Amber Archive Apr 2007: by subject

amber mm-pbsa problem
- odde (Tue Apr 17 2007 - 06:57:37 PDT)
- Jiten (Mon Apr 16 2007 - 18:39:26 PDT)
AMBER: .prmtop entries
- Andy Purkiss-Trew (Mon Apr 23 2007 - 04:13:18 PDT)
- Neelanjana Sengupta (Sun Apr 22 2007 - 22:53:46 PDT)
AMBER: a problem of surface area calulated by MM/PBSA
- David A. Case (Mon Apr 30 2007 - 08:20:43 PDT)
- Chengwen Chen (Mon Apr 30 2007 - 00:34:38 PDT)
AMBER: A test email
- Ruchi Sachdeva (Thu Apr 19 2007 - 23:54:55 PDT)
AMBER: about define improper torsion in .frcmod file
- David A. Case (Wed Apr 04 2007 - 08:25:11 PDT)
- Chengwen Chen (Wed Apr 04 2007 - 02:02:57 PDT)
AMBER: AIX 5 test failures: -NaNQ
- Patrick McCarren (Wed Apr 25 2007 - 16:44:15 PDT)
- Ross Walker (Mon Apr 23 2007 - 15:47:20 PDT)
- Patrick McCarren (Mon Apr 23 2007 - 14:51:46 PDT)
- Scott Brozell (Mon Apr 23 2007 - 10:10:23 PDT)
- Patrick McCarren (Fri Apr 20 2007 - 16:01:53 PDT)
- Ross Walker (Thu Apr 19 2007 - 18:20:46 PDT)
- David A. Case (Thu Apr 19 2007 - 18:13:46 PDT)
- Scott Brozell (Thu Apr 19 2007 - 17:13:54 PDT)
- Patrick McCarren (Thu Apr 19 2007 - 16:30:35 PDT)
AMBER: Amber 8 support of CHARMM ff?
- David A. Case (Sat Apr 14 2007 - 12:21:23 PDT)
- Seth Lilavivat (Sat Apr 14 2007 - 11:36:35 PDT)
AMBER: amber 9 installation: broken pipe
- Scott Brozell (Thu Apr 05 2007 - 18:46:09 PDT)
- Stern, Julie (Thu Apr 05 2007 - 16:54:16 PDT)
AMBER: amber equation of ff99
- Chengwen Chen (Tue Apr 24 2007 - 19:19:15 PDT)
- Carlos Simmerling (Tue Apr 24 2007 - 09:18:57 PDT)
- Chengwen Chen (Tue Apr 24 2007 - 09:13:54 PDT)
AMBER: AMBER MINIMIZATION
- gsciaini.qi.fcen.uba.ar (Mon Apr 30 2007 - 14:08:47 PDT)
- Sophie Barbe (Mon Apr 30 2007 - 09:23:41 PDT)
- David A. Case (Mon Apr 30 2007 - 08:24:34 PDT)
- Sophie Barbe (Mon Apr 30 2007 - 06:55:53 PDT)
AMBER: AMBER9 installation error on dual core AMD Opteron(tm) processor 275
- Arvind Marathe (Fri Apr 13 2007 - 08:59:35 PDT)
- Mark Williamson (Fri Apr 13 2007 - 05:51:54 PDT)
- Arvind Marathe (Fri Apr 13 2007 - 03:23:38 PDT)
AMBER: amber9: running parallel error
- Khatcharin Siriwong (Wed Apr 18 2007 - 00:03:13 PDT)
- Khatcharin Siriwong (Wed Apr 18 2007 - 00:00:29 PDT)
- Benjamin Juhl (Thu Apr 12 2007 - 01:33:48 PDT)
- Khatcharin Siriwong (Wed Apr 11 2007 - 20:40:27 PDT)
- Ross Walker (Wed Apr 11 2007 - 06:43:19 PDT)
- Khatcharin Siriwong (Wed Apr 11 2007 - 01:08:16 PDT)
AMBER: Amber:PBSA&Extract_coords problem (Needed help)
- Jiten (Sat Apr 14 2007 - 06:51:58 PDT)
- odde (Fri Apr 13 2007 - 12:06:42 PDT)
AMBER: Antechamber
- Junmei Wang (Thu Apr 19 2007 - 06:58:14 PDT)
- Beale, John (Thu Apr 19 2007 - 06:51:03 PDT)
AMBER: Antechamber Warning
- Beale, John (Wed Apr 18 2007 - 12:39:31 PDT)
AMBER: Attaching capping groups
- Ross Walker (Sun Apr 15 2007 - 20:49:26 PDT)
- Neelanjana Sengupta (Thu Apr 12 2007 - 19:54:30 PDT)
- Ross Walker (Wed Apr 11 2007 - 20:49:36 PDT)
- Kristina Furse (Wed Apr 11 2007 - 19:30:30 PDT)
- Neelanjana Sengupta (Wed Apr 11 2007 - 18:28:33 PDT)
AMBER: bad atom type errors in GB for halides?
