AMBER Archive (2009) - Jul 2009 By Subject

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About this archive

Starting: Wed Jul 01 2009 - 04:17:51 CDT
Ending: Fri Jul 31 2009 - 22:33:10 CDT

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- vitor.felix (Tue Jul 21 2009 - 22:15:06 CDT)
[AMBER] (no subject)
- gunajyoti das (Sun Jul 19 2009 - 10:13:01 CDT)
- gunajyoti das (Sun Jul 19 2009 - 10:14:20 CDT)
- Beale, John (Mon Jul 13 2009 - 12:35:46 CDT)
[AMBER] -a flag :RESP
- Jio M (Sun Jul 19 2009 - 05:48:20 CDT)
[AMBER] [ALERT]: It's the time to come out on streets and stop the complete nation on it's place - Take immediate actions at once with full force.
- Organization (Wed Jul 22 2009 - 14:13:37 CDT)
[AMBER] Acetylate and Amidate
- Carlos Simmerling (Thu Jul 09 2009 - 06:52:28 CDT)
- Bill Ross (Wed Jul 08 2009 - 18:13:09 CDT)
- Alison Saunders (Wed Jul 08 2009 - 17:47:59 CDT)
- Carlos Simmerling (Wed Jul 08 2009 - 17:22:58 CDT)
- Alison Saunders (Wed Jul 08 2009 - 17:19:44 CDT)
[AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S"
- Bill Ross (Wed Jul 15 2009 - 11:53:41 CDT)
- Sushil Mishra (Wed Jul 15 2009 - 08:58:13 CDT)
- Shubhra Gupta (Wed Jul 15 2009 - 07:38:34 CDT)
- Sushil Mishra (Wed Jul 15 2009 - 05:36:26 CDT)
[AMBER] Am I doing the right thing
- nicholus bhattacharjee (Tue Jul 28 2009 - 23:36:31 CDT)
- Ashish Runthala (Tue Jul 28 2009 - 22:44:59 CDT)
- Bill Ross (Tue Jul 28 2009 - 21:39:48 CDT)
- Ashish Runthala (Tue Jul 28 2009 - 20:35:09 CDT)
- nicholus bhattacharjee (Tue Jul 28 2009 - 12:20:57 CDT)
[AMBER] amber dihedral format
- case (Sun Jul 12 2009 - 16:49:12 CDT)
- s. Bill (Sun Jul 12 2009 - 09:05:23 CDT)
[AMBER] AMBER windows version ?
- Siddharth Rastogi (Thu Jul 09 2009 - 18:17:33 CDT)
- Ross Walker (Thu Jul 09 2009 - 17:45:49 CDT)
- Siddharth Rastogi (Thu Jul 09 2009 - 16:14:05 CDT)
[AMBER] amber10 installation problem
- Lan JIN (Fri Jul 10 2009 - 02:41:34 CDT)
- case (Thu Jul 09 2009 - 07:38:01 CDT)
- Lan JIN (Wed Jul 08 2009 - 21:46:22 CDT)
- case (Wed Jul 08 2009 - 06:56:19 CDT)
- Lan JIN (Wed Jul 08 2009 - 01:49:05 CDT)
[AMBER] amber10 parallel compiling error
- nam kim (Thu Jul 23 2009 - 23:32:14 CDT)
- case (Wed Jul 22 2009 - 21:15:50 CDT)
- nam kim (Tue Jul 21 2009 - 12:06:32 CDT)
- Toshifumi Yui (Tue Jul 21 2009 - 00:46:11 CDT)
- nam kim (Mon Jul 20 2009 - 17:53:24 CDT)
- nam kim (Mon Jul 20 2009 - 13:34:41 CDT)
- nam kim (Mon Jul 20 2009 - 13:15:16 CDT)
- Ross Walker (Mon Jul 20 2009 - 12:33:08 CDT)
- nam kim (Mon Jul 20 2009 - 12:24:14 CDT)
- nam kim (Sat Jul 18 2009 - 12:19:39 CDT)
- Ross Walker (Thu Jul 16 2009 - 22:43:15 CDT)
- Nam Kim (Thu Jul 16 2009 - 19:50:57 CDT)
[AMBER] Amber10, Serial compilation with ifort
- Ross Walker (Sun Jul 12 2009 - 16:41:07 CDT)
- Aldo Humberto Romero (Sun Jul 12 2009 - 15:57:40 CDT)
[AMBER] amber9 in fedora10
- Bala subramanian (Thu Jul 02 2009 - 03:05:55 CDT)
- Bala subramanian (Thu Jul 02 2009 - 02:02:54 CDT)
- Ross Walker (Wed Jul 01 2009 - 11:36:33 CDT)
- Bala subramanian (Wed Jul 01 2009 - 09:09:15 CDT)
[AMBER] ambpdb problem
- Ashish Runthala (Fri Jul 31 2009 - 20:28:42 CDT)
- Jordan Monnet (Fri Jul 31 2009 - 09:30:54 CDT)
- Jio M (Fri Jul 31 2009 - 02:11:32 CDT)
- Ashish Runthala (Thu Jul 30 2009 - 22:44:10 CDT)
- Jordan Monnet (Thu Jul 30 2009 - 14:32:57 CDT)
- Jio M (Thu Jul 30 2009 - 14:12:10 CDT)
[AMBER] amino acids caps for truncated proteins
- FyD (Thu Jul 16 2009 - 11:58:32 CDT)
- Andrew Voronkov (Thu Jul 16 2009 - 11:31:18 CDT)
[AMBER] analysis of QM/MM - LCOD
- Aust, Susanne (Fri Jul 03 2009 - 04:51:34 CDT)
[AMBER] antechamber
- R. A. (Thu Jul 02 2009 - 19:35:42 CDT)
- Alan (Thu Jul 02 2009 - 05:16:55 CDT)
- FyD (Thu Jul 02 2009 - 01:33:46 CDT)
- R. A. (Wed Jul 01 2009 - 19:46:19 CDT)
- FyD (Wed Jul 01 2009 - 07:26:39 CDT)
- gilbert_at_bluemarble.net (Wed Jul 01 2009 - 07:11:17 CDT)
- case (Wed Jul 01 2009 - 07:04:02 CDT)
- Alan (Wed Jul 01 2009 - 06:37:40 CDT)
- R. A. (Wed Jul 01 2009 - 04:19:54 CDT)
- R. A. (Wed Jul 01 2009 - 04:17:51 CDT)
[AMBER] Antechamber prep question
- FyD (Fri Jul 10 2009 - 10:24:08 CDT)
- Andrew Olson (Fri Jul 10 2009 - 08:33:09 CDT)
- gilbert_at_bluemarble.net (Fri Jul 10 2009 - 08:10:32 CDT)
- FyD (Fri Jul 10 2009 - 00:52:12 CDT)
- case (Thu Jul 09 2009 - 13:54:44 CDT)
- Andrew Olson (Thu Jul 09 2009 - 12:00:19 CDT)
- case (Thu Jul 09 2009 - 11:48:44 CDT)
- Andrew Olson (Thu Jul 09 2009 - 10:22:18 CDT)
- case (Thu Jul 09 2009 - 10:16:17 CDT)
- Andrew Olson (Thu Jul 09 2009 - 09:39:25 CDT)
[AMBER] Average structure over simulation
- Olotu Odunayo (Mon Jul 27 2009 - 08:38:59 CDT)
[AMBER] Boundary Condition Problem
- case (Sat Jul 04 2009 - 08:45:45 CDT)
- Pepe` Falahat (Sat Jul 04 2009 - 07:10:59 CDT)
[AMBER] Box shape change
- Hemant Kumar (Sun Jul 19 2009 - 12:38:43 CDT)
- Carlos Simmerling (Sun Jul 19 2009 - 08:51:44 CDT)
- Hemant Kumar (Sun Jul 19 2009 - 07:05:04 CDT)
- Carlos Simmerling (Sun Jul 19 2009 - 06:40:03 CDT)
- Hemant Kumar (Sun Jul 19 2009 - 06:00:18 CDT)
- Carlos Simmerling (Sat Jul 18 2009 - 20:35:41 CDT)
- Hemant Kumar (Sat Jul 18 2009 - 14:38:46 CDT)
[AMBER] bug in antechamber
- David Mobley (Wed Jul 08 2009 - 11:19:12 CDT)
[AMBER] bugfix 10 failing for ambertools1.2
- Alan (Mon Jul 20 2009 - 03:14:16 CDT)
[AMBER] calculation of binding energy for lectin and fucuse..
