds in PyMol?
- de Waal, Parker (Mon Feb 24 2014 - 05:11:09 PST)
- David A Case (Mon Feb 24 2014 - 04:43:51 PST)
- de Waal, Parker (Sun Feb 23 2014 - 20:37:02 PST)
[AMBER] no pdb file after running nab /AMBER11
- David A Case (Wed Feb 26 2014 - 04:54:19 PST)
- Urszula Uciechowska (Wed Feb 26 2014 - 00:57:04 PST)
[AMBER] optimise ligand geomatry before MD
- Nitin Sharma (Wed Feb 05 2014 - 09:14:42 PST)
[AMBER] optimization of the ligand
- Mary Varughese (Thu Feb 06 2014 - 07:08:34 PST)
- David A Case (Thu Feb 06 2014 - 05:07:27 PST)
- Jason Swails (Thu Feb 06 2014 - 04:49:16 PST)
- Mary Varughese (Thu Feb 06 2014 - 02:04:41 PST)
[AMBER] Parallel running problem of MMPBSA
- zhongqiao hu (Tue Feb 04 2014 - 00:12:07 PST)
- Jason Swails (Mon Feb 03 2014 - 04:29:24 PST)
- zhongqiao hu (Mon Feb 03 2014 - 01:35:47 PST)
- zhongqiao hu (Mon Feb 03 2014 - 00:47:45 PST)
[AMBER] pbsa calculation using sander
- Sun (Mon Feb 24 2014 - 05:29:48 PST)
- Jason Swails (Mon Feb 24 2014 - 05:11:13 PST)
- Sun (Mon Feb 24 2014 - 04:58:43 PST)
- David A Case (Mon Feb 24 2014 - 04:47:09 PST)
- Sun (Mon Feb 24 2014 - 00:01:20 PST)
[AMBER] PDB to prmtop inpcrd using tleap
- David A Case (Tue Feb 11 2014 - 03:41:20 PST)
- Jheng Wei Li (Tue Feb 11 2014 - 02:58:20 PST)
[AMBER] PDDG-PM3/MMGBSA calculation
- Jason Swails (Sat Feb 15 2014 - 09:08:16 PST)
- Jason Swails (Sat Feb 15 2014 - 08:13:13 PST)
- Giovanni Grazioso (Fri Feb 14 2014 - 08:26:49 PST)
[AMBER] PME with cutoff = 0
- Jason Swails (Wed Feb 26 2014 - 05:03:33 PST)
- FyD (Tue Feb 25 2014 - 22:34:17 PST)
- FyD (Tue Feb 25 2014 - 22:19:35 PST)
- Ross Walker (Mon Feb 24 2014 - 09:54:00 PST)
- Duke, Robert E Jr (Mon Feb 24 2014 - 09:44:49 PST)
- Jason Swails (Mon Feb 24 2014 - 05:45:57 PST)
- FyD (Mon Feb 24 2014 - 04:52:45 PST)
- FyD (Mon Feb 24 2014 - 01:31:26 PST)
- Duke, Robert E Jr (Sun Feb 23 2014 - 11:06:33 PST)
- Ross Walker (Sun Feb 23 2014 - 09:38:49 PST)
- FyD (Sun Feb 23 2014 - 09:19:23 PST)
[AMBER] pmemd.CUDA.mpi micro-second long simulation
- Carlos Simmerling (Mon Feb 24 2014 - 07:33:23 PST)
- Ross Walker (Mon Feb 24 2014 - 07:26:46 PST)
- psu4.uic.edu (Sun Feb 23 2014 - 22:58:42 PST)
[AMBER] Pmf ....restrain
- David A Case (Wed Feb 26 2014 - 04:58:05 PST)
- Rasha Alqus (Wed Feb 26 2014 - 03:29:02 PST)
[AMBER] Postdoctoral position
- Fernando Martín García (Tue Feb 18 2014 - 08:30:00 PST)
[AMBER] Print Pressure value by using PMEMD
- kurisaki (Tue Feb 18 2014 - 22:22:32 PST)
- Daniel Roe (Tue Feb 18 2014 - 21:53:41 PST)
- Ross Walker (Tue Feb 18 2014 - 21:52:05 PST)
- kurisaki (Tue Feb 18 2014 - 21:42:33 PST)
[AMBER] Problem running amber on some gpu's
- David A Case (Thu Feb 27 2014 - 04:55:32 PST)
- Ross Walker (Wed Feb 26 2014 - 21:43:49 PST)
- Jagga Soorma (Wed Feb 26 2014 - 21:31:01 PST)
[AMBER] problem with installing amber
- David A Case (Thu Feb 06 2014 - 05:11:21 PST)
- Jason Swails (Thu Feb 06 2014 - 05:01:28 PST)
- Hanna Thamleena (Thu Feb 06 2014 - 02:49:19 PST)
[AMBER] Problems with mmpbsa
- Jason Swails (Wed Feb 19 2014 - 04:53:05 PST)
[AMBER] protein amide conjugate parameters