- David A. Case (Thu Apr 12 2007 - 17:04:55 PDT)
- Ilyas Yildirim (Thu Apr 12 2007 - 12:57:13 PDT)
- David Mobley (Thu Apr 12 2007 - 10:19:51 PDT)
AMBER: Binding free energy errors: Grid setting fail
- jitrayut jitonnom (Sun Apr 29 2007 - 06:48:17 PDT)
AMBER: Blue Gene, compile Amber9?
- Mike Hanby (Fri Apr 20 2007 - 12:33:39 PDT)
- David A. Case (Thu Apr 19 2007 - 14:31:25 PDT)
- Mike Hanby (Thu Apr 19 2007 - 07:34:46 PDT)
- Robert Duke (Tue Apr 10 2007 - 08:42:11 PDT)
- Mike Hanby (Tue Apr 10 2007 - 08:13:11 PDT)
- Mike Hanby (Tue Apr 10 2007 - 07:04:13 PDT)
- Ross Walker (Fri Apr 06 2007 - 14:23:33 PDT)
- Carlos P. Sosa (Fri Apr 06 2007 - 11:55:28 PDT)
- Mike Hanby (Fri Apr 06 2007 - 10:22:57 PDT)
AMBER: Charges in antechamber
- Scott Brozell (Thu Apr 05 2007 - 13:43:59 PDT)
- Beale, John (Thu Apr 05 2007 - 08:46:34 PDT)
AMBER: CHARMM vs. AMBER ff literature
- Jiri Sponer (Thu Apr 12 2007 - 05:58:32 PDT)
- Thomas Cheatham (Wed Apr 11 2007 - 14:21:14 PDT)
- Seth Lilavivat (Wed Apr 11 2007 - 08:21:07 PDT)
AMBER: choice of alpha carbons vs side chains
- Bill Ross (Wed Apr 04 2007 - 16:28:34 PDT)
- Christopher Gaughan (Wed Apr 04 2007 - 15:34:31 PDT)
AMBER: Constant volume simulations
- Christopher Gaughan (Tue Apr 10 2007 - 10:12:14 PDT)
- Vlad Cojocaru (Tue Apr 10 2007 - 09:02:42 PDT)
- Christopher Gaughan (Tue Apr 10 2007 - 08:50:39 PDT)
- Vlad Cojocaru (Tue Apr 10 2007 - 08:39:45 PDT)
- Carlos Simmerling (Tue Apr 10 2007 - 08:35:14 PDT)
- Christopher Gaughan (Tue Apr 10 2007 - 08:31:58 PDT)
- David A. Case (Mon Apr 09 2007 - 13:24:09 PDT)
- Christopher Gaughan (Mon Apr 09 2007 - 11:59:26 PDT)
AMBER: Cut off for cavities
- Sangwai, Ashishvikas (Mon Apr 02 2007 - 11:47:30 PDT)
AMBER: dihedral angles restraint for DNA
- Hu, Shaowen (JSC-SK)[USRA] (Tue Apr 10 2007 - 10:51:13 PDT)
AMBER: Employing SCC-DFTB with a periodic boundary condtion
- Gustavo Seabra (Thu Apr 26 2007 - 06:18:32 PDT)
- 한재범 (Wed Apr 25 2007 - 23:48:58 PDT)
AMBER: Energy minimization problem
- Bo Baker (Thu Apr 05 2007 - 03:14:31 PDT)
- David A. Case (Wed Apr 04 2007 - 18:25:26 PDT)
- Bo Baker (Wed Apr 04 2007 - 17:02:42 PDT)
- David A. Case (Tue Apr 03 2007 - 18:39:37 PDT)
- Bo Baker (Tue Apr 03 2007 - 18:24:05 PDT)
AMBER: enzyme kinetics in silico
- Sean Rathlef (Tue Apr 03 2007 - 14:08:10 PDT)
- Xu, Yong (Tue Apr 03 2007 - 12:26:45 PDT)
AMBER: Error at Equilibration....
- David A. Case (Mon Apr 02 2007 - 08:45:57 PDT)
- Sandeep Kaushik (Mon Apr 02 2007 - 00:14:17 PDT)
AMBER: Error in protonating
- David A. Case (Sat Apr 28 2007 - 14:26:08 PDT)
- Ross Walker (Fri Apr 27 2007 - 08:46:50 PDT)
- Neelanjana Sengupta (Fri Apr 27 2007 - 04:31:52 PDT)
AMBER: Error on compile amber8
- tri nam Vo (Mon Apr 23 2007 - 23:47:27 PDT)
- David LeBard (Mon Apr 23 2007 - 22:45:45 PDT)
- tri nam Vo (Mon Apr 23 2007 - 22:04:34 PDT)
AMBER: Error on compiling AMBER8
- David A. Case (Wed Apr 25 2007 - 11:33:11 PDT)
- tri nam Vo (Wed Apr 25 2007 - 09:35:31 PDT)
- David A. Case (Tue Apr 24 2007 - 20:31:44 PDT)
- tri nam Vo (Tue Apr 24 2007 - 19:03:16 PDT)
AMBER: Error: "Suspended (tty input)" & "Unit 6 Error on OPEN: md.out"
- Khatcharin Siriwong (Sat Apr 21 2007 - 20:57:18 PDT)
- David A. Case (Sat Apr 21 2007 - 12:04:23 PDT)
- Khatcharin Siriwong (Sat Apr 21 2007 - 00:42:14 PDT)
AMBER: Ewald BOMB....... what is this..