- Sushil Mishra (Fri Jul 10 2009 - 13:26:20 CDT)
[AMBER] calculation of the solvent accessibility
- Rilei Yu (Sat Jul 04 2009 - 03:54:23 CDT)
[AMBER] Can I get the torsion angle between base-pairs using ptraj ?
- Jordan Monnet (Wed Jul 15 2009 - 17:56:12 CDT)
- Myeong Lee (Wed Jul 15 2009 - 16:51:02 CDT)
[AMBER] carbonic anhydrase (CA) simulation
- case (Thu Jul 16 2009 - 06:36:17 CDT)
- vhakkim boy (Thu Jul 16 2009 - 02:03:23 CDT)
[AMBER] charge not zero on group: RESP
- Ben Roberts (Sat Jul 18 2009 - 07:45:10 CDT)
- Jio M (Sat Jul 18 2009 - 00:14:58 CDT)
[AMBER] charged or not
- case (Thu Jul 09 2009 - 10:10:14 CDT)
- s. Bill (Thu Jul 09 2009 - 07:33:05 CDT)
[AMBER] charges in topology file
- Carlos Simmerling (Fri Jul 10 2009 - 11:36:30 CDT)
- Jeffrey (Fri Jul 10 2009 - 11:20:01 CDT)
[AMBER] command for RESP fitting
- bharat lakhani (Mon Jul 20 2009 - 02:01:23 CDT)
- FyD (Thu Jul 16 2009 - 09:34:28 CDT)
- bharat lakhani (Thu Jul 16 2009 - 02:10:33 CDT)
[AMBER] Compilation error with pmemd (amber10) on fedora9 64 bits
- Nicolas SAPAY (Fri Jul 31 2009 - 07:55:18 CDT)
- Robert Duke (Fri Jul 31 2009 - 07:33:52 CDT)
- Nicolas SAPAY (Fri Jul 31 2009 - 04:41:21 CDT)
[AMBER] Compiling AMBER 10 (parallel, MPICH2) on Mac OS X Intel w/gcc, ifort, icc
- David Watson (Thu Jul 23 2009 - 15:03:59 CDT)
[AMBER] Compiling Amber 10 (serial) on Mac OS X 10.5.7 w/ gcc, Intel Fortan 11.0 and MKL 10.0
- Scott Brozell (Wed Jul 22 2009 - 14:52:59 CDT)
- David Watson (Tue Jul 21 2009 - 16:20:36 CDT)
[AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits
- David Watson (Thu Jul 30 2009 - 14:10:39 CDT)
- Alan (Thu Jul 30 2009 - 08:39:03 CDT)
- David Watson (Wed Jul 29 2009 - 11:21:50 CDT)
- Alan (Wed Jul 29 2009 - 11:00:42 CDT)
[AMBER] Coordinate resetting (SHAKE) cannot be accomplished,
- steinbrt_at_rci.rutgers.edu (Thu Jul 16 2009 - 04:01:15 CDT)
- Zhongjie Liang (Thu Jul 16 2009 - 03:37:29 CDT)
[AMBER] Could not find bond parameter for O2 - ca
- Yogesh Aher (Fri Jul 17 2009 - 01:37:52 CDT)
- case (Tue Jul 14 2009 - 22:28:02 CDT)
- Yogesh Aher (Tue Jul 14 2009 - 07:53:35 CDT)
[AMBER] Could not find type: MG Parameter file was not saved.
- Mannan (Sat Jul 25 2009 - 22:41:24 CDT)
[AMBER] Could not find type: MG Parameter file was not saved. though it was loaded
- FyD (Mon Jul 27 2009 - 00:03:00 CDT)
- Mannan (Sun Jul 26 2009 - 22:49:54 CDT)
[AMBER] Counterion release and Free energy of binding ?
- Marek Maly (Fri Jul 17 2009 - 06:10:40 CDT)
- case (Tue Jul 14 2009 - 22:10:18 CDT)
- Marek Maly (Tue Jul 14 2009 - 17:27:18 CDT)
[AMBER] cpin error
- Rukman Hertadi (Tue Jul 28 2009 - 00:22:18 CDT)
- case (Fri Jul 24 2009 - 14:41:00 CDT)
- Rukman Hertadi (Fri Jul 24 2009 - 02:18:52 CDT)
[AMBER] DCCM
- Duggan, Brendan M. (Wed Jul 15 2009 - 11:06:57 CDT)
- Raja Pandian (Tue Jul 07 2009 - 06:05:20 CDT)
[AMBER] default integration scheme in 7 vs. 10
- case (Thu Jul 02 2009 - 06:37:17 CDT)
- Ross Walker (Wed Jul 01 2009 - 16:29:12 CDT)
- Paul Brandt (Wed Jul 01 2009 - 15:48:46 CDT)
[AMBER] Different machines
- Ross Walker (Sun Jul 19 2009 - 11:28:52 CDT)
- s. Bill (Sun Jul 19 2009 - 04:55:48 CDT)
[AMBER] different results for antechamber/mopac for the same input
- case (Thu Jul 16 2009 - 06:30:08 CDT)
- Alan (Wed Jul 15 2009 - 17:05:07 CDT)
[AMBER] diffusion coeficients
- felix (Fri Jul 17 2009 - 08:41:43 CDT)
- case (Fri Jul 17 2009 - 06:59:41 CDT)
- felix (Fri Jul 17 2009 - 03:15:35 CDT)
[AMBER] Directory - GAFF Parameter File?
