Amber Archive Oct 2006: by subject

Amber8: problem related to antechamber
- David A. Case (Sun Oct 01 2006 - 06:34:45 PDT)
- David A. Case (Sun Oct 01 2006 - 06:35:55 PDT)
AMBER: (no subject)
- David A. Case (Fri Oct 06 2006 - 09:20:03 PDT)
- Prashanth Athri (Thu Oct 05 2006 - 19:34:47 PDT)
AMBER: adding polar hydrogens
- Sean Rathlef (Wed Oct 11 2006 - 11:35:47 PDT)
- David A. Case (Wed Oct 11 2006 - 11:28:11 PDT)
- Sean Rathlef (Wed Oct 11 2006 - 11:02:28 PDT)
- David A. Case (Wed Oct 11 2006 - 09:14:29 PDT)
- Sean Rathlef (Tue Oct 10 2006 - 19:43:39 PDT)
AMBER: alanine scan (mm/pbsa)
- rob yang (Wed Oct 18 2006 - 07:46:47 PDT)
AMBER: Amber 9 installation problem
- Cenk Andac (Thu Oct 19 2006 - 12:13:58 PDT)
- David A. Case (Thu Oct 19 2006 - 11:43:35 PDT)
- Cenk Andac (Thu Oct 19 2006 - 10:55:54 PDT)
- Mark Williamson (Thu Oct 19 2006 - 09:12:01 PDT)
- Cenk Andac (Thu Oct 19 2006 - 08:43:02 PDT)
AMBER: amber force field
- Carlos Simmerling (Wed Oct 11 2006 - 11:33:36 PDT)
- Noriaki Okimoto (Wed Oct 11 2006 - 11:21:03 PDT)
AMBER: AMBER minimization vs. Gaussian optimization
- FyD (Wed Oct 04 2006 - 22:14:07 PDT)
- Ilyas Yildirim (Wed Oct 04 2006 - 15:17:51 PDT)
- Thomas Cheatham (Wed Oct 04 2006 - 13:45:59 PDT)
- Ilyas Yildirim (Wed Oct 04 2006 - 13:27:48 PDT)
AMBER: Amber8: how to do Simulated Annealing and Equilibration
- priya priya (Mon Oct 16 2006 - 21:42:15 PDT)
- Ross Walker (Mon Oct 16 2006 - 08:32:20 PDT)
- priya priya (Mon Oct 16 2006 - 01:32:18 PDT)
AMBER: Amber8: problem related to antechamber
- David A. Case (Tue Oct 17 2006 - 08:10:43 PDT)
- priya priya (Mon Oct 16 2006 - 23:49:03 PDT)
- Ross Walker (Mon Oct 16 2006 - 08:32:20 PDT)
- David A. Case (Mon Oct 16 2006 - 08:29:19 PDT)
- priya priya (Mon Oct 16 2006 - 00:00:38 PDT)
AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred
- Ross Walker (Tue Oct 24 2006 - 08:33:45 PDT)
- Maniopoulou, A \(Mina\) (Tue Oct 24 2006 - 06:59:26 PDT)
- Ross Walker (Fri Oct 20 2006 - 09:06:49 PDT)
- Maniopoulou, A \(Mina\) (Fri Oct 20 2006 - 03:27:29 PDT)
- Ross Walker (Thu Oct 19 2006 - 12:24:43 PDT)
- David A. Case (Thu Oct 19 2006 - 12:22:47 PDT)
- Maniopoulou, A \(Mina\) (Thu Oct 19 2006 - 05:48:08 PDT)
AMBER: amber9: SA Bomb in sa_arc
- Ray Luo (Tue Oct 31 2006 - 00:29:27 PST)
- Ross Walker (Thu Oct 26 2006 - 09:35:19 PDT)
- Ray Luo (Wed Oct 25 2006 - 02:14:08 PDT)
- Giulio Rastelli (Thu Oct 26 2006 - 08:58:50 PDT)
- Ross Walker (Thu Oct 26 2006 - 08:38:05 PDT)
- Giulio Rastelli (Thu Oct 26 2006 - 03:56:43 PDT)
- Ray Luo (Tue Oct 24 2006 - 14:55:24 PDT)
- Giulio Rastelli (Wed Oct 25 2006 - 04:03:54 PDT)
AMBER: Amber: Parallel Installation Problems
- Ross Walker (Fri Oct 27 2006 - 10:53:10 PDT)
- Maniopoulou, A \(Mina\) (Fri Oct 27 2006 - 10:13:56 PDT)
AMBER: angle between two vectors
- Myunggi Yi (Mon Oct 16 2006 - 09:15:59 PDT)
- David A. Case (Thu Oct 12 2006 - 11:14:14 PDT)
- M. L. Dodson (Thu Oct 12 2006 - 10:40:35 PDT)
- Lwin, ThuZar (Thu Oct 12 2006 - 09:51:15 PDT)
AMBER: angle between two vectors. .