- Ross Walker (Sat Apr 21 2007 - 10:08:15 PDT)
- Vijay Manickam Achari (Wed Apr 18 2007 - 20:13:38 PDT)
AMBER: Explicit water opinion
- David Cerutti (Fri Apr 13 2007 - 15:58:32 PDT)
- Hayden Eastwood (Fri Apr 13 2007 - 11:39:19 PDT)
AMBER: Extra Points... How to Deal with Them
- David Cerutti (Mon Apr 02 2007 - 23:39:23 PDT)
AMBER: Extra points... virial computation
- David Cerutti (Sat Apr 07 2007 - 23:48:11 PDT)
AMBER: Extracting Coords&MMPBSA&ambpdb
- Srinivas Odde (Tue Apr 24 2007 - 08:51:48 PDT)
AMBER: Fails to load libraries present in /leap/lib/
- Ross Walker (Tue Apr 10 2007 - 15:53:07 PDT)
- David A. Case (Mon Apr 09 2007 - 10:25:41 PDT)
- Neelanjana Sengupta (Mon Apr 09 2007 - 02:33:29 PDT)
AMBER: ff02 + POL3 - polar interactions !!
- Pradipta Bandyopadhyay (Wed Apr 18 2007 - 09:04:22 PDT)
AMBER: frcmod file
- Ross Walker (Wed Apr 18 2007 - 08:51:20 PDT)
- David A. Case (Wed Apr 18 2007 - 08:22:01 PDT)
- deepti nayar (Tue Apr 17 2007 - 23:31:52 PDT)
AMBER: H-bond analysis............acceptorH absent..!!!
- Sandeep Kaushik (Sun Apr 15 2007 - 23:32:28 PDT)
AMBER: How can I modify the frcmod file of ligand with a nonstandard guanidine
- tonglei (Thu Apr 12 2007 - 00:13:34 PDT)
AMBER: how to modify map.DG-AMBER file?
- A Box (Tue Apr 10 2007 - 16:56:21 PDT)
AMBER: I'm sorry ... please ignore the junk !!
- Vlad Cojocaru (Mon Apr 09 2007 - 03:50:54 PDT)
AMBER: is possible to compile pmemd using scali MPI?
- Andrea Bortolato (Mon Apr 23 2007 - 05:31:53 PDT)
AMBER: MD at constan pH
- tri nam Vo (Fri Apr 06 2007 - 21:05:20 PDT)
- tri nam Vo (Fri Apr 06 2007 - 20:53:52 PDT)
- Scott Brozell (Fri Apr 06 2007 - 09:41:39 PDT)
- tri nam Vo (Fri Apr 06 2007 - 07:10:18 PDT)
AMBER: mdfil.f
- David A. Case (Mon Apr 16 2007 - 10:25:02 PDT)
- Robert Duke (Mon Apr 16 2007 - 10:02:28 PDT)
- Ross Walker (Mon Apr 16 2007 - 09:43:01 PDT)
- Peljidiyn Genden (Sat Apr 14 2007 - 00:43:27 PDT)
AMBER: membrane simulation
- nag raj (Thu Apr 19 2007 - 05:51:56 PDT)
- Vlad Cojocaru (Thu Apr 19 2007 - 02:07:52 PDT)
- nag raj (Wed Apr 18 2007 - 19:53:27 PDT)
- Florian Haberl (Mon Apr 16 2007 - 07:04:04 PDT)
- nag raj (Sun Apr 15 2007 - 22:29:32 PDT)
- Jojart Balazs (Sun Apr 15 2007 - 11:06:31 PDT)
AMBER: MM-PBSA: Can't finish the binding energy process
- Navnit Kumar Mishra (Mon Apr 23 2007 - 07:04:12 PDT)
- jitrayut jitonnom (Mon Apr 23 2007 - 05:34:48 PDT)
AMBER: MM-PBSA: decompose energy error
- Sergey Samsonov (Mon Apr 23 2007 - 04:56:30 PDT)
- jitrayut jitonnom (Mon Apr 23 2007 - 04:31:43 PDT)
AMBER: MM-PBSA_binding energy script error
- odde (Mon Apr 16 2007 - 16:33:14 PDT)
AMBER: mobile proton algorithm
- HL Eastwood (Tue Apr 24 2007 - 12:25:10 PDT)
AMBER: mol2 format
- j j (Mon Apr 23 2007 - 02:04:53 PDT)
- Jardas sucuriba (Sun Apr 22 2007 - 15:57:12 PDT)
AMBER: Multiple Bonds to one Atom
- crowfoot.unr.nevada.edu (Thu Apr 12 2007 - 13:41:36 PDT)