- Patrick Gedeon (Mon Jul 06 2009 - 18:31:49 CDT)
[AMBER] Disappearing common atoms in Amber 10 with TI
- steinbrt_at_rci.rutgers.edu (Mon Jul 20 2009 - 07:05:24 CDT)
- Khavrutskii, Ilja (Mon Jul 20 2009 - 06:46:38 CDT)
- case (Fri Jul 17 2009 - 06:41:39 CDT)
- steinbrt_at_rci.rutgers.edu (Fri Jul 17 2009 - 03:53:19 CDT)
- Khavrutskii, Ilja (Thu Jul 16 2009 - 16:02:10 CDT)
- steinbrt_at_rci.rutgers.edu (Thu Jul 16 2009 - 09:09:39 CDT)
- Khavrutskii, Ilja (Thu Jul 16 2009 - 08:38:43 CDT)
[AMBER] DNA + intercalator
- Ashish Runthala (Fri Jul 24 2009 - 22:12:27 CDT)
- Bill Ross (Fri Jul 24 2009 - 18:03:06 CDT)
- Rodrigo Galindo (Fri Jul 24 2009 - 17:22:35 CDT)
[AMBER] EPtot for Alpha-L- methyl fucose
- Sushil Mishra (Fri Jul 10 2009 - 09:12:28 CDT)
- Carlos Simmerling (Fri Jul 10 2009 - 08:57:34 CDT)
- Sushil Mishra (Fri Jul 10 2009 - 08:47:26 CDT)
[AMBER] Equilibration step
- Olotu Odunayo (Thu Jul 23 2009 - 01:52:50 CDT)
- Tom Joseph (Wed Jul 22 2009 - 14:05:58 CDT)
- Olotu Odunayo (Wed Jul 22 2009 - 11:46:12 CDT)
- Olotu Odunayo (Wed Jul 22 2009 - 11:41:13 CDT)
- Tom Joseph (Wed Jul 22 2009 - 07:35:15 CDT)
- Olotu Odunayo (Wed Jul 22 2009 - 04:47:37 CDT)
[AMBER] Equilibrium water density
- case (Wed Jul 15 2009 - 14:53:54 CDT)
- Myeong Lee (Wed Jul 15 2009 - 03:58:52 CDT)
[AMBER] equivalent atoms
- Ye MEI (Mon Jul 20 2009 - 23:56:52 CDT)
[AMBER] error in antechamber
- Qinghua Liao (Tue Jul 28 2009 - 00:13:49 CDT)
- case (Mon Jul 27 2009 - 23:23:54 CDT)
- Qinghua Liao (Mon Jul 27 2009 - 20:02:26 CDT)
- Mengjuei Hsieh (Mon Jul 27 2009 - 17:29:06 CDT)
- Qinghua Liao (Mon Jul 27 2009 - 06:57:50 CDT)
[AMBER] Error in Sander Output File
- Alison Saunders (Tue Jul 28 2009 - 12:00:12 CDT)
[AMBER] errors of PMEMD installation
- Mengjuei Hsieh (Sat Jul 25 2009 - 22:10:11 CDT)
- Mengjuei Hsieh (Thu Jul 23 2009 - 14:25:27 CDT)
- å»–é’åŽ (Wed Jul 22 2009 - 09:28:45 CDT)
[AMBER] ESP charges of Fe4S4
- subarna thakur (Wed Jul 22 2009 - 00:19:48 CDT)
[AMBER] Exclamation marks in trajectory
- Ross Walker (Mon Jul 13 2009 - 14:20:37 CDT)
- Hugh Heldenbrand (Mon Jul 13 2009 - 13:52:37 CDT)
- Ross Walker (Mon Jul 13 2009 - 13:13:17 CDT)
- Hugh Heldenbrand (Mon Jul 13 2009 - 10:16:26 CDT)
[AMBER] ff parameters
- case (Thu Jul 09 2009 - 08:23:31 CDT)
- oguz gurbulak (Wed Jul 08 2009 - 09:35:40 CDT)
[AMBER] File conversion for from Amber to Charmm
- case (Fri Jul 17 2009 - 06:53:06 CDT)
- Yogesh Aher (Fri Jul 17 2009 - 01:45:11 CDT)
[AMBER] file truncated : Output file truncated during equilibration of salivated complex in MM-PBSA
- Sushil Mishra (Mon Jul 20 2009 - 07:26:27 CDT)
[AMBER] GAFF and NME, ACE terminal res
- FyD (Thu Jul 16 2009 - 01:25:03 CDT)
- Jio M (Wed Jul 15 2009 - 23:29:08 CDT)
- FyD (Tue Jul 14 2009 - 02:40:00 CDT)
- Jio M (Mon Jul 13 2009 - 15:51:06 CDT)
[AMBER] H-bond vs. VdW
- case (Mon Jul 06 2009 - 12:29:49 CDT)
- Cihan Aydin (Mon Jul 06 2009 - 10:13:39 CDT)
- FyD (Sat Jul 04 2009 - 00:01:58 CDT)
- Taufik Al-Sarraj (Fri Jul 03 2009 - 13:48:12 CDT)
[AMBER] help needed for HID
- FyD (Mon Jul 13 2009 - 15:27:13 CDT)
- Marius Retegan (Sun Jul 12 2009 - 13:24:40 CDT)
- s. Bill (Sun Jul 12 2009 - 13:16:08 CDT)
[AMBER] Holding ligand rigid for minimization
- Andrew Olson (Tue Jul 14 2009 - 13:23:31 CDT)
- Andrew Olson (Tue Jul 14 2009 - 10:23:01 CDT)
- Andrew Olson (Tue Jul 14 2009 - 10:14:38 CDT)
[AMBER] how to choose exclusion policy for GPCR
- xueqin pang (Tue Jul 28 2009 - 21:12:33 CDT)
[AMBER] How to fix specific atoms? (not residue)
- Tom Joseph (Sat Jul 11 2009 - 17:01:04 CDT)
- Myeong Lee (Sat Jul 11 2009 - 06:46:06 CDT)
[AMBER] how to launch XLEaP from SSH Secure Shell?
- Thomas Patko (Wed Jul 22 2009 - 19:47:51 CDT)
- David Watson (Wed Jul 22 2009 - 19:30:12 CDT)
- Tom Joseph (Wed Jul 22 2009 - 18:24:56 CDT)
- Robert Duke (Wed Jul 22 2009 - 18:07:24 CDT)
- Yana Berezovskaya (Wed Jul 22 2009 - 17:44:45 CDT)
[AMBER] How to read md trajectory for each time slice as an input coordinate
- Myeong Lee (Mon Jul 27 2009 - 03:16:47 CDT)
[AMBER] How to visualize PCA results without IED?
- Shozeb Haider (Tue Jul 28 2009 - 06:02:22 CDT)
- Vlad Cojocaru (Tue Jul 28 2009 - 05:42:05 CDT)
- Hannes Loeffler (Tue Jul 28 2009 - 05:12:04 CDT)
- Vlad Cojocaru (Tue Jul 28 2009 - 04:58:50 CDT)
- Catein Catherine (Tue Jul 28 2009 - 04:30:22 CDT)
[AMBER] IDIVF and PN
- Ross Walker (Thu Jul 16 2009 - 22:40:11 CDT)
- s. Bill (Thu Jul 16 2009 - 07:11:27 CDT)
[AMBER] IGB=7 vs IGB=5
- Carlos Simmerling (Tue Jul 21 2009 - 08:51:22 CDT)
[AMBER] implicit solvent (GB version2) MD simulation
- Carlos Simmerling (Fri Jul 10 2009 - 10:57:57 CDT)
- workalemahu berhanu (Fri Jul 10 2009 - 10:53:47 CDT)
[AMBER] Installing Amber10 on Ubuntu
- Rodrigo Galindo (Wed Jul 29 2009 - 14:49:33 CDT)
- David Dubins (Wed Jul 29 2009 - 13:50:12 CDT)
[AMBER] Installing of amber10
- case (Wed Jul 08 2009 - 06:42:02 CDT)
- Rilei Yu (Wed Jul 08 2009 - 03:34:24 CDT)
[AMBER] installing of amber10 problem
- Rilei Yu (Wed Jul 08 2009 - 03:47:13 CDT)
[AMBER] Is rmsd ~ 3 A reasonable for a 4ns simulation?