- Lwin, ThuZar (Mon Oct 16 2006 - 13:51:28 PDT)
AMBER: Announcement: Parameters for Modified Nucleosides in RNA
- Raviprasad Aduri (Mon Oct 09 2006 - 14:13:56 PDT)
AMBER: atom nomination in the PDB file produced by Amber
- Fenghui Fan (Wed Oct 04 2006 - 08:37:45 PDT)
AMBER: atom type nh vs. n2
- sethl.gatech.edu (Fri Oct 20 2006 - 14:31:09 PDT)
AMBER: BioBlade
- Sean Rathlef (Thu Oct 12 2006 - 20:12:41 PDT)
AMBER: Building polymer with sequence command
- David A. Case (Thu Oct 05 2006 - 17:31:36 PDT)
- gtg549i.mail.gatech.edu (Thu Oct 05 2006 - 09:46:11 PDT)
AMBER: C -N -CT-CT torsion parameters
- John Vieceli (Sun Oct 29 2006 - 17:10:49 PST)
AMBER: Calculating native contacts for mdcrd files
- Anna Bowman (Thu Oct 26 2006 - 08:20:50 PDT)
AMBER: Calculation of Dihedral constants
- Prashanth Athri (Thu Oct 05 2006 - 19:36:15 PDT)
AMBER: CARNAL: carnal source code
- Keerthi Gottipati (Thu Oct 26 2006 - 05:41:21 PDT)
- Carlos Simmerling (Wed Oct 25 2006 - 16:06:08 PDT)
- Keerthi Gottipati (Wed Oct 25 2006 - 15:14:41 PDT)
AMBER: change from .rst file to .mdcrd file
- JunJun Liu (Wed Oct 04 2006 - 13:14:22 PDT)
- Wang, Xuelin (Wed Oct 04 2006 - 08:52:56 PDT)
AMBER: charge models in antechamber
- David Mobley (Thu Oct 19 2006 - 10:48:14 PDT)
- Sean Rathlef (Wed Oct 18 2006 - 16:48:00 PDT)
- Sean Rathlef (Wed Oct 18 2006 - 16:29:02 PDT)
- Eric Hu (Wed Oct 18 2006 - 15:51:00 PDT)
AMBER: chemical shift restrains
- David A. Case (Sun Oct 01 2006 - 06:35:01 PDT)
AMBER: Closest(closest water)
- Mingfeng Yang (Mon Oct 30 2006 - 12:29:00 PST)
- Sergey Samsonov (Mon Oct 30 2006 - 06:27:40 PST)
- Adrian Roitberg (Mon Oct 30 2006 - 05:12:13 PST)
- Sergey Samsonov (Mon Oct 30 2006 - 04:58:11 PST)
AMBER: Compile AMBER 8
- Esther Brugger (Mon Oct 30 2006 - 10:14:05 PST)
- HL Eastwood (Mon Oct 30 2006 - 09:37:22 PST)
- Esther Brugger (Mon Oct 30 2006 - 09:24:59 PST)
- HL Eastwood (Mon Oct 30 2006 - 08:43:51 PST)
- Esther Brugger (Mon Oct 30 2006 - 07:28:08 PST)
- David A. Case (Fri Oct 27 2006 - 13:46:07 PDT)
- Esther Brugger (Fri Oct 27 2006 - 13:18:00 PDT)
- David A. Case (Fri Oct 27 2006 - 12:12:35 PDT)
- Esther Brugger (Fri Oct 27 2006 - 11:21:13 PDT)
- David A. Case (Fri Oct 27 2006 - 09:45:36 PDT)
- Mark Williamson (Fri Oct 27 2006 - 09:03:07 PDT)
- Esther Brugger (Fri Oct 27 2006 - 08:44:51 PDT)
AMBER: Curve fitting during dihedral parameter calculation
- Prashanth Athri (Thu Oct 19 2006 - 12:15:21 PDT)
AMBER: Density calculation
- David A. Case (Mon Oct 16 2006 - 15:26:49 PDT)
- Jianhui (Mon Oct 16 2006 - 14:12:24 PDT)
AMBER: DIST_RST
- Cenk Andac (Tue Oct 24 2006 - 03:51:01 PDT)
- Urszula Uciechowska (Tue Oct 24 2006 - 01:32:03 PDT)
AMBER: Distance between 2 atoms
- Fenghui Fan (Wed Oct 04 2006 - 06:52:16 PDT)
AMBER: Distance between two atoms
- Fenghui Fan (Tue Oct 03 2006 - 16:59:17 PDT)
AMBER: error estimate for free energy perturbation calculation
- Ilyas Yildirim (Wed Oct 25 2006 - 16:17:36 PDT)
- Fenghui Fan (Wed Oct 25 2006 - 13:34:42 PDT)
- David A. Case (Wed Oct 25 2006 - 11:40:47 PDT)
- Chris Moth (Wed Oct 25 2006 - 09:58:14 PDT)
- jz7.duke.edu (Tue Oct 24 2006 - 21:15:26 PDT)
AMBER: error GRID command in ptraj
- Andres Palencia (Thu Oct 26 2006 - 10:39:19 PDT)
AMBER: ff for drug-dna complex and drug atom types assignment
- Barbault Florent (Mon Oct 23 2006 - 11:37:53 PDT)
- Kateryna Miroshnychenko (Mon Oct 23 2006 - 09:08:59 PDT)
AMBER: ff02 force fields
- norberto.ualberta.ca (Mon Oct 30 2006 - 10:37:57 PST)
- David A. Case (Sun Oct 29 2006 - 21:17:44 PST)
- norberto.ualberta.ca (Sun Oct 29 2006 - 12:18:25 PST)
AMBER: ff99SB vs ff02 (ff02pol.rl)
- Thomas Cheatham (Mon Oct 30 2006 - 21:07:46 PST)
- David A. Case (Mon Oct 30 2006 - 18:57:48 PST)
- Thomas Cheatham (Mon Oct 30 2006 - 18:15:18 PST)
- Nicolas Lux Fawzi (Mon Oct 30 2006 - 17:48:32 PST)
AMBER: force fiels for a-rna
- Jiri Sponer (Sat Oct 14 2006 - 00:59:13 PDT)
- asli ertekin (Fri Oct 13 2006 - 16:20:32 PDT)
- Carlos Simmerling (Fri Oct 13 2006 - 15:41:21 PDT)
- asli ertekin (Fri Oct 13 2006 - 15:28:58 PDT)
AMBER: Free-energy using MM-PBSA
- Yongmei Pan (Thu Oct 19 2006 - 06:20:07 PDT)
- mathew k varghese (Thu Oct 19 2006 - 01:05:45 PDT)