AMBER: NAD parameters
- Jardas sucuriba (Wed Apr 25 2007 - 15:46:17 PDT)
- Ross Walker (Tue Apr 24 2007 - 12:32:27 PDT)
- Jardas sucuriba (Tue Apr 24 2007 - 11:02:56 PDT)
AMBER: Needed help regardng Simulated Annealing
- Anju Sharma (Wed Apr 11 2007 - 22:07:14 PDT)
AMBER: netcdf support needed (Amber 9, sander imin = 5, -y flag)
- Chris Moth (Fri Apr 06 2007 - 11:50:29 PDT)
AMBER: nmode
- David A. Case (Tue Apr 03 2007 - 09:31:54 PDT)
- Marie Brut (Tue Apr 03 2007 - 08:42:17 PDT)
- David A. Case (Tue Apr 03 2007 - 08:25:52 PDT)
- Marie Brut (Tue Apr 03 2007 - 03:17:39 PDT)
AMBER: nscm in simulation annealing
- Hu, Shaowen (JSC-SK)[USRA] (Tue Apr 17 2007 - 09:59:43 PDT)
- Ross Walker (Tue Apr 17 2007 - 09:25:35 PDT)
- Hu, Shaowen (JSC-SK)[USRA] (Tue Apr 17 2007 - 09:26:01 PDT)
- Hu, Shaowen (JSC-SK)[USRA] (Tue Apr 17 2007 - 08:25:05 PDT)
- David A. Case (Tue Apr 17 2007 - 09:18:02 PDT)
- Hu, Shaowen (JSC-SK)[USRA] (Fri Apr 13 2007 - 13:13:07 PDT)
- David A. Case (Fri Apr 13 2007 - 12:48:13 PDT)
- Hu, Shaowen (JSC-SK)[USRA] (Fri Apr 13 2007 - 11:36:59 PDT)
- David A. Case (Fri Apr 13 2007 - 10:22:32 PDT)
- Hu, Shaowen (JSC-SK)[USRA] (Fri Apr 13 2007 - 08:32:26 PDT)
- David A. Case (Thu Apr 12 2007 - 17:05:01 PDT)
- Hu, Shaowen (JSC-SK)[USRA] (Thu Apr 12 2007 - 10:53:18 PDT)
- David A. Case (Thu Apr 12 2007 - 09:41:03 PDT)
- Hu, Shaowen (JSC-SK)[USRA] (Thu Apr 12 2007 - 07:38:09 PDT)
AMBER: NTX=7 ?............lastist= ?...........lastrst= ?????
- Sandeep Kaushik (Wed Apr 11 2007 - 23:11:40 PDT)
- Ross Walker (Tue Apr 10 2007 - 15:53:19 PDT)
- David A. Case (Mon Apr 09 2007 - 10:21:21 PDT)
- j j (Mon Apr 09 2007 - 07:18:58 PDT)
- Sandeep Kaushik (Mon Apr 09 2007 - 03:35:54 PDT)
AMBER: parse radii
- Gohlke.bioinformatik.uni-frankfurt.de (Mon Apr 09 2007 - 02:35:06 PDT)
- AYTUG TUNCEL (Mon Apr 09 2007 - 01:02:59 PDT)
- Holger Gohlke (Wed Apr 04 2007 - 02:24:17 PDT)
- AYTUG TUNCEL (Wed Apr 04 2007 - 02:10:10 PDT)
AMBER: PDB file format for AMBER
- David A. Case (Sat Apr 07 2007 - 08:56:18 PDT)
- Neelanjana Sengupta (Fri Apr 06 2007 - 19:41:43 PDT)
AMBER: PDB files
- David A. Case (Mon Apr 30 2007 - 13:00:33 PDT)
- Hayden Eastwood (Mon Apr 30 2007 - 10:20:14 PDT)
- Hayden Eastwood (Mon Apr 30 2007 - 10:12:01 PDT)
- Beale, John (Mon Apr 30 2007 - 09:16:59 PDT)
AMBER: PDBs
- John E. Kerrigan (Tue Apr 17 2007 - 05:40:54 PDT)
- Beale, John (Tue Apr 17 2007 - 05:22:42 PDT)
AMBER: pH effect on protein folding
- tri nam Vo (Fri Apr 06 2007 - 23:27:40 PDT)
AMBER: phosphorylated residues
- yxamber (Tue Apr 03 2007 - 06:12:35 PDT)
- David A. Case (Mon Apr 02 2007 - 15:13:37 PDT)
- yxamber (Sun Apr 01 2007 - 22:13:17 PDT)
AMBER: polarization and water density
- David A. Case (Fri Apr 13 2007 - 12:53:42 PDT)
- Thérèse Malliavin (Fri Apr 13 2007 - 02:36:44 PDT)
AMBER: Prblm rgrdng Simulated Annealing
- Anju Sharma (Wed Apr 11 2007 - 04:46:08 PDT)