- FyD (Thu Feb 06 2014 - 22:31:22 PST)
- Nahoum Anthony (Thu Feb 06 2014 - 04:55:33 PST)
- Jason Swails (Thu Feb 06 2014 - 04:54:50 PST)
- Nahoum Anthony (Thu Feb 06 2014 - 01:41:58 PST)
[AMBER] Protein insertion into a membrane
- Stéphane Azoulay (Tue Feb 11 2014 - 03:05:51 PST)
- Stéphane Azoulay (Tue Feb 11 2014 - 00:51:33 PST)
- Stéphane Azoulay (Mon Feb 03 2014 - 05:50:52 PST)
[AMBER] Query on introducing a protein
- Aditya Padhi (Wed Feb 05 2014 - 05:01:02 PST)
- David A Case (Wed Feb 05 2014 - 04:31:17 PST)
- Aditya Padhi (Tue Feb 04 2014 - 21:12:10 PST)
[AMBER] Question about force field parameters for RDX and PETN
- FyD (Tue Feb 18 2014 - 22:40:19 PST)
- Ganesh Kamath (Tue Feb 18 2014 - 13:38:23 PST)
- FyD (Tue Feb 18 2014 - 12:19:21 PST)
- ABEL Stephane 175950 (Tue Feb 18 2014 - 07:24:16 PST)
- Ilyas Yildirim (Tue Feb 18 2014 - 07:05:22 PST)
- Ganesh Kamath (Tue Feb 18 2014 - 06:51:56 PST)
- ABEL Stephane 175950 (Tue Feb 18 2014 - 06:30:20 PST)
- Ganesh Kamath (Tue Feb 18 2014 - 06:23:16 PST)
[AMBER] R.E.D. server seems to be down?
- psu4.uic.edu (Fri Feb 14 2014 - 09:40:14 PST)
- FyD (Fri Feb 14 2014 - 09:32:41 PST)
- psu4.uic.edu (Thu Feb 13 2014 - 21:31:33 PST)
[AMBER] RE : Protein insertion into a membrane
- Stéphane Azoulay (Tue Feb 11 2014 - 05:44:23 PST)
- ABEL Stephane 175950 (Tue Feb 11 2014 - 03:41:40 PST)
- ABEL Stephane 175950 (Tue Feb 11 2014 - 02:51:16 PST)
[AMBER] RE : RE : Protein insertion into a membrane
- Benjamin Madej (Tue Feb 11 2014 - 14:41:50 PST)
- Stéphane Azoulay (Tue Feb 11 2014 - 07:43:42 PST)
- ABEL Stephane 175950 (Tue Feb 11 2014 - 06:00:54 PST)
[AMBER] reg: the charges for methylated cytosine atoms
- Jason Swails (Thu Feb 20 2014 - 05:25:48 PST)
- Filip Lankas (Thu Feb 20 2014 - 04:34:47 PST)
- Jason Swails (Fri Feb 14 2014 - 03:04:43 PST)
- satyanarayan rao (Thu Feb 13 2014 - 16:40:18 PST)
[AMBER] Regarding MD simulation input files
- richa anand (Wed Feb 12 2014 - 20:12:39 PST)
[AMBER] request for help in analysis
- Daniel Roe (Wed Feb 26 2014 - 07:17:06 PST)
- Robin Jain (Mon Feb 24 2014 - 01:11:49 PST)
[AMBER] rewriting trajectory
- Christina Bergonzo (Thu Feb 13 2014 - 07:31:58 PST)
- Hector A. Baldoni (Thu Feb 13 2014 - 04:51:36 PST)
[AMBER] sander minimization issue
- David A Case (Fri Feb 07 2014 - 18:06:21 PST)
- Arjun Sharma (Fri Feb 07 2014 - 13:38:45 PST)
[AMBER] Shake problem: Coordinate resetting (SHAKE) cannot be accomplished
- Jason Swails (Tue Feb 25 2014 - 10:04:46 PST)
- Thomas Cheatham (Tue Feb 25 2014 - 09:54:05 PST)
- Mele N. (Tue Feb 25 2014 - 09:42:24 PST)
- Jason Swails (Tue Feb 25 2014 - 09:28:58 PST)
- ABEL Stephane 175950 (Tue Feb 25 2014 - 08:59:00 PST)
- Mele N. (Tue Feb 25 2014 - 08:18:22 PST)
- Jason Swails (Tue Feb 25 2014 - 04:56:24 PST)
- Mele N. (Tue Feb 25 2014 - 02:47:24 PST)
- Mele N. (Tue Feb 25 2014 - 01:58:35 PST)
- David A Case (Mon Feb 24 2014 - 10:32:28 PST)
- Jason Swails (Mon Feb 24 2014 - 09:55:47 PST)
- Mele N. (Mon Feb 24 2014 - 09:22:06 PST)
- Jason Swails (Mon Feb 24 2014 - 09:10:04 PST)
- Mele N. (Mon Feb 24 2014 - 08:56:44 PST)