AMBER: General Coding Problem
- Bill Ross (Mon Oct 16 2006 - 17:56:37 PDT)
- David A. Case (Mon Oct 16 2006 - 17:27:56 PDT)
- Elijah Gregory (Mon Oct 16 2006 - 16:53:27 PDT)
AMBER: generalized born model for organic solvent
- Eric Hu (Thu Oct 12 2006 - 16:32:16 PDT)
- David A. Case (Thu Oct 12 2006 - 11:00:00 PDT)
- Eric Hu (Thu Oct 12 2006 - 10:47:44 PDT)
- Adrian Roitberg (Wed Oct 11 2006 - 17:11:33 PDT)
- David A. Case (Wed Oct 11 2006 - 16:53:49 PDT)
- Eric Hu (Wed Oct 11 2006 - 16:37:01 PDT)
- David A. Case (Wed Oct 11 2006 - 09:16:23 PDT)
- Eric Hu (Tue Oct 10 2006 - 18:29:12 PDT)
AMBER: generating resp input files with antechamber
- dhruva chakravorty (Thu Oct 05 2006 - 12:53:03 PDT)
AMBER: Grid command of ptraj
- Thomas Cheatham (Mon Oct 23 2006 - 09:24:20 PDT)
- Atsutoshi Okabe (Tue Oct 17 2006 - 21:19:13 PDT)
- Thomas Cheatham (Tue Oct 17 2006 - 08:40:22 PDT)
- Atsutoshi Okabe (Mon Oct 16 2006 - 02:26:55 PDT)
- Sean Rathlef (Sat Oct 14 2006 - 03:25:59 PDT)
- Atsutoshi Okabe (Sat Oct 14 2006 - 00:31:01 PDT)
AMBER: halogen bondi radii in mm_pbsa_calceneent.pm
- Giulio Rastelli (Fri Oct 27 2006 - 01:46:30 PDT)
AMBER: HBON in frcmod file
- David A. Case (Sun Oct 22 2006 - 22:11:58 PDT)
- Bill Ross (Sat Oct 21 2006 - 12:57:48 PDT)
- Ilyas Yildirim (Sat Oct 21 2006 - 01:24:42 PDT)
- Bill Ross (Sat Oct 21 2006 - 00:41:55 PDT)
- Ilyas Yildirim (Fri Oct 20 2006 - 22:46:31 PDT)
AMBER: hbond analysis
- Sergey Samsonov (Wed Oct 04 2006 - 23:40:59 PDT)
- Thomas Cheatham (Wed Oct 04 2006 - 14:00:02 PDT)
- Vlad Cojocaru (Wed Oct 04 2006 - 08:26:32 PDT)
- Sergey Samsonov (Wed Oct 04 2006 - 07:49:35 PDT)
- Vlad Cojocaru (Tue Oct 03 2006 - 09:35:32 PDT)
- Thomas Cheatham (Tue Oct 03 2006 - 09:27:56 PDT)
- Vlad Cojocaru (Tue Oct 03 2006 - 09:18:28 PDT)
- Thomas Cheatham (Tue Oct 03 2006 - 09:05:00 PDT)
- Vlad Cojocaru (Tue Oct 03 2006 - 08:45:23 PDT)
AMBER: Help with polarization force field
- norberto.ualberta.ca (Fri Oct 27 2006 - 16:20:09 PDT)
AMBER: High Values in MMPBSA
- Thomas Steinbrecher (Thu Oct 12 2006 - 08:36:31 PDT)
- Shozeb Haider (Thu Oct 12 2006 - 09:55:15 PDT)
AMBER: How did the coordinates change in xleap?
- David A. Case (Tue Oct 17 2006 - 08:28:52 PDT)
- Zhihong Yu (Tue Oct 17 2006 - 08:03:47 PDT)
AMBER: How do we simulate deletion mutations
- Dave, Sonya (Thu Oct 26 2006 - 11:05:01 PDT)
- Fenghui Fan (Wed Oct 25 2006 - 15:43:49 PDT)
- Dave, Sonya (Wed Oct 25 2006 - 14:41:48 PDT)
- Fenghui Fan (Wed Oct 25 2006 - 13:13:20 PDT)
- Dave, Sonya (Wed Oct 25 2006 - 11:47:38 PDT)
AMBER: how to add hydrogen molecules in the protein
- David A. Case (Thu Oct 26 2006 - 17:57:22 PDT)
- Rachel (Thu Oct 26 2006 - 09:28:16 PDT)
AMBER: How to calculate RDF based on the center of mass of specific solute atoms?
- Xioling Chuang (Mon Oct 16 2006 - 01:48:04 PDT)
- Fenghui Fan (Sun Oct 15 2006 - 21:36:25 PDT)
- Xioling Chuang (Sun Oct 15 2006 - 21:04:10 PDT)
AMBER: how to calculate rmsd for non hydrogen at oms?
- JunJun Liu (Tue Oct 03 2006 - 12:10:25 PDT)
- Viktor Hornak (Tue Oct 03 2006 - 09:51:53 PDT)
- yxiong99 (Tue Oct 03 2006 - 09:43:49 PDT)
AMBER: how to combine NEB method with QM/MM approach
- Ross Walker (Mon Oct 09 2006 - 15:33:00 PDT)
- caoch.cherry.bio.titech.ac.jp (Mon Oct 09 2006 - 09:23:07 PDT)
AMBER: How to find equillibration time for my system in a generalised born solvation model
- David A. Case (Mon Oct 16 2006 - 15:33:14 PDT)
- Gobind Singh Bisht (Mon Oct 16 2006 - 14:34:11 PDT)
AMBER: How to get the VDW contacts' messages from the mdcrd files
- Jiapu.Zhang.csiro.au (Mon Oct 02 2006 - 23:11:03 PDT)
AMBER: How to merge two molecules to one
- Myunggi Yi (Fri Oct 06 2006 - 11:51:19 PDT)
AMBER: how to restrain some residues in a NPT MD?
- Ross Walker (Mon Oct 30 2006 - 08:34:46 PST)
- Zhihong Yu (Mon Oct 30 2006 - 07:20:38 PST)
AMBER: how to run a mm_pbsa on a minimized structure?
- Wang, Xuelin (Mon Oct 02 2006 - 14:50:02 PDT)
AMBER: how to select the problematic residues(atoms) in VMD
- Ross Walker (Thu Oct 26 2006 - 08:26:22 PDT)
- Andres Palencia (Thu Oct 26 2006 - 04:56:31 PDT)
- Rachel (Thu Oct 26 2006 - 04:00:21 PDT)
AMBER: how to simulate water flow inside a channel?