- Carlos Simmerling (Wed Apr 11 2007 - 04:39:30 PDT)
- Anju Sharma (Wed Apr 11 2007 - 04:33:03 PDT)
- Carlos Simmerling (Wed Apr 11 2007 - 04:23:43 PDT)
- Anju Sharma (Wed Apr 11 2007 - 03:06:08 PDT)
AMBER: prep file new residue
- David A. Case (Tue Apr 24 2007 - 12:12:44 PDT)
- Dr M. Blomberg (Mon Apr 23 2007 - 01:48:27 PDT)
AMBER: pressure tensor in a slab configuration
- rdauria.uci.edu (Mon Apr 30 2007 - 19:16:08 PDT)
AMBER: principal axis calculation in Ptraj
- Esther Brugger (Tue Apr 03 2007 - 14:05:44 PDT)
AMBER: principal mask dorotation
- Esther Brugger (Thu Apr 05 2007 - 14:46:51 PDT)
AMBER: Print individual free energies in MD trajectories using MM_PBSA
- Giulio Rastelli (Fri Apr 27 2007 - 09:05:39 PDT)
AMBER: printcharges option when using QM/MM simulation
- Ross Walker (Wed Apr 18 2007 - 08:31:17 PDT)
- 한재범 (Tue Apr 17 2007 - 23:41:33 PDT)
AMBER: problem regarding implicit simulation
- Carlos Simmerling (Tue Apr 24 2007 - 04:25:31 PDT)
- gurpreet singh (Tue Apr 24 2007 - 04:18:57 PDT)
- Carlos Simmerling (Mon Apr 23 2007 - 04:30:34 PDT)
- gurpreet singh (Sun Apr 22 2007 - 23:16:35 PDT)
AMBER: problem related to visualizing of structure
- deepti nayar (Tue Apr 10 2007 - 02:42:58 PDT)
- Vlad Cojocaru (Tue Apr 10 2007 - 02:32:01 PDT)
- deepti nayar (Tue Apr 10 2007 - 02:18:38 PDT)
- Vlad Cojocaru (Tue Apr 10 2007 - 01:25:06 PDT)
- deepti nayar (Mon Apr 09 2007 - 23:33:40 PDT)
AMBER: Problem using Ptraj
- Thomas Cheatham III (Mon Apr 23 2007 - 10:02:17 PDT)
- j j (Mon Apr 23 2007 - 09:47:50 PDT)
- alfredoq.fcq.unc.edu.ar (Mon Apr 23 2007 - 08:41:56 PDT)
AMBER: Problem while using antechamber
- Anju Sharma (Tue Apr 10 2007 - 02:18:07 PDT)
- Benjamin Juhl (Tue Apr 10 2007 - 00:12:13 PDT)
- Anju Sharma (Mon Apr 09 2007 - 23:15:47 PDT)
AMBER: Problem with calcpka.pl and constant pH
- Hayden Eastwood (Mon Apr 30 2007 - 06:04:11 PDT)
- Hayden Eastwood (Mon Apr 30 2007 - 04:35:23 PDT)
AMBER: problem with calculating RMSD
- Ross Walker (Wed Apr 18 2007 - 09:03:37 PDT)
- Gustavo Seabra (Wed Apr 18 2007 - 07:50:21 PDT)
- tri nam Vo (Wed Apr 18 2007 - 01:22:45 PDT)
- Gustavo Seabra (Tue Apr 17 2007 - 05:41:26 PDT)
- tri nam Vo (Tue Apr 17 2007 - 00:01:35 PDT)
AMBER: Problem with MM-PBSA statistics
- Henar Martínez García (Mon Apr 30 2007 - 02:53:38 PDT)
AMBER: Problem with PCSHIFT module
- David A. Case (Sun Apr 15 2007 - 21:24:01 PDT)
- Edoardo Saccenti (Thu Apr 12 2007 - 05:40:55 PDT)
- Edoardo Saccenti (Tue Apr 03 2007 - 01:08:38 PDT)
AMBER: Problem with Sander restart file.
- David A. Case (Wed Apr 11 2007 - 11:11:40 PDT)
- Martin Stennett (Wed Apr 11 2007 - 04:45:03 PDT)
- Navnit Kumar Mishra (Wed Apr 11 2007 - 04:19:20 PDT)
- Martin Stennett (Wed Apr 11 2007 - 03:56:37 PDT)
AMBER: Problem with sander.MPI
- Sandeep Kaushik (Mon Apr 02 2007 - 06:06:21 PDT)
AMBER: Problems during compilation and test.