- David A Case (Mon Feb 24 2014 - 04:54:50 PST)
- Mele N. (Mon Feb 24 2014 - 01:45:58 PST)
[AMBER] SMD Problem: r4 and r4a values are not read from the restraint file
- Jason Swails (Sun Feb 23 2014 - 17:52:09 PST)
- Ali M. Naserian-Nik (Sun Feb 23 2014 - 11:45:57 PST)
- Ali M. Naserian-Nik (Sun Feb 23 2014 - 11:33:33 PST)
- Jason Swails (Sun Feb 23 2014 - 10:12:05 PST)
- Adrian Roitberg (Sun Feb 23 2014 - 09:53:02 PST)
- Ali M. Naserian-Nik (Sun Feb 23 2014 - 09:48:51 PST)
- Jason Swails (Sun Feb 23 2014 - 07:42:17 PST)
- Ali M. Naserian-Nik (Sun Feb 23 2014 - 00:16:10 PST)
[AMBER] Specifying the number of water molecules for solvateBox
- Pawel (Wed Feb 05 2014 - 20:40:33 PST)
- Yip Yew Mun (Wed Feb 05 2014 - 20:23:03 PST)
- Pawel (Wed Feb 05 2014 - 19:47:03 PST)
- Jason Swails (Wed Feb 05 2014 - 19:29:02 PST)
- Yip Yew Mun (Wed Feb 05 2014 - 19:01:24 PST)
[AMBER] TACC Stampede AMBER
- Ross Walker (Thu Feb 13 2014 - 10:06:47 PST)
- Ross Walker (Thu Feb 13 2014 - 09:59:14 PST)
- de Waal, Parker (Thu Feb 13 2014 - 09:57:01 PST)
- de Waal, Parker (Thu Feb 13 2014 - 08:55:30 PST)
- David Cowburn (Thu Feb 13 2014 - 08:40:40 PST)
[AMBER] Tesla K40
- Ross Walker (Thu Feb 13 2014 - 09:52:10 PST)
- Ross Walker (Thu Feb 13 2014 - 09:39:35 PST)
- Scott Le Grand (Wed Feb 12 2014 - 18:26:56 PST)
- Gustavo Seabra (Wed Feb 12 2014 - 17:02:11 PST)
- Scott Le Grand (Wed Feb 12 2014 - 15:48:04 PST)
- Chinthaka Ratnaweera (Wed Feb 12 2014 - 15:39:27 PST)
- Scott Le Grand (Wed Feb 12 2014 - 14:47:36 PST)
- Shaw, Sharon (Wed Feb 12 2014 - 14:42:56 PST)
- Chinthaka Ratnaweera (Wed Feb 12 2014 - 13:58:46 PST)
[AMBER] The unperturbed charge of the unit
- Nitin Sharma (Thu Feb 13 2014 - 10:46:31 PST)
- Jason Swails (Thu Feb 13 2014 - 10:23:52 PST)
- Nitin Sharma (Thu Feb 13 2014 - 09:18:51 PST)
[AMBER] TI calculation Fatal error in PMPI_Bcast
- Jason Swails (Fri Feb 28 2014 - 05:12:43 PST)
- Jason Swails (Fri Feb 28 2014 - 05:11:54 PST)
- David A Case (Fri Feb 28 2014 - 05:04:44 PST)
- Ying-Chieh Sun (Fri Feb 28 2014 - 00:29:03 PST)
- Changqing Yan (Thu Feb 27 2014 - 23:40:33 PST)
[AMBER] To post to amber list
- Jason Swails (Wed Feb 12 2014 - 05:05:53 PST)
- richa anand (Wed Feb 12 2014 - 03:17:26 PST)
[AMBER] Total charge not zero
- FyD (Wed Feb 12 2014 - 22:08:55 PST)
- Ross Walker (Wed Feb 12 2014 - 10:05:39 PST)
- George Patargias (Wed Feb 12 2014 - 09:46:44 PST)
- Ross Walker (Wed Feb 12 2014 - 09:39:15 PST)
- George Patargias (Wed Feb 12 2014 - 09:33:26 PST)
- George Patargias (Wed Feb 12 2014 - 06:33:00 PST)
- George Patargias (Wed Feb 12 2014 - 06:13:05 PST)
- FyD (Wed Feb 12 2014 - 05:19:17 PST)
- Jason Swails (Wed Feb 12 2014 - 05:11:34 PST)
- George Patargias (Wed Feb 12 2014 - 02:42:10 PST)
[AMBER] tracking ions in protein channel
- Daniel Roe (Wed Feb 05 2014 - 12:41:01 PST)
- Jio M (Wed Feb 05 2014 - 03:22:24 PST)
[AMBER] Unable to apply patches on AmberTools 13
- Jason Swails (Fri Feb 21 2014 - 19:37:30 PST)
- George Tzotzos (Fri Feb 21 2014 - 16:17:56 PST)
[AMBER] Unable to read coords from XXX.rst - How can I resolve this once and for all?