- Gobind Singh Bisht (Wed Oct 18 2006 - 07:33:51 PDT)
AMBER: imaging issue
- Thomas Cheatham (Mon Oct 30 2006 - 12:54:20 PST)
- Kristina Furse (Mon Oct 30 2006 - 10:30:25 PST)
- David Smith (Sun Oct 29 2006 - 08:26:07 PST)
AMBER: Installation amber 9 on IBM SP4
- Scott Brozell (Fri Oct 06 2006 - 10:13:15 PDT)
AMBER: Interbox interactions
- Austin B. Yongye (Tue Oct 17 2006 - 09:03:18 PDT)
- Thomas Cheatham (Tue Oct 17 2006 - 08:34:50 PDT)
- Austin B. Yongye (Mon Oct 16 2006 - 10:15:04 PDT)
AMBER: Is GB/SANDER slower than TIP3P/PMEMD
- Ross Walker (Wed Oct 04 2006 - 10:51:24 PDT)
- Robert Duke (Wed Oct 04 2006 - 10:45:06 PDT)
- b86203054.ntu.edu.tw (Wed Oct 04 2006 - 10:21:39 PDT)
AMBER: Issue with installation of Amber v9.0 parallel compilation
- Ross Walker (Thu Oct 19 2006 - 21:55:00 PDT)
- Pravin_Kumar.jubilantbiosys.com (Thu Oct 19 2006 - 21:17:51 PDT)
- Pravin_Kumar.jubilantbiosys.com (Thu Oct 19 2006 - 21:02:42 PDT)
AMBER: klambda
- Sergey Samsonov (Fri Oct 13 2006 - 07:49:05 PDT)
AMBER: LEAP error
- David A. Case (Sun Oct 08 2006 - 21:28:36 PDT)
- Ilyas Yildirim (Fri Oct 06 2006 - 21:26:29 PDT)
- Akshay Patny (Fri Oct 06 2006 - 16:17:05 PDT)
- Scott Brozell (Fri Oct 06 2006 - 10:30:34 PDT)
- Akshay Patny (Fri Oct 06 2006 - 09:49:42 PDT)
AMBER: LEAP error (Test Case)
- Akshay Patny (Mon Oct 09 2006 - 08:37:18 PDT)
AMBER: load charges to antechamber calculations
- David A. Case (Tue Oct 24 2006 - 15:55:29 PDT)
- Wang, Xuelin (Tue Oct 24 2006 - 12:30:24 PDT)
AMBER: md and implicit solvation
- Thomas Cheatham (Tue Oct 24 2006 - 18:50:43 PDT)
- David A. Case (Tue Oct 24 2006 - 18:47:18 PDT)
- Jardas sucuriba (Tue Oct 24 2006 - 18:29:35 PDT)
- David A. Case (Tue Oct 24 2006 - 18:26:15 PDT)
- Adrian Roitberg (Tue Oct 24 2006 - 17:19:34 PDT)
- Jardas sucuriba (Tue Oct 24 2006 - 16:57:24 PDT)
AMBER: mdcrd file
- Ross Walker (Mon Oct 02 2006 - 21:31:03 PDT)
- Bill Ross (Mon Oct 02 2006 - 19:46:15 PDT)
- Fenghui Fan (Mon Oct 02 2006 - 19:17:12 PDT)
- Bill Ross (Mon Oct 02 2006 - 17:23:18 PDT)
- Fenghui Fan (Mon Oct 02 2006 - 17:09:37 PDT)
AMBER: Missing values for MM VDW
- bala (Thu Oct 05 2006 - 04:33:14 PDT)
AMBER: MM-PBSA memory usage
- Stefano Pieraccini (Thu Oct 26 2006 - 05:33:41 PDT)
AMBER: MM_PBSA
- Rajendra P. OJHA (Sat Oct 07 2006 - 09:21:49 PDT)
AMBER: mm_pbsa does not terminate
- Holly Freedman (Tue Oct 31 2006 - 16:51:19 PST)
AMBER: MM_PBSA error
- Shozeb Haider (Tue Oct 03 2006 - 14:04:57 PDT)
AMBER: mm_pbsa PBCAL
- William Wei (Tue Oct 03 2006 - 12:23:18 PDT)
AMBER: mm_pbsa reference
- Angelo (Fri Oct 27 2006 - 05:47:07 PDT)
AMBER: mm_pbsa: binding energy calculation
- Angelo (Mon Oct 30 2006 - 01:36:25 PST)
- Varsha Goyal (Sat Oct 28 2006 - 14:41:02 PDT)
- Angelo (Thu Oct 26 2006 - 06:04:18 PDT)
- Varsha Goyal (Wed Oct 25 2006 - 11:51:57 PDT)
AMBER: MMPBSA entropy question
- David A. Case (Tue Oct 31 2006 - 17:04:29 PST)
- Barbault Florent (Tue Oct 31 2006 - 01:08:55 PST)
AMBER: mmpbsa in parallell
- Olayiwola Adekoya (Thu Oct 19 2006 - 00:57:07 PDT)
AMBER: MMPBSA vDW error
- Shozeb Haider (Mon Oct 09 2006 - 16:08:27 PDT)
AMBER: mmpbsa: fail to run heat in tutorial A3
- Ross Walker (Mon Oct 23 2006 - 08:39:26 PDT)
- jitrayut jitonnom (Sun Oct 22 2006 - 10:31:53 PDT)
AMBER: modeling of ligand concentrations
- Sean Rathlef (Tue Oct 24 2006 - 19:30:54 PDT)
- Sean Rathlef (Tue Oct 24 2006 - 19:29:43 PDT)
- David A. Case (Tue Oct 24 2006 - 18:56:14 PDT)
- Thomas Steinbrecher (Tue Oct 24 2006 - 18:11:05 PDT)
- Sean Rathlef (Tue Oct 24 2006 - 16:47:03 PDT)