- David A. Case (Tue Apr 10 2007 - 18:27:39 PDT)
- Liang, Lei (Mon Apr 09 2007 - 10:21:39 PDT)
- Scott Brozell (Thu Apr 05 2007 - 19:11:30 PDT)
- Liang, Lei (Thu Apr 05 2007 - 13:43:23 PDT)
AMBER: Problems installing Amber9
- Ângela dos Reis (Fri Apr 27 2007 - 10:34:38 PDT)
- Ross Walker (Fri Apr 27 2007 - 08:56:41 PDT)
- Andreas Svrcek-Seiler (Fri Apr 27 2007 - 05:52:05 PDT)
- Ângela dos Reis (Fri Apr 27 2007 - 04:14:05 PDT)
AMBER: Problems with AMBER8 on 32-bit FC6
- David A. Case (Mon Apr 23 2007 - 14:17:09 PDT)
- David LeBard (Mon Apr 23 2007 - 11:51:02 PDT)
AMBER: Problems with Machine file for sander.MPI
- Terry Lang (Tue Apr 24 2007 - 16:55:11 PDT)
- Ross Walker (Thu Apr 19 2007 - 14:02:24 PDT)
- Terry Lang (Thu Apr 19 2007 - 13:15:45 PDT)
AMBER: process and plot matrix data
- Vlad Cojocaru (Fri Apr 20 2007 - 06:18:46 PDT)
- Patrick McCarren (Fri Apr 20 2007 - 03:02:15 PDT)
- Vlad Cojocaru (Fri Apr 20 2007 - 02:28:12 PDT)
AMBER: Projecting trajectories onto normal modes
- M. L. Dodson (Mon Apr 16 2007 - 08:41:50 PDT)
- Harald Lanig (Mon Apr 16 2007 - 07:50:38 PDT)
AMBER: protein-rna interaction & mmpbsa
- Antonio Morreale (Thu Apr 26 2007 - 01:28:19 PDT)
AMBER: Protonation/deprotonation of terminal residues
- FyD (Wed Apr 18 2007 - 11:26:47 PDT)
- Jesper Soerensen (Wed Apr 18 2007 - 05:56:26 PDT)
AMBER: ptraj and quasi harmonic analysis
- David A. Case (Fri Apr 20 2007 - 09:49:26 PDT)
- Hans Lee (Fri Apr 20 2007 - 09:35:49 PDT)
- David A. Case (Fri Apr 20 2007 - 08:23:34 PDT)
- Hans Lee (Thu Apr 19 2007 - 18:46:38 PDT)
- Thomas Cheatham III (Thu Apr 19 2007 - 13:26:35 PDT)
- Chris Moth (Thu Apr 19 2007 - 12:58:52 PDT)
- Myunggi Yi (Wed Apr 18 2007 - 09:46:22 PDT)
- Hans Lee (Wed Apr 18 2007 - 07:47:11 PDT)
- Hans Lee (Mon Apr 16 2007 - 14:19:34 PDT)
AMBER: ptraj bug?
- Tamara Rogers (Wed Apr 18 2007 - 15:09:39 PDT)
AMBER: ptraj error- glibc detected free(): invalid pointer: 0x0812bb38
- Bill Ross (Fri Apr 27 2007 - 16:07:54 PDT)
- Bill Ross (Fri Apr 27 2007 - 13:41:20 PDT)
- Scott Brozell (Fri Apr 27 2007 - 13:25:23 PDT)
- Ruchi Sachdeva (Tue Apr 24 2007 - 20:54:14 PDT)
AMBER: ptraj hbond
- Evan Kelly (Sun Apr 08 2007 - 19:00:29 PDT)
- Evan Kelly (Sun Apr 08 2007 - 17:37:04 PDT)
AMBER: ptraj secstruct core dumped error
- vijayaraj.clri.info (Tue Apr 17 2007 - 06:45:04 PDT)
AMBER: ptraj:problems with time correlation calculation (comp. with NMR experiments)
- David A. Case (Mon Apr 09 2007 - 10:27:59 PDT)
- anna.schrey.gmx.de (Sun Apr 08 2007 - 05:21:38 PDT)
AMBER: QM/MM NPT Simulation
- Ross Walker (Fri Apr 20 2007 - 08:22:25 PDT)
- Daniel Oehme (Thu Apr 19 2007 - 21:46:14 PDT)
AMBER: QM/MM simulation with SCC-DFTB
- Gustavo Seabra (Tue Apr 24 2007 - 03:48:11 PDT)
- 한재범 (Tue Apr 24 2007 - 01:19:25 PDT)
AMBER: QM/MM Umbrella sampling
- Jerome.GOLEBIOWSKI.unice.fr (Sat Apr 28 2007 - 00:55:49 PDT)
- Ross Walker (Fri Apr 27 2007 - 15:01:46 PDT)
- Jason DeChancie (Fri Apr 27 2007 - 13:53:08 PDT)
AMBER: QMMM with printcharges
- Ross Walker (Thu Apr 19 2007 - 09:42:15 PDT)
- Kijeong Kwac (Thu Apr 19 2007 - 08:42:38 PDT)
- Ross Walker (Tue Apr 17 2007 - 14:37:27 PDT)
- Kijeong Kwac (Fri Apr 13 2007 - 17:37:45 PDT)
AMBER: Question about MMPBSA v9
- Cenk Andac (Wed Apr 11 2007 - 03:38:12 PDT)