- Catein Catherine (Wed Jul 08 2009 - 04:45:41 CDT)
[AMBER] Langevin Dynamics in AMBER10
- Carlos Simmerling (Fri Jul 24 2009 - 07:01:28 CDT)
- Biswaranjan Meher (Thu Jul 23 2009 - 18:12:59 CDT)
- Carlos Simmerling (Thu Jul 23 2009 - 16:57:44 CDT)
- Biswaranjan Meher (Thu Jul 23 2009 - 16:54:58 CDT)
[AMBER] Leap Questions...
- Ross Walker (Sun Jul 05 2009 - 23:01:34 CDT)
- Cihan Aydin (Sat Jul 04 2009 - 20:41:39 CDT)
[AMBER] ligand/protein minimization
- Andrew Olson (Mon Jul 13 2009 - 12:10:18 CDT)
- case (Mon Jul 13 2009 - 11:29:06 CDT)
- Andrew Olson (Mon Jul 13 2009 - 10:53:11 CDT)
- case (Sun Jul 12 2009 - 21:32:29 CDT)
- Andrew Olson (Fri Jul 10 2009 - 16:00:26 CDT)
[AMBER] loading a mol2 file in xleap
- FyD (Mon Jul 27 2009 - 08:44:50 CDT)
- vallespardojl_at_chem.leidenuniv.nl (Mon Jul 27 2009 - 07:40:13 CDT)
- FyD (Fri Jul 24 2009 - 15:00:41 CDT)
- vallespardojl_at_chem.leidenuniv.nl (Fri Jul 24 2009 - 12:40:13 CDT)
[AMBER] mailing list
- Qinghua Liao (Thu Jul 23 2009 - 20:45:50 CDT)
[AMBER] Manganese
- Chunliyan (Fri Jul 10 2009 - 08:39:51 CDT)
[AMBER] Manganese bondi radii
- Chunliyan (Fri Jul 10 2009 - 08:39:51 CDT)
[AMBER] Manganese bondi radii for mm/pbsa calculation
- Chunliyan (Fri Jul 10 2009 - 08:39:51 CDT)
[AMBER] manganese bondi radii for mm_pbsa calculation
- Chunliyan (Fri Jul 10 2009 - 08:39:51 CDT)
[AMBER] Metalloproteins - Ligand Protonation
- s. Bill (Fri Jul 31 2009 - 13:01:42 CDT)
[AMBER] missing Halogen parameters (radii) for PBSA/GBSA calculations - PB Bomb in pb_aaradi(): No radius assigned for atom
- suhaib sh (Thu Jul 02 2009 - 08:18:05 CDT)
[AMBER] MM-PBSA cannot finish without error message.
- Catein Catherine (Thu Jul 23 2009 - 04:57:00 CDT)
[AMBER] MM-PBSA delphi.crg and delphi.siz
- Manish Kumar (Wed Jul 08 2009 - 16:29:40 CDT)
[AMBER] MM-PBSA problem
- Giorgos Lamprinidis (Mon Jul 06 2009 - 03:07:14 CDT)
- Rubben Torella (Fri Jul 03 2009 - 08:57:09 CDT)
- Giorgos Lamprinidis (Fri Jul 03 2009 - 08:50:36 CDT)
[AMBER] MM-PBSA tail: equil.out: file truncated during equilibration of salivated complex
- Sushil Mishra (Mon Jul 20 2009 - 03:32:32 CDT)
[AMBER] MM/PBSA, MM/GBSA and NMODE Analysis
- Ray Luo (Wed Jul 29 2009 - 19:25:14 CDT)
- Matthias Negri (Wed Jul 29 2009 - 05:55:46 CDT)
[AMBER] Molecular Modeling Workshop and Model(l)ing'09 in Erlangen, Germany
- Harald Lanig (Tue Jul 14 2009 - 09:02:16 CDT)
[AMBER] MPI error
- Robert Duke (Wed Jul 29 2009 - 07:05:57 CDT)
- vhakkim boy (Wed Jul 29 2009 - 04:44:35 CDT)
[AMBER] MPI process terminated unexpectedly forrtl: error (69): process interrupted (SIGINT)
- Ross Walker (Wed Jul 08 2009 - 10:01:24 CDT)
- Andrew Voronkov (Wed Jul 08 2009 - 05:05:52 CDT)
- Andrew Voronkov (Wed Jul 08 2009 - 04:39:03 CDT)
[AMBER] mpirun noticed that process rank 1 ... on signal 1 (Hangup).
- Naser Alijabbari (Tue Jul 14 2009 - 05:41:39 CDT)
[AMBER] nasty memory bug in calculatePrincipalAxis
- Hannes Loeffler (Mon Jul 20 2009 - 03:30:38 CDT)
[AMBER] need charges of FE-S cluster
- Markus Kaukonen (Tue Jul 21 2009 - 13:50:39 CDT)
- case (Mon Jul 06 2009 - 07:35:19 CDT)
- subarna thakur (Mon Jul 06 2009 - 05:44:05 CDT)
[AMBER] Need help for PMEMD 10 installation
- Robert Duke (Tue Jul 14 2009 - 06:50:26 CDT)
- Giorgos Lamprinidis (Tue Jul 14 2009 - 02:29:09 CDT)
- Ross Walker (Mon Jul 13 2009 - 14:18:26 CDT)
- Jun Dong (Mon Jul 13 2009 - 13:10:34 CDT)
- Ross Walker (Fri Jul 10 2009 - 13:52:13 CDT)
- Jun Dong (Fri Jul 10 2009 - 12:25:03 CDT)
- Ross Walker (Fri Jul 10 2009 - 11:26:29 CDT)
- Jun Dong (Fri Jul 10 2009 - 11:05:49 CDT)
[AMBER] non standard residue
- FyD (Tue Jul 14 2009 - 15:01:32 CDT)
- FyD (Tue Jul 14 2009 - 01:47:00 CDT)
- FyD (Tue Jul 07 2009 - 02:50:09 CDT)
- Neha Gandhi (Mon Jul 06 2009 - 03:07:35 CDT)
[AMBER] Non-Standard Amino Acid Residue LEAP ERROR
- Ashish Runthala (Fri Jul 31 2009 - 20:39:54 CDT)
- Brothers, Michael Charles (Fri Jul 31 2009 - 12:36:10 CDT)
- Ashish Runthala (Thu Jul 30 2009 - 22:40:45 CDT)
- Brothers, Michael Charles (Thu Jul 30 2009 - 17:28:43 CDT)
[AMBER] nonbon.f question
- Carlos Simmerling (Mon Jul 27 2009 - 14:34:20 CDT)
- Rizwan Tai (Mon Jul 27 2009 - 14:30:12 CDT)
- Rizwan Tai (Mon Jul 20 2009 - 14:31:17 CDT)
[AMBER] Nonstandard molecules simulated with parm99EP ?