- Adrian Roitberg (Mon Oct 23 2006 - 16:44:46 PDT)
- Thomas Cheatham (Mon Oct 23 2006 - 15:51:28 PDT)
- Carlos Simmerling (Mon Oct 23 2006 - 15:38:22 PDT)
- Sean Rathlef (Mon Oct 23 2006 - 15:19:18 PDT)
- Thomas Cheatham (Mon Oct 23 2006 - 09:38:55 PDT)
- David A. Case (Tue Oct 17 2006 - 09:41:24 PDT)
- Sean Rathlef (Tue Oct 17 2006 - 09:07:18 PDT)
- David A. Case (Tue Oct 17 2006 - 08:38:07 PDT)
- Sean Rathlef (Mon Oct 16 2006 - 18:37:25 PDT)
- David A. Case (Mon Oct 16 2006 - 17:33:54 PDT)
- Sean Rathlef (Mon Oct 16 2006 - 15:48:16 PDT)
- David A. Case (Mon Oct 16 2006 - 15:24:34 PDT)
- Sean Rathlef (Mon Oct 16 2006 - 13:43:51 PDT)
AMBER: Multiple Timestep MD
- Robert Duke (Sun Oct 01 2006 - 07:22:34 PDT)
- David A. Case (Sun Oct 01 2006 - 06:35:25 PDT)
AMBER: N1-protonated adenosine, N-terminal myristyl group
- Michael F. Summers (Tue Oct 31 2006 - 12:54:49 PST)
AMBER: Not getting proper structure after minimization
- Giulio Rastelli (Wed Oct 25 2006 - 06:52:48 PDT)
- Carlos Simmerling (Wed Oct 25 2006 - 06:45:38 PDT)
- Elijah Gregory (Tue Oct 24 2006 - 16:17:14 PDT)
- Elijah Gregory (Tue Oct 24 2006 - 16:12:35 PDT)
- Dave, Sonya (Tue Oct 24 2006 - 15:46:45 PDT)
- Elijah Gregory (Tue Oct 24 2006 - 14:39:08 PDT)
- Gustavo Seabra (Tue Oct 24 2006 - 14:28:27 PDT)
- Carlos Simmerling (Tue Oct 24 2006 - 14:06:14 PDT)
- Dave, Sonya (Tue Oct 24 2006 - 13:50:04 PDT)
AMBER: on rst file
- Bill Ross (Wed Oct 04 2006 - 10:17:10 PDT)
- Fenghui Fan (Wed Oct 04 2006 - 07:02:40 PDT)
AMBER: parameters !!??
- Ross Walker (Wed Oct 25 2006 - 08:53:01 PDT)
- Urszula Uciechowska (Wed Oct 25 2006 - 06:32:49 PDT)
- cristian obiol (Wed Oct 25 2006 - 03:29:42 PDT)
- Urszula Uciechowska (Wed Oct 25 2006 - 02:27:22 PDT)
AMBER: parameters for fluoromolecules with more than one single carbon?
- Jones de Andrade (Thu Oct 26 2006 - 14:51:27 PDT)
AMBER: Parameters for Nickel
- a a (Wed Oct 11 2006 - 02:05:15 PDT)
AMBER: partial charges
- David A. Case (Wed Oct 11 2006 - 09:17:48 PDT)
- Fabian Alejandro Rodriguez (Tue Oct 10 2006 - 09:35:53 PDT)
AMBER: PBSA calculation fail ....
- Ray Luo (Fri Oct 06 2006 - 09:22:11 PDT)
- Changge Ji (Thu Oct 05 2006 - 19:36:34 PDT)
- Ray Luo (Thu Oct 05 2006 - 09:36:32 PDT)
- Changge Ji (Thu Oct 05 2006 - 06:42:39 PDT)
AMBER: periodic boundary condition question...
- HL Eastwood (Mon Oct 30 2006 - 08:52:04 PST)
- David A. Case (Mon Oct 30 2006 - 08:32:56 PST)
- Ross Walker (Mon Oct 30 2006 - 08:24:26 PST)
- Sergey Samsonov (Mon Oct 30 2006 - 07:36:29 PST)
- HL Eastwood (Mon Oct 30 2006 - 07:19:16 PST)
- Sergey Samsonov (Mon Oct 30 2006 - 07:04:12 PST)
- HL Eastwood (Mon Oct 30 2006 - 06:42:53 PST)
AMBER: Phenyl Ring atom types
- sethl.gatech.edu (Thu Oct 12 2006 - 11:59:24 PDT)
AMBER: Phosphorylated protein MD simulation
- Myunggi Yi (Thu Oct 26 2006 - 08:13:17 PDT)
- Myunggi Yi (Thu Oct 26 2006 - 08:18:26 PDT)
- Fenghui Fan (Wed Oct 25 2006 - 14:16:50 PDT)
AMBER: PKDIV lone pair dihedrals
- darden (Mon Oct 23 2006 - 14:05:37 PDT)
- David A. Case (Mon Oct 23 2006 - 13:26:58 PDT)
- Lorenzo Gontrani (Mon Oct 23 2006 - 10:16:25 PDT)
AMBER: pmemd installation on linux_p3_athlon ifort
- Shuting Wei (Tue Oct 24 2006 - 12:19:31 PDT)
- Robert Duke (Tue Oct 24 2006 - 10:08:58 PDT)
- gtg549i.mail.gatech.edu (Tue Oct 24 2006 - 09:20:30 PDT)
AMBER: polarization effects
- Vitor Manuel Sousa F?x (Sun Oct 01 2006 - 07:08:55 PDT)
AMBER: Potential of Mean Force calculation or Steered molecular dynamics
- a a (Sun Oct 08 2006 - 23:07:25 PDT)
AMBER: Pressure in MD