- David A. Case (Tue Apr 10 2007 - 19:20:58 PDT)
- Cenk Andac (Mon Apr 09 2007 - 03:54:39 PDT)
AMBER: regarding frcmod file
- David A. Case (Thu Apr 19 2007 - 09:14:03 PDT)
- Gustavo Seabra (Thu Apr 19 2007 - 08:50:44 PDT)
- Santanu Roy (Thu Apr 19 2007 - 08:28:01 PDT)
AMBER: Regarding Simulated Annealing
- Ross Walker (Tue Apr 03 2007 - 08:43:55 PDT)
- Anju Sharma (Tue Apr 03 2007 - 05:27:18 PDT)
AMBER: Release of the R.E.D.-III tools
- FyD (Sun Apr 15 2007 - 03:10:25 PDT)
AMBER: Request for addition of a useful command in ptraj module of AMBER
- Cenk Andac (Tue Apr 17 2007 - 10:18:30 PDT)
AMBER: Request for addition of a useful command in ptraj module of AMBER #2
- Vlad Cojocaru (Tue Apr 24 2007 - 01:30:40 PDT)
- Cenk Andac (Mon Apr 23 2007 - 15:35:36 PDT)
- Melinda Layten (Mon Apr 23 2007 - 14:52:26 PDT)
- Cenk Andac (Tue Apr 17 2007 - 10:24:37 PDT)
AMBER: restraint command not taken
- Vlad Cojocaru (Mon Apr 02 2007 - 09:57:37 PDT)
- deepti nayar (Mon Apr 02 2007 - 02:54:44 PDT)
- deepti nayar (Mon Apr 02 2007 - 02:25:12 PDT)
- Vlad Cojocaru (Mon Apr 02 2007 - 09:16:16 PDT)
- deepti nayar (Mon Apr 02 2007 - 03:21:51 PDT)
AMBER: restraint value: written but none specified
- Ben Sattelle (Fri Apr 20 2007 - 16:05:47 PDT)
- Ross Walker (Fri Apr 20 2007 - 15:37:01 PDT)
- Ben Sattelle (Fri Apr 20 2007 - 15:08:55 PDT)
- Ben Sattelle (Fri Apr 20 2007 - 14:51:30 PDT)
- David A. Case (Fri Apr 20 2007 - 14:15:05 PDT)
- Chris Moth (Fri Apr 20 2007 - 14:16:52 PDT)
- Ben Sattelle (Fri Apr 20 2007 - 13:42:56 PDT)
AMBER: Restraints and free energy
- David A. Case (Fri Apr 13 2007 - 10:22:49 PDT)
- Sophie Barbe (Fri Apr 13 2007 - 09:05:06 PDT)
AMBER: rigid epoxide substrate
- David A. Case (Fri Apr 20 2007 - 08:30:42 PDT)
- Dr M. Blomberg (Fri Apr 20 2007 - 04:24:13 PDT)
AMBER: sander (AMBER 9) and -y flag -- not working?
- David Mobley (Tue Apr 10 2007 - 12:31:56 PDT)
- Carlos Simmerling (Tue Apr 10 2007 - 12:10:41 PDT)
- David Mobley (Tue Apr 10 2007 - 12:04:52 PDT)
- David Mobley (Tue Apr 10 2007 - 11:52:29 PDT)
- Chris Moth (Tue Apr 10 2007 - 11:36:22 PDT)
- David Mobley (Tue Apr 10 2007 - 11:22:39 PDT)
AMBER: sander bomb
- Ross Walker (Tue Apr 03 2007 - 08:35:40 PDT)
- janavi raghavan (Tue Apr 03 2007 - 07:28:39 PDT)
AMBER: Sander Bomb in subroutine nonbond_list
- Jingyuan Luke (Mon Apr 09 2007 - 19:34:51 PDT)
AMBER: Sander BOMB.. simulation terminates by itself...
- Vijay Manickam Achari (Wed Apr 18 2007 - 18:24:28 PDT)
AMBER: SANDER PMEMD ntpr ntwx discrepancy (?bug? report)
- Chris Moth (Mon Apr 09 2007 - 10:32:35 PDT)
- David A. Case (Fri Apr 06 2007 - 15:37:46 PDT)
- Chris Moth (Fri Apr 06 2007 - 14:07:17 PDT)
AMBER: Sander....
- Ross Walker (Tue Apr 03 2007 - 08:28:51 PDT)
- Rita Cassia (Tue Apr 03 2007 - 01:23:06 PDT)
AMBER: signal SIGSEGV(11)
- Ross Walker (Tue Apr 24 2007 - 12:43:49 PDT)
- Pankaj R. Daga (Tue Apr 24 2007 - 07:55:14 PDT)
- Chris Moth (Wed Apr 18 2007 - 13:22:58 PDT)
- Pankaj R. Daga (Wed Apr 18 2007 - 12:16:48 PDT)
- Ross Walker (Wed Apr 18 2007 - 09:09:10 PDT)
- David A. Case (Wed Apr 18 2007 - 08:49:24 PDT)
- Pankaj R. Daga (Wed Apr 18 2007 - 08:25:55 PDT)
AMBER: single solvated glycine simulation - zwitterion, cation, anion parameters?