- Marek Maly (Wed Jul 01 2009 - 11:02:29 CDT)
- Marek Maly (Wed Jul 01 2009 - 10:47:04 CDT)
[AMBER] Normal mode analysis of water
- case (Thu Jul 30 2009 - 09:11:23 CDT)
- bharat lakhani (Thu Jul 30 2009 - 04:27:19 CDT)
[AMBER] ntt=3 and ibelly=1
- Kristina Furse (Fri Jul 17 2009 - 11:41:29 CDT)
- Ross Walker (Thu Jul 16 2009 - 22:44:47 CDT)
- Kristina Furse (Thu Jul 16 2009 - 11:07:23 CDT)
[AMBER] only ff94 and ff99 for GBSA?
- FyD (Tue Jul 28 2009 - 02:32:52 CDT)
- Andrew Voronkov (Tue Jul 28 2009 - 01:12:15 CDT)
- case (Mon Jul 27 2009 - 12:05:48 CDT)
- Andrew Voronkov (Mon Jul 27 2009 - 11:41:27 CDT)
[AMBER] ouput trajectory of only CA atom
- Jordan Monnet (Wed Jul 08 2009 - 11:03:32 CDT)
- Vlad Cojocaru (Wed Jul 08 2009 - 10:07:30 CDT)
- Bala subramanian (Wed Jul 08 2009 - 10:01:27 CDT)
- Carlos Simmerling (Wed Jul 08 2009 - 09:41:25 CDT)
- Bala subramanian (Wed Jul 08 2009 - 08:24:56 CDT)
[AMBER] Output file truncated during equilibration of salivated complex in MM-PBSA
- Sushil Mishra (Mon Jul 20 2009 - 05:40:51 CDT)
[AMBER] Output forces in Sander
- case (Mon Jul 27 2009 - 10:11:30 CDT)
- Frank X. Vázquez (Tue Jul 21 2009 - 16:58:36 CDT)
[AMBER] Patching terminal
- Manish Kumar (Tue Jul 21 2009 - 18:53:54 CDT)
[AMBER] PCA analysis: the first vector is the movement of whole molecule.
- Hannes Loeffler (Fri Jul 31 2009 - 02:27:54 CDT)
- Catein Catherine (Thu Jul 30 2009 - 22:46:49 CDT)
- Hannes Loeffler (Thu Jul 30 2009 - 05:52:48 CDT)
- Catein Catherine (Thu Jul 30 2009 - 05:37:49 CDT)
[AMBER] pdb file no bond and charges
- Jio M (Wed Jul 29 2009 - 01:28:48 CDT)
[AMBER] Peptide bond broken
- Syed Tarique Moin (Mon Jul 13 2009 - 08:20:02 CDT)
- Shubhra Gupta (Sun Jul 12 2009 - 23:17:31 CDT)
- case (Sun Jul 12 2009 - 21:35:35 CDT)
- FyD (Sat Jul 11 2009 - 01:58:06 CDT)
- Syed Tarique Moin (Fri Jul 10 2009 - 13:19:02 CDT)
[AMBER] Please help me out
- case (Wed Jul 15 2009 - 14:55:21 CDT)
- bharat lakhani (Wed Jul 15 2009 - 05:43:21 CDT)
[AMBER] PLUMED release 1.1.0 available
- Massimiliano Bonomi (Tue Jul 28 2009 - 03:10:39 CDT)
[AMBER] PMEMD in a Cygwin Environment
- Robert Duke (Tue Jul 14 2009 - 15:16:46 CDT)
- Hopkins, Robert (Tue Jul 14 2009 - 14:48:41 CDT)
[AMBER] PMEMD in a Cygwin Environment 8%
- Hopkins, Robert (Thu Jul 23 2009 - 15:37:12 CDT)
[AMBER] pmemd/bintraj and ifort 10.1.0.21
- Robert Duke (Wed Jul 01 2009 - 13:54:52 CDT)
- Peter Varnai (Wed Jul 01 2009 - 13:28:30 CDT)
[AMBER] position v time graph
- Shozeb Haider (Wed Jul 15 2009 - 13:21:35 CDT)
[AMBER] Principle Questions
- Ross Walker (Tue Jul 07 2009 - 18:42:42 CDT)
- s_bill36_at_yahoo.co.uk (Tue Jul 07 2009 - 02:50:53 CDT)
[AMBER] problem from xleap
- Ashish Runthala (Fri Jul 31 2009 - 22:33:10 CDT)
- Qinghua Liao (Fri Jul 31 2009 - 20:38:19 CDT)
- Tom Joseph (Fri Jul 31 2009 - 11:41:49 CDT)
- Qinghua Liao (Fri Jul 31 2009 - 09:38:18 CDT)
[AMBER] Problem with amber9 installation
- moitrayee_at_mbu.iisc.ernet.in (Tue Jul 14 2009 - 02:02:39 CDT)
- Ross Walker (Mon Jul 13 2009 - 22:34:54 CDT)
- moitrayee_at_mbu.iisc.ernet.in (Mon Jul 13 2009 - 15:31:18 CDT)
[AMBER] problem with energy calculations
- Carlos Simmerling (Sun Jul 12 2009 - 09:15:39 CDT)
- Thomas Lake (Sun Jul 12 2009 - 09:10:58 CDT)
- Carlos Simmerling (Sun Jul 12 2009 - 08:42:35 CDT)
- Lake, Thomas (Sun Jul 12 2009 - 08:35:33 CDT)
- Carlos Simmerling (Fri Jul 10 2009 - 12:25:56 CDT)
- Thomas Lake (Fri Jul 10 2009 - 11:13:55 CDT)
[AMBER] problem with the energetics of the system
- Mahmoud A. A. Ibrahim (Sun Jul 12 2009 - 05:37:37 CDT)
- Ross Walker (Sat Jul 11 2009 - 18:52:42 CDT)
- Mahmoud A. A. Ibrahim (Sat Jul 11 2009 - 18:23:13 CDT)
[AMBER] production phase
- Ross Walker (Thu Jul 16 2009 - 22:56:13 CDT)
- s. Bill (Thu Jul 16 2009 - 07:18:25 CDT)
[AMBER] Protonated or not