- Thomas Steinbrecher (Mon Oct 02 2006 - 14:24:30 PDT)
- Fenghui Fan (Mon Oct 02 2006 - 13:55:16 PDT)
AMBER: Pressure problem with restraint
- David A. Case (Wed Oct 04 2006 - 15:19:50 PDT)
- Jianhui (Wed Oct 04 2006 - 12:24:35 PDT)
- David A. Case (Wed Oct 04 2006 - 11:03:45 PDT)
- Jianhui (Wed Oct 04 2006 - 10:49:29 PDT)
- David A. Case (Wed Oct 04 2006 - 08:06:38 PDT)
- Jianhui (Tue Oct 03 2006 - 07:41:46 PDT)
AMBER: Probelm with running Amber 9 parallelly
- David A. Case (Fri Oct 20 2006 - 08:24:16 PDT)
- Rafi Ahmad (Fri Oct 20 2006 - 07:29:14 PDT)
AMBER: problem installing amber9 with g95 gcc on a fc5 m/c
- David A. Case (Fri Oct 27 2006 - 21:42:08 PDT)
- Sayandeep Purkayasth (Fri Oct 27 2006 - 18:25:37 PDT)
- David A. Case (Mon Oct 16 2006 - 09:41:31 PDT)
- Sayandeep Purkayasth (Sun Oct 15 2006 - 23:32:04 PDT)
- Scott Brozell (Mon Oct 09 2006 - 18:14:54 PDT)
- Sayandeep Purkayasth (Mon Oct 09 2006 - 01:59:18 PDT)
- Scott Brozell (Wed Oct 04 2006 - 01:16:09 PDT)
- Sayandeep Purkayasth (Tue Oct 03 2006 - 22:14:06 PDT)
- Sayandeep Purkayasth (Mon Oct 02 2006 - 17:30:40 PDT)
- David A. Case (Mon Oct 02 2006 - 08:28:25 PDT)
- Sayandeep Purkayasth (Sun Oct 01 2006 - 19:15:54 PDT)
AMBER: Problem loading peptoid residues with antechamber
- nur avneet (Wed Oct 18 2006 - 21:05:15 PDT)
- Junmei Wang (Wed Oct 18 2006 - 09:05:24 PDT)
- nur avneet (Tue Oct 17 2006 - 23:23:42 PDT)
AMBER: problem of installing carnal on macosx
- Shuting Wei (Fri Oct 20 2006 - 12:45:03 PDT)
- Bill Ross (Fri Oct 20 2006 - 11:50:19 PDT)
- gtg549i.mail.gatech.edu (Fri Oct 20 2006 - 11:37:39 PDT)
AMBER: problem to center solvateshell
- Bonnet, Pascal [PRDBE] (Mon Oct 02 2006 - 23:30:53 PDT)
- David A. Case (Mon Oct 02 2006 - 09:01:44 PDT)
AMBER: problem with calcpka.pl
- Amber admin (Tue Oct 31 2006 - 16:33:09 PST)
- Benjamin Juhl (Mon Oct 30 2006 - 05:57:42 PST)
- David A. Case (Sun Oct 29 2006 - 20:33:54 PST)
- Benjamin Juhl (Tue Oct 24 2006 - 04:58:27 PDT)
AMBER: Problem working with Antechamber
- nur avneet (Tue Oct 17 2006 - 00:44:54 PDT)
AMBER: problems for running sander.MPI
- Ross Walker (Mon Oct 30 2006 - 10:40:06 PST)
- Christophe Deprez (Mon Oct 30 2006 - 10:27:12 PST)
- Ross Walker (Thu Oct 12 2006 - 10:41:19 PDT)
- Christophe Deprez (Thu Oct 12 2006 - 06:54:41 PDT)
- Ross Walker (Wed Oct 11 2006 - 15:18:14 PDT)
- Qizhi Cui (Wed Oct 11 2006 - 13:39:36 PDT)
AMBER: Problems with carnal (Amber7)
- Bill Ross (Tue Oct 31 2006 - 09:09:57 PST)
- anna.schrey.gmx.de (Tue Oct 31 2006 - 07:24:29 PST)
AMBER: proposed patch for ptraj/evec.c (Amber 9.0)
- David A. Case (Mon Oct 02 2006 - 08:51:53 PDT)
AMBER: ptraj atomicfluct
- Myunggi Yi (Wed Oct 18 2006 - 12:13:36 PDT)
- Myunggi Yi (Wed Oct 18 2006 - 11:59:22 PDT)
AMBER: ptraj hbond analysis troubles
- Reinhard Klement (Wed Oct 11 2006 - 01:25:27 PDT)
- Sayandeep Purkayasth (Mon Oct 09 2006 - 01:11:56 PDT)
- Robert Duke (Thu Oct 05 2006 - 18:55:42 PDT)
- Thomas Cheatham (Thu Oct 05 2006 - 12:43:37 PDT)
- Robert Duke (Thu Oct 05 2006 - 11:35:20 PDT)
- Thomas Cheatham (Thu Oct 05 2006 - 08:21:40 PDT)
- Robert Duke (Thu Oct 05 2006 - 06:58:50 PDT)
- Sayandeep Purkayasth (Thu Oct 05 2006 - 06:37:07 PDT)
- Thomas Cheatham (Wed Oct 04 2006 - 15:41:55 PDT)
- Thomas Cheatham (Wed Oct 04 2006 - 14:36:49 PDT)
- Sayandeep Purkayasth (Wed Oct 04 2006 - 14:14:10 PDT)
AMBER: Ptraj problems
- Charlisa Daniels (Thu Oct 12 2006 - 13:01:30 PDT)
AMBER: ptraj radial problem: Segmentation fault
- Jianhui Tian (Mon Oct 23 2006 - 14:48:43 PDT)
AMBER: puzzles about solvatoct or solvatebox