- Nicolas Lux Fawzi (Tue Apr 17 2007 - 12:00:18 PDT)
AMBER: single solvated glycine simulation - zwitterion, cation, anion parameters? 2nd try
- Pradipta Bandyopadhyay (Tue Apr 17 2007 - 21:33:52 PDT)
- Nicolas Lux Fawzi (Tue Apr 17 2007 - 14:50:07 PDT)
AMBER: supplement ptraj:problems with time correlation calculation (comp. with NMR experiments)
- David A. Case (Mon Apr 09 2007 - 07:56:56 PDT)
- anna.schrey.gmx.de (Sun Apr 08 2007 - 07:15:22 PDT)
AMBER: temperature artifacts with andersen and GB?
- David Mobley (Wed Apr 11 2007 - 09:50:17 PDT)
AMBER: thermodynamic integration
- David A. Case (Sat Apr 28 2007 - 14:26:28 PDT)
- Servaas Michielssens (Sat Apr 28 2007 - 10:48:10 PDT)
AMBER: topology for postprocessed files?
- anna.schrey.gmx.de (Wed Apr 18 2007 - 10:40:51 PDT)
- anna.schrey.gmx.de (Thu Apr 12 2007 - 03:42:41 PDT)
- Vlad Cojocaru (Thu Apr 12 2007 - 03:07:08 PDT)
- anna.schrey.gmx.de (Thu Apr 12 2007 - 02:57:28 PDT)
AMBER: using glycam04 parameters
- kkirschn.hamilton.edu (Wed Apr 25 2007 - 13:02:49 PDT)
- Ross Walker (Thu Apr 19 2007 - 12:00:01 PDT)
- Sara Alexandra Moura (Thu Apr 19 2007 - 11:35:16 PDT)
- kkirschn.hamilton.edu (Thu Apr 19 2007 - 10:53:37 PDT)
- Sara Alexandra Moura (Thu Apr 19 2007 - 09:27:38 PDT)
- Austin B. Yongye (Wed Apr 18 2007 - 09:03:35 PDT)
- David A. Case (Wed Apr 18 2007 - 08:28:27 PDT)
- Sara Alexandra Moura (Wed Apr 18 2007 - 08:10:35 PDT)
- Sara Alexandra Moura (Wed Apr 18 2007 - 07:59:10 PDT)
- Austin B. Yongye (Wed Apr 18 2007 - 06:24:38 PDT)
- FyD (Wed Apr 18 2007 - 03:57:02 PDT)
- David A. Case (Tue Apr 17 2007 - 14:37:35 PDT)
- Sara Alexandra Moura (Tue Apr 17 2007 - 12:17:44 PDT)
AMBER: Vlad has Tagged you! :)
- Vlad Cojocaru (Mon Apr 09 2007 - 03:06:37 PDT)
AMBER: vmd and amber
- Gustavo Seabra (Tue Apr 17 2007 - 05:33:48 PDT)
- deepti nayar (Tue Apr 17 2007 - 04:58:51 PDT)
AMBER: Work with constand pH
- Myunggi Yi (Fri Apr 27 2007 - 18:42:32 PDT)
- tri nam Vo (Thu Apr 26 2007 - 20:37:53 PDT)
- Myunggi Yi (Wed Apr 25 2007 - 06:49:59 PDT)
- tri nam Vo (Wed Apr 25 2007 - 01:13:05 PDT)
AMBER: working with Antechamber
- David A. Case (Wed Apr 11 2007 - 12:56:00 PDT)
- Atila Iamarino (Wed Apr 11 2007 - 11:59:03 PDT)
- David Mobley (Wed Apr 11 2007 - 11:34:55 PDT)
- Atila Iamarino (Wed Apr 11 2007 - 10:45:20 PDT)
AMBER: Xleap errors
- David A. Case (Mon Apr 02 2007 - 10:32:47 PDT)
- Beale, John (Mon Apr 02 2007 - 10:20:43 PDT)
AMBER:a question about RMSD
- Carlos Simmerling (Tue Apr 24 2007 - 06:06:40 PDT)
dihedral term charge dependence
- Kateryna Miroshnychenko (Tue Apr 03 2007 - 06:59:08 PDT)
- Carlos Simmerling (Mon Apr 02 2007 - 09:14:15 PDT)
- Williamson, Mark (Mon Apr 02 2007 - 09:07:29 PDT)
MM-PBSA amber script problem
- David A. Case (Tue Apr 17 2007 - 14:35:59 PDT)
- odde (Tue Apr 17 2007 - 11:45:06 PDT)
parameter
- Ross Walker (Wed Apr 04 2007 - 08:18:07 PDT)

Amber Archive Apr 2007 by subject