- Adrian Roitberg (Fri Jul 31 2009 - 12:32:50 CDT)
- s. Bill (Fri Jul 31 2009 - 12:15:32 CDT)
[AMBER] ptraj - cluster
- Cihan Aydin (Fri Jul 17 2009 - 09:22:37 CDT)
- Wei Huang (Fri Jul 17 2009 - 07:34:00 CDT)
- Cihan Aydin (Thu Jul 16 2009 - 00:55:07 CDT)
[AMBER] ptraj grid option
- Youn Kyeung Lee (Tue Jul 21 2009 - 02:15:11 CDT)
[AMBER] ptraj mask selection
- Patrick Gedeon (Mon Jul 13 2009 - 14:58:18 CDT)
- Jianyin Shao (Mon Jul 13 2009 - 14:02:03 CDT)
- case (Mon Jul 13 2009 - 13:10:46 CDT)
- Jianyin Shao (Mon Jul 13 2009 - 12:57:23 CDT)
- Patrick Gedeon (Sun Jul 12 2009 - 22:45:56 CDT)
[AMBER] ptraj-radial distribution function
- Christof Jaeger (Thu Jul 16 2009 - 03:22:02 CDT)
- Nancy (Thu Jul 16 2009 - 01:34:12 CDT)
[AMBER] pulling two atoms in SMD
- Santosh Mogurampelly (Tue Jul 28 2009 - 07:10:12 CDT)
[AMBER] QM/MM
- steinbrt_at_rci.rutgers.edu (Tue Jul 28 2009 - 02:19:32 CDT)
- s. Bill (Tue Jul 28 2009 - 01:44:15 CDT)
[AMBER] QMMM outupts
- Gustavo Seabra (Thu Jul 09 2009 - 11:58:30 CDT)
- Myeong Lee (Tue Jul 07 2009 - 12:13:27 CDT)
[AMBER] query
- Ashish Runthala (Fri Jul 31 2009 - 20:23:07 CDT)
- Pansy Patel (Fri Jul 31 2009 - 09:41:05 CDT)
- bharat lakhani (Fri Jul 31 2009 - 02:42:04 CDT)
[AMBER] query regarding FE4S4
- case (Thu Jul 16 2009 - 06:45:06 CDT)
- subarna thakur (Thu Jul 16 2009 - 02:14:27 CDT)
[AMBER] question of ibelly used in pmemd
- Kristina Furse (Tue Jul 21 2009 - 11:27:29 CDT)
- Robert Duke (Tue Jul 21 2009 - 09:16:21 CDT)
- Kristina Furse (Tue Jul 21 2009 - 08:53:21 CDT)
- Robert Duke (Tue Jul 21 2009 - 08:15:20 CDT)
- Robert Duke (Mon Jul 20 2009 - 12:55:23 CDT)
- xiaoqin huang (Mon Jul 20 2009 - 12:39:16 CDT)
- Ross Walker (Mon Jul 20 2009 - 12:32:08 CDT)
- xiaoqin huang (Mon Jul 20 2009 - 12:20:36 CDT)
- Robert Duke (Mon Jul 20 2009 - 12:10:03 CDT)
- Kristina Furse (Mon Jul 20 2009 - 11:56:26 CDT)
- Robert Duke (Mon Jul 20 2009 - 11:42:08 CDT)
- xiaoqin huang (Mon Jul 20 2009 - 11:28:42 CDT)
- Robert Duke (Mon Jul 20 2009 - 10:53:50 CDT)
- xiaoqin huang (Mon Jul 20 2009 - 10:20:32 CDT)
- Robert Duke (Mon Jul 20 2009 - 09:42:15 CDT)
- xiaoqin huang (Mon Jul 20 2009 - 09:21:20 CDT)
- Robert Duke (Fri Jul 17 2009 - 10:48:41 CDT)
- xiaoqin huang (Fri Jul 17 2009 - 09:54:55 CDT)
- xiaoqin huang (Fri Jul 17 2009 - 09:36:06 CDT)
- Ross Walker (Wed Jul 15 2009 - 20:32:07 CDT)
- Robert Duke (Wed Jul 15 2009 - 16:56:00 CDT)
- xiaoqin huang (Wed Jul 15 2009 - 16:28:52 CDT)
- Robert Duke (Wed Jul 15 2009 - 13:22:23 CDT)
- xiaoqin huang (Wed Jul 15 2009 - 12:34:20 CDT)
[AMBER] question of mm_pbsa
- Ray Luo (Fri Jul 10 2009 - 11:47:12 CDT)
- Hannes Kopitz (Fri Jul 10 2009 - 04:36:44 CDT)
- å»–é’åŽ (Thu Jul 09 2009 - 20:49:40 CDT)
[AMBER] Question on REST and VALUE1 keywords
- Ashish Runthala (Tue Jul 28 2009 - 20:26:19 CDT)
- Carlos Simmerling (Tue Jul 28 2009 - 16:14:20 CDT)
- hwu_at_clarku.edu (Tue Jul 28 2009 - 16:06:34 CDT)
[AMBER] questions about RESP
- FyD (Thu Jul 23 2009 - 12:49:23 CDT)
- Jeffrey (Thu Jul 23 2009 - 07:51:34 CDT)
- FyD (Mon Jul 20 2009 - 15:46:04 CDT)
- Jeffrey (Mon Jul 20 2009 - 02:42:29 CDT)
- FyD (Thu Jul 16 2009 - 09:27:44 CDT)
- Jeffrey (Thu Jul 16 2009 - 01:57:28 CDT)
[AMBER] R.E.D intra-mcc and reorientation
- Ganesh Krishnan (Sat Jul 11 2009 - 17:56:18 CDT)
- FyD (Sat Jul 11 2009 - 03:05:56 CDT)
- Ganesh Krishnan (Fri Jul 10 2009 - 17:00:35 CDT)
[AMBER] R.E.D. help please
- FyD (Wed Jul 15 2009 - 11:35:57 CDT)
- s. Bill (Wed Jul 15 2009 - 09:11:46 CDT)
[AMBER] radical simulation
- Jeffrey (Sun Jul 26 2009 - 07:28:39 CDT)
- FyD (Fri Jul 24 2009 - 05:27:34 CDT)
- Manish Kumar (Fri Jul 24 2009 - 02:48:01 CDT)
- Jeffrey (Fri Jul 24 2009 - 02:34:53 CDT)
[AMBER] radius for Manganese ion
- Chunliyan (Fri Jul 10 2009 - 08:39:51 CDT)
[AMBER] rdparm bug?