- Daniel Roe (Thu Feb 27 2014 - 08:21:29 PST)
- Nitin Sharma (Thu Feb 27 2014 - 08:11:35 PST)
- Yip Yew Mun (Thu Feb 27 2014 - 08:05:31 PST)
- Nitin Sharma (Thu Feb 27 2014 - 07:58:21 PST)
- Daniel Roe (Thu Feb 27 2014 - 07:55:45 PST)
- Yew Mun Yip (Thu Feb 27 2014 - 07:11:00 PST)
[AMBER] using chamber to convert psf generated by VMD
- Yi Shang (Sun Feb 23 2014 - 21:32:44 PST)
- Ross Walker (Fri Feb 14 2014 - 11:23:52 PST)
- Jason Swails (Fri Feb 14 2014 - 11:09:36 PST)
- Yi Shang (Fri Feb 14 2014 - 10:51:27 PST)
- Ross Walker (Fri Feb 14 2014 - 10:29:01 PST)
- Jason Swails (Fri Feb 14 2014 - 08:24:30 PST)
- Yi Shang (Fri Feb 14 2014 - 08:15:53 PST)
[AMBER] using ff99SB forcefiled to a complex where ligand charge is from Glycam_04
- Arun Kumar Somavarapu (Mon Feb 24 2014 - 08:47:54 PST)
- Karl Kirschner (Mon Feb 24 2014 - 06:50:43 PST)
- Arun Kumar Somavarapu (Mon Feb 24 2014 - 05:08:28 PST)
- David A Case (Mon Feb 24 2014 - 04:50:53 PST)
- FyD (Mon Feb 24 2014 - 02:49:54 PST)
- Arun Kumar Somavarapu (Mon Feb 24 2014 - 02:20:09 PST)
- Karl Kirschner (Mon Feb 24 2014 - 01:57:18 PST)
- Arun Kumar Somavarapu (Mon Feb 24 2014 - 01:12:04 PST)
[AMBER] What does "Bond types are assigned for valence state 1 with penalty of 1" mean?
- David A Case (Thu Feb 20 2014 - 09:22:46 PST)
- Yew Mun Yip (Wed Feb 19 2014 - 20:37:13 PST)
[AMBER] XLeap in Cygwin - Does it work?
- Bill Ross (Tue Feb 11 2014 - 21:05:43 PST)
- Ilyas Yildirim (Sat Feb 08 2014 - 13:34:48 PST)
- Daniel Roe (Sat Feb 08 2014 - 13:30:19 PST)
- Ilyas Yildirim (Sat Feb 08 2014 - 06:16:30 PST)
ERROR in sidechain.bcl file in MCPB
- nalini chauhan (Mon Feb 24 2014 - 22:43:44 PST)
error with md simulation
- David A Case (Mon Feb 17 2014 - 17:23:47 PST)
- Zahra Khatti (Mon Feb 17 2014 - 09:00:37 PST)
PDDG-PM3/MMGBSA calculation
- Giovanni Grazioso (Tue Feb 18 2014 - 08:05:37 PST)
- Jason Swails (Sat Feb 15 2014 - 18:13:13 PST)
- Giovanni Grazioso (Sat Feb 15 2014 - 11:49:44 PST)

Amber Archive Feb 2014 by subject