- Bill Ross (Tue Oct 17 2006 - 09:13:58 PDT)
- Thomas Cheatham (Tue Oct 17 2006 - 08:05:08 PDT)
- Zhihong Yu (Tue Oct 17 2006 - 07:42:54 PDT)
- Bill Ross (Thu Oct 12 2006 - 10:43:38 PDT)
- Zhihong Yu (Thu Oct 12 2006 - 03:00:08 PDT)
AMBER: question about building molecules
- Rita Cassia (Mon Oct 09 2006 - 08:49:10 PDT)
- David A. Case (Sun Oct 08 2006 - 09:31:27 PDT)
- Rita Cassia (Sun Oct 08 2006 - 04:05:59 PDT)
AMBER: Question about sander code
- David A. Case (Fri Oct 20 2006 - 15:55:05 PDT)
- Kijeong Kwac (Fri Oct 20 2006 - 15:48:07 PDT)
- Kijeong Kwac (Fri Oct 20 2006 - 15:32:00 PDT)
- David A. Case (Fri Oct 20 2006 - 14:47:50 PDT)
- Kijeong Kwac (Fri Oct 20 2006 - 14:08:17 PDT)
- David A. Case (Fri Oct 20 2006 - 11:37:51 PDT)
- Kijeong Kwac (Fri Oct 20 2006 - 11:13:49 PDT)
AMBER: question on mm_pbsa_statistics.pl
- Yongmei Pan (Tue Oct 17 2006 - 15:36:23 PDT)
AMBER: question on molsurf
- Yongmei Pan (Fri Oct 20 2006 - 15:38:38 PDT)
AMBER: Question regarding lastrst and taup
- Priti Hansia (Wed Oct 25 2006 - 21:58:10 PDT)
- Ross Walker (Wed Oct 25 2006 - 08:46:52 PDT)
- Priti Hansia (Tue Oct 24 2006 - 23:37:09 PDT)
AMBER: questions on mm_pbsa_statitistics.pl
- Holger Gohlke (Wed Oct 18 2006 - 11:19:20 PDT)
- Yongmei Pan (Wed Oct 18 2006 - 08:12:58 PDT)
- Holger Gohlke (Wed Oct 18 2006 - 00:42:52 PDT)
- Yongmei Pan (Tue Oct 17 2006 - 15:57:59 PDT)
AMBER: rbornstat average and fluctuations incorrect when nrespa != nrespai
- David A. Case (Fri Oct 20 2006 - 10:27:50 PDT)
- Ingvar Lagerstedt (Fri Oct 20 2006 - 09:17:08 PDT)
AMBER: RDF calculation
- Thomas Cheatham (Tue Oct 17 2006 - 08:23:05 PDT)
- Xioling Chuang (Tue Oct 17 2006 - 03:54:02 PDT)
AMBER: Reducind trajectory
- Sergey Samsonov (Wed Oct 11 2006 - 00:03:49 PDT)
AMBER: Reducing trajectory
- Sergey Samsonov (Wed Oct 11 2006 - 00:36:15 PDT)
AMBER: regarding PBCAL in MM-PBSA
- Cenk Andac (Mon Oct 16 2006 - 18:15:20 PDT)
- Ray Luo (Mon Oct 16 2006 - 17:35:42 PDT)
- Cenk Andac (Mon Oct 16 2006 - 16:11:33 PDT)
AMBER: reinstall amber8
- Wei Zhang (Wed Oct 25 2006 - 08:13:01 PDT)
- Rachel (Wed Oct 25 2006 - 07:57:59 PDT)
AMBER: residence time& hydration density
- Myunggi Yi (Thu Oct 26 2006 - 08:27:26 PDT)
- Andres Palencia (Wed Oct 25 2006 - 07:16:53 PDT)
AMBER: RESP charge fitting
- FyD (Fri Oct 27 2006 - 23:37:59 PDT)
- Mingfeng Yang (Fri Oct 27 2006 - 17:35:37 PDT)
AMBER: RESP charges of iron-porphyrin system
- Marcelo Puiatti (Wed Oct 25 2006 - 10:42:07 PDT)
- FyD (Thu Oct 19 2006 - 22:23:14 PDT)
- Shin Tokumoto (Thu Oct 19 2006 - 21:45:08 PDT)
- Chris Moth (Thu Oct 19 2006 - 09:39:24 PDT)
- Gustavo Seabra (Thu Oct 19 2006 - 06:40:20 PDT)
- Shin Tokumoto (Wed Oct 18 2006 - 19:50:26 PDT)
AMBER: restraints and constant pressure
- Joshua (Fri Oct 13 2006 - 15:46:26 PDT)
AMBER: RMSD: is it related to flexibility?
- Feng X Zhou (Fri Oct 06 2006 - 09:28:36 PDT)
- a a (Thu Oct 05 2006 - 19:50:43 PDT)
- Gustavo Seabra (Thu Oct 05 2006 - 09:08:05 PDT)
- a a (Wed Oct 04 2006 - 21:15:20 PDT)
- David A. Case (Wed Oct 04 2006 - 08:08:32 PDT)
- Carlos Simmerling (Wed Oct 04 2006 - 04:40:04 PDT)
- a a (Wed Oct 04 2006 - 02:42:12 PDT)
AMBER: sander/topology problem
- David A. Case (Tue Oct 17 2006 - 10:31:25 PDT)
- Lorenzo Gontrani (Tue Oct 17 2006 - 09:51:39 PDT)
AMBER: Shake&Lone Pairs
- David A. Case (Wed Oct 25 2006 - 11:21:02 PDT)
- Lorenzo Gontrani (Wed Oct 25 2006 - 03:58:59 PDT)
AMBER: simulation of protein in non-aq or organic solvent bath
- Smriti Sharma (Sun Oct 15 2006 - 21:06:53 PDT)
AMBER: single or dual topology for TI?