- Paul Mortenson (Tue Jul 07 2009 - 11:29:44 CDT)
[AMBER] RED.III: Invalid Optimization OUTPUT
- s. Bill (Wed Jul 29 2009 - 03:37:27 CDT)
[AMBER] RED: Charge derivation of transtion state analogue
- FyD (Mon Jul 06 2009 - 01:45:13 CDT)
- FyD (Mon Jul 06 2009 - 01:29:11 CDT)
- manoj singh (Mon Jul 06 2009 - 00:03:27 CDT)
- FyD (Sun Jul 05 2009 - 04:39:13 CDT)
- manoj singh (Sun Jul 05 2009 - 01:10:57 CDT)
[AMBER] reference re. determining size of timestep
- Gustavo Seabra (Fri Jul 17 2009 - 11:53:46 CDT)
- Paul Brandt (Thu Jul 09 2009 - 13:07:50 CDT)
[AMBER] Regarding Hbond interactions
- Thomas Cheatham (Thu Jul 23 2009 - 17:57:57 CDT)
- aneesh cna (Wed Jul 22 2009 - 01:30:10 CDT)
[AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10
- Keith Van Nostrand (Wed Jul 22 2009 - 10:58:08 CDT)
- Ross Walker (Thu Jul 16 2009 - 22:34:13 CDT)
- Keith Van Nostrand (Thu Jul 16 2009 - 16:08:04 CDT)
- Ross Walker (Fri Jul 10 2009 - 11:21:11 CDT)
- Keith Van Nostrand (Fri Jul 10 2009 - 10:27:12 CDT)
[AMBER] Removed proton in protein (Advanced Tutorials A1 old)
- albert albert (Fri Jul 31 2009 - 14:27:02 CDT)
- Ashish Runthala (Tue Jul 28 2009 - 08:08:48 CDT)
- FyD (Tue Jul 28 2009 - 06:59:51 CDT)
- Ashish Runthala (Tue Jul 28 2009 - 05:28:40 CDT)
- Bill Ross (Mon Jul 27 2009 - 11:17:29 CDT)
- Ashish Runthala (Mon Jul 27 2009 - 04:09:23 CDT)
- albert albert (Mon Jul 27 2009 - 01:57:20 CDT)
[AMBER] Replacing DNA base with analog
- Kristina Furse (Thu Jul 23 2009 - 09:36:26 CDT)
- amoreno_at_wesleyan.edu (Thu Jul 23 2009 - 09:20:08 CDT)
[AMBER] residues lacking connect0/connect1
- Bill Ross (Mon Jul 27 2009 - 11:40:31 CDT)
- Jio M (Mon Jul 27 2009 - 11:10:06 CDT)
[AMBER] RESP fit
- FyD (Sat Jul 18 2009 - 01:29:56 CDT)
- E.M. (Fri Jul 17 2009 - 18:00:08 CDT)
[AMBER] Restrained backbone conformation MD simulation"
- Carlos Simmerling (Fri Jul 10 2009 - 06:47:20 CDT)
- Prem Prakash Pathak (Fri Jul 10 2009 - 06:27:38 CDT)
[AMBER] rmsd_dna
- balaji nagarajan (Wed Jul 08 2009 - 20:55:53 CDT)
- Carlos Simmerling (Wed Jul 08 2009 - 13:21:29 CDT)
- balaji nagarajan (Wed Jul 08 2009 - 11:15:02 CDT)
[AMBER] rmsd_ptraj
- Thomas Cheatham (Thu Jul 09 2009 - 02:08:53 CDT)
- balaji nagarajan (Thu Jul 09 2009 - 00:50:10 CDT)
- Ross Walker (Wed Jul 08 2009 - 23:35:59 CDT)
- balaji nagarajan (Wed Jul 08 2009 - 23:19:56 CDT)
[AMBER] saquinavir parameterization with antechamber
- Oliver Kuhn (Thu Jul 23 2009 - 03:06:00 CDT)
- FyD (Thu Jul 23 2009 - 02:29:57 CDT)
- Oliver Kuhn (Thu Jul 23 2009 - 02:02:49 CDT)
- FyD (Wed Jul 22 2009 - 13:41:21 CDT)
- Oliver Kuhn (Wed Jul 22 2009 - 10:42:49 CDT)
[AMBER] setting AMBERHOME
- case (Wed Jul 22 2009 - 21:15:34 CDT)
[AMBER] Simulation with United atom force field in Implicit solvent.
- Manish Kumar (Sun Jul 26 2009 - 13:22:40 CDT)
- Ray Luo (Sun Jul 26 2009 - 02:09:07 CDT)
- Manish Kumar (Sat Jul 25 2009 - 22:55:42 CDT)
[AMBER] Steered MD---more than one pair of atoms
- Hlengisizwe Ndlovu (Tue Jul 07 2009 - 08:27:59 CDT)
[AMBER] Steered MD.....SHAKE error!!
- case (Fri Jul 17 2009 - 07:01:03 CDT)
- Hlengisizwe Ndlovu (Fri Jul 17 2009 - 03:50:11 CDT)
[AMBER] Steps for NMR structure minimization
- case (Wed Jul 01 2009 - 07:48:13 CDT)
[AMBER] suitable force field
- Jio M (Wed Jul 08 2009 - 02:14:12 CDT)
- Jio M (Wed Jul 08 2009 - 05:06:35 CDT)
[AMBER] Syntax Bellymask
- Brothers, Michael Charles (Fri Jul 10 2009 - 18:59:01 CDT)
[AMBER] The problem of restart file
- Jeffrey (Wed Jul 01 2009 - 09:07:08 CDT)
- Carlos Simmerling (Wed Jul 01 2009 - 07:49:32 CDT)
- Jeffrey (Wed Jul 01 2009 - 07:15:34 CDT)
[AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ?
- Andrew Voronkov (Tue Jul 28 2009 - 23:19:41 CDT)
- Marek Maly (Fri Jul 17 2009 - 13:37:02 CDT)
- Thomas Cheatham III (Fri Jul 17 2009 - 11:50:15 CDT)
- Marek Maly (Fri Jul 17 2009 - 11:34:44 CDT)
[AMBER] thymidine monophosphate parametrization
- Yvonne.Westermaier_at_unige.ch (Tue Jul 28 2009 - 07:10:43 CDT)
- case (Mon Jul 27 2009 - 09:47:38 CDT)
- Yvonne.Westermaier_at_unige.ch (Fri Jul 24 2009 - 10:18:18 CDT)
[AMBER] Tleap input error, atom not found in residue template
- Brothers, Michael Charles (Tue Jul 07 2009 - 11:08:00 CDT)
- Ross Walker (Mon Jul 06 2009 - 23:28:46 CDT)
- Brothers, Michael Charles (Mon Jul 06 2009 - 20:25:00 CDT)
[AMBER] TMD: solvation and equilibration questions
- Jeffrey (Fri Jul 10 2009 - 20:07:55 CDT)
[AMBER] Trouble saving amberparm files
- Alison Saunders (Mon Jul 13 2009 - 16:43:40 CDT)
- Tom Joseph (Mon Jul 13 2009 - 16:14:39 CDT)
- Tom Joseph (Mon Jul 13 2009 - 16:13:14 CDT)
- Alison Saunders (Mon Jul 13 2009 - 16:06:12 CDT)
- Tom Joseph (Mon Jul 13 2009 - 15:16:27 CDT)
- Alison Saunders (Mon Jul 13 2009 - 12:07:28 CDT)
[AMBER] Tutorial A3
- Ross Walker (Mon Jul 20 2009 - 14:03:44 CDT)
- s. Bill (Sun Jul 19 2009 - 14:33:58 CDT)
[AMBER] Umbrella Sampling
- Hemant Kumar (Sat Jul 18 2009 - 14:28:19 CDT)