- David Mobley (Sat Oct 21 2006 - 13:58:41 PDT)
- Holly Freedman (Sat Oct 21 2006 - 13:32:42 PDT)
- David Mobley (Sat Oct 21 2006 - 12:17:50 PDT)
- Holly Freedman (Sat Oct 21 2006 - 11:20:51 PDT)
AMBER: solvation and His protonation
- David A. Case (Tue Oct 31 2006 - 07:57:53 PST)
- Jardas sucuriba (Tue Oct 31 2006 - 05:07:24 PST)
- David A. Case (Mon Oct 30 2006 - 16:34:05 PST)
- Jardas sucuriba (Sat Oct 28 2006 - 07:00:44 PDT)
AMBER: some puzzles in equilibration MD
- Bill Ross (Mon Oct 09 2006 - 20:14:39 PDT)
- Ross Walker (Mon Oct 09 2006 - 15:41:54 PDT)
- Zhihong Yu (Mon Oct 09 2006 - 08:19:15 PDT)
- Ross Walker (Mon Oct 09 2006 - 07:53:20 PDT)
- Zhihong Yu (Mon Oct 09 2006 - 06:58:06 PDT)
AMBER: splitting LES with ptraj in amber9
- bala (Mon Oct 23 2006 - 22:18:16 PDT)
AMBER: Steered molecular dynamics with Amber 8.0
- a a (Tue Oct 10 2006 - 02:44:56 PDT)
AMBER: SURFTEN/SURFOFF values in amber9
- ferranna.unimo.it (Sat Oct 14 2006 - 00:27:42 PDT)
AMBER: TFE parameters for Amber
- Mingfeng Yang (Thu Oct 12 2006 - 16:33:21 PDT)
AMBER: To create methanol solvent box
- Smriti Sharma (Wed Oct 18 2006 - 01:14:38 PDT)
- Atsutoshi Okabe (Tue Oct 17 2006 - 23:31:02 PDT)
AMBER: Trouble with Leap
- Ilyas Yildirim (Thu Oct 19 2006 - 01:04:59 PDT)
- Biswa Ranjan Meher (Wed Oct 18 2006 - 22:28:46 PDT)
- Biswa Ranjan Meher (Tue Oct 17 2006 - 22:35:48 PDT)
- Scott Brozell (Mon Oct 09 2006 - 18:42:38 PDT)
- Biswa Ranjan Meher (Mon Oct 09 2006 - 07:28:28 PDT)
AMBER: Two different HIS ligands
- David LeBard (Thu Oct 26 2006 - 16:16:42 PDT)
- Kristina Furse (Thu Oct 26 2006 - 14:41:49 PDT)
- David LeBard (Thu Oct 26 2006 - 14:16:09 PDT)
AMBER: Unstable RMS trajectory
- Dave, Sonya (Tue Oct 17 2006 - 11:14:44 PDT)
- Gustavo Seabra (Tue Oct 17 2006 - 10:41:43 PDT)
- Adrian Roitberg (Tue Oct 17 2006 - 10:41:31 PDT)
- Dave, Sonya (Tue Oct 17 2006 - 10:17:59 PDT)
- Dave, Sonya (Tue Oct 17 2006 - 10:10:03 PDT)
- Gustavo Seabra (Tue Oct 17 2006 - 09:56:23 PDT)
- Adrian Roitberg (Tue Oct 17 2006 - 09:46:48 PDT)
- Ross Walker (Tue Oct 17 2006 - 09:40:43 PDT)
- Carlos Simmerling (Tue Oct 17 2006 - 09:33:40 PDT)
- Bill Ross (Tue Oct 17 2006 - 09:26:18 PDT)
- Gustavo Seabra (Tue Oct 17 2006 - 09:22:31 PDT)
- Carlos Simmerling (Tue Oct 17 2006 - 09:10:52 PDT)
- Dave, Sonya (Tue Oct 17 2006 - 09:03:59 PDT)
AMBER: Updated Tutorials Page
- Ross Walker (Fri Oct 13 2006 - 12:17:07 PDT)
AMBER: Using modified NA bases
- Qizhi Cui (Wed Oct 25 2006 - 08:51:32 PDT)
- FyD (Tue Oct 24 2006 - 11:14:54 PDT)
- Franck_Vendeix.ncsu.edu (Tue Oct 24 2006 - 06:03:36 PDT)
- Fabian Alejandro Rodriguez (Mon Oct 23 2006 - 16:17:41 PDT)
- sethl.gatech.edu (Mon Oct 23 2006 - 12:59:15 PDT)
AMBER: Virus?
- Peter Gannett (Mon Oct 23 2006 - 05:34:29 PDT)
AMBER: VMD PDB into LEAP Readable PDB
- David A. Case (Thu Oct 05 2006 - 08:13:41 PDT)
- Akshay Patny (Wed Oct 04 2006 - 18:07:11 PDT)
AMBER: water prmtop/inpcrd problem
- Akshay Patny (Fri Oct 06 2006 - 07:49:22 PDT)
- Ilyas Yildirim (Fri Oct 06 2006 - 02:17:11 PDT)
- David A. Case (Thu Oct 05 2006 - 19:01:22 PDT)
- Akshay Patny (Thu Oct 05 2006 - 18:08:59 PDT)
AMBER: what is the RMS value in resp charge fitting ?
- jitrayut jitonnom (Tue Oct 31 2006 - 00:46:31 PST)
AMBER: where to set bondi radii for halogens
- David A. Case (Fri Oct 27 2006 - 17:24:12 PDT)
- Giulio Rastelli (Fri Oct 27 2006 - 14:10:32 PDT)
- David A. Case (Fri Oct 27 2006 - 11:58:04 PDT)
- Giulio Rastelli (Fri Oct 27 2006 - 09:59:00 PDT)
AMBER: Ｆｅ complex
- Toshifumi Yui (Tue Oct 10 2006 - 18:09:36 PDT)
AMBER: Ｆｅ complex　(correction)
- Toshifumi Yui (Tue Oct 10 2006 - 18:41:05 PDT)
AMBER:pls help load peptoid residues in antechamber
- nur avneet (Tue Oct 24 2006 - 22:29:55 PDT)
atom nomination in the PDB file produced by Amber
- Fenghui Fan (Wed Oct 04 2006 - 08:41:11 PDT)
Distance between two atoms
- Fenghui Fan (Tue Oct 03 2006 - 23:41:27 PDT)
- Fenghui Fan (Tue Oct 03 2006 - 23:12:06 PDT)
Problems installing antechamber 1.27
- andrea carotti (Tue Oct 31 2006 - 00:17:49 PST)

Amber Archive Oct 2006 by subject