- Seetin, Matthew (Thu Jul 16 2009 - 15:13:59 CDT)
- case (Thu Jul 16 2009 - 15:03:29 CDT)
- Hemant Kumar (Thu Jul 16 2009 - 13:01:40 CDT)
[AMBER] unable to read MM charges
- Vishal Maingi (Mon Jul 06 2009 - 04:32:29 CDT)
[AMBER] unable to read MM charges (no reply yet)
- Vishal Maingi (Mon Jul 06 2009 - 22:32:07 CDT)
[AMBER] unexplained blow-up at restart
- case (Mon Jul 13 2009 - 11:51:46 CDT)
- Sally Pias (Mon Jul 13 2009 - 11:11:08 CDT)
- Carlos Simmerling (Mon Jul 13 2009 - 05:24:23 CDT)
- Sally Pias (Mon Jul 13 2009 - 02:01:29 CDT)
- Sally Pias (Fri Jul 10 2009 - 13:59:24 CDT)
- Carlos Simmerling (Fri Jul 10 2009 - 12:58:15 CDT)
- Carlos Simmerling (Fri Jul 10 2009 - 12:25:10 CDT)
- Sally Pias (Fri Jul 10 2009 - 12:20:27 CDT)
- Carlos Simmerling (Fri Jul 10 2009 - 12:02:39 CDT)
- Sally Pias (Fri Jul 10 2009 - 11:31:59 CDT)
- Sally Pias (Fri Jul 10 2009 - 10:29:01 CDT)
- Simon Becker (Fri Jul 10 2009 - 08:24:13 CDT)
- Carlos Simmerling (Fri Jul 10 2009 - 05:55:51 CDT)
- Sally Pias (Fri Jul 10 2009 - 03:02:42 CDT)
[AMBER] unsolved verbosity when running minimization
- Carlos Simmerling (Wed Jul 08 2009 - 06:34:20 CDT)
- albert albert (Wed Jul 08 2009 - 06:10:43 CDT)
- Carlos Simmerling (Mon Jul 06 2009 - 14:28:08 CDT)
- albert albert (Mon Jul 06 2009 - 14:09:02 CDT)
[AMBER] Using idecomp=3 with igb=10 (PB)
- Ashish Runthala (Tue Jul 28 2009 - 09:33:02 CDT)
- Hannes Kopitz (Tue Jul 28 2009 - 07:47:15 CDT)
- Chris Whittleston (Tue Jul 28 2009 - 05:54:09 CDT)
- Hannes Kopitz (Tue Jul 28 2009 - 05:09:01 CDT)
- Chris Whittleston (Mon Jul 27 2009 - 15:04:14 CDT)
[AMBER] vertex atom mismatch
- Guillermo Mulliert Carlín (Fri Jul 31 2009 - 09:33:46 CDT)
- Clark, Tiffany D (Fri Jul 31 2009 - 08:14:15 CDT)
[AMBER] vlimit error after heating restart
- AL Olson (Fri Jul 17 2009 - 09:26:05 CDT)
[AMBER] vlimit exceeded....nscu_SMD!!
- Hlengisizwe Ndlovu (Thu Jul 16 2009 - 07:53:50 CDT)
[AMBER] What is the meaning of "rms first *"
- Catein Catherine (Thu Jul 30 2009 - 22:49:17 CDT)
[AMBER] which keyword
- s. Bill (Sun Jul 19 2009 - 07:21:23 CDT)
[AMBER] xleap facility to insert a residue
- Sergey Samsonov (Fri Jul 24 2009 - 08:07:27 CDT)
[AMBER] Zinc ion, help
- FyD (Wed Jul 08 2009 - 04:43:26 CDT)
- Mahmoud A. A. Ibrahim (Tue Jul 07 2009 - 09:26:48 CDT)
[q4md-fft] Charge calculation or non standard residue
- FyD (Sun Jul 05 2009 - 03:30:50 CDT)
Ambertools 1.2 installation error
- case (Mon Jul 27 2009 - 09:38:28 CDT)
- Bokun Cho (Mon Jul 27 2009 - 01:51:49 CDT)
ask for help (zn parameters)
- Ross Walker (Sun Jul 05 2009 - 21:56:50 CDT)
Average structure over simulation
- Olotu Odunayo (Mon Jul 27 2009 - 10:47:20 CDT)
- Niel Henriksen (Mon Jul 27 2009 - 09:56:40 CDT)
AW: [AMBER] Steered MD---more than one pair of atoms
- Aust, Susanne (Wed Jul 08 2009 - 01:47:56 CDT)
bug in antechamber
- David Mobley (Mon Jul 13 2009 - 12:41:01 CDT)
bugfix 10 failing for ambertools1.2
- case (Mon Jul 27 2009 - 10:03:24 CDT)
- Alan (Mon Jul 20 2009 - 03:25:55 CDT)
charge not zero on group:''''.respin1 attached
- FyD (Sun Jul 19 2009 - 02:41:17 CDT)
- Jio M (Sat Jul 18 2009 - 09:40:18 CDT)
DCCM
- Duggan, Brendan M. (Mon Jul 20 2009 - 09:29:46 CDT)
Directory - GAFF Parameter File?
- Patrick Gedeon (Mon Jul 06 2009 - 18:38:57 CDT)
Error in REDIII
- FyD (Fri Jul 03 2009 - 09:59:30 CDT)
MM-PBSA delphi.crg and delphi.siz
- Manish Kumar (Thu Jul 23 2009 - 02:10:51 CDT)
- Ray Luo (Tue Jul 21 2009 - 09:24:40 CDT)
- Manish Kumar (Mon Jul 20 2009 - 16:11:20 CDT)
- Ray Luo (Sun Jul 19 2009 - 17:45:29 CDT)
- Manish Kumar (Sun Jul 19 2009 - 14:36:35 CDT)
- Ray Luo (Fri Jul 10 2009 - 11:32:18 CDT)
- suhaib sh (Fri Jul 10 2009 - 09:17:52 CDT)
- Manish Kumar (Thu Jul 09 2009 - 22:33:01 CDT)
MM-PBSA test jobs error messages
- Catein Catherine (Tue Jul 28 2009 - 04:24:31 CDT)
MM-PBSA test jobs error messages (Can i fix the problem without recompile the amber?)
- Catein Catherine (Wed Jul 29 2009 - 04:39:02 CDT)
MM-PBSA test jobs error messages (with bugfix.all)
- Catein Catherine (Wed Jul 29 2009 - 00:50:50 CDT)
mpirun noticed that process rank 1 ... on signal 1 (Hangup).
- Naser Alijabbari (Tue Jul 14 2009 - 11:30:55 CDT)
- Ross Walker (Tue Jul 14 2009 - 07:33:49 CDT)
- Naser Alijabbari (Tue Jul 14 2009 - 05:49:14 CDT)
non aminoacid Residue
- Ross Walker (Mon Jul 06 2009 - 11:21:44 CDT)
- Neha Gandhi (Mon Jul 06 2009 - 03:43:56 CDT)
pls help and suggest
- Gustavo Seabra (Fri Jul 17 2009 - 11:50:59 CDT)
- Vishal Maingi (Thu Jul 09 2009 - 13:45:21 CDT)
- Gustavo Seabra (Thu Jul 09 2009 - 11:14:42 CDT)
pmemd parallel
- Jun Dong (Wed Jul 15 2009 - 10:00:49 CDT)
- Ross Walker (Tue Jul 14 2009 - 07:24:06 CDT)
problem of installation of amber10
- Mengjuei Hsieh (Wed Jul 29 2009 - 14:41:52 CDT)
question about TUTORIAL A1
- Ross Walker (Mon Jul 06 2009 - 11:58:47 CDT)
- Ross Walker (Sun Jul 05 2009 - 21:29:38 CDT)
Questions about QMMM
- Ross Walker (Tue Jul 21 2009 - 17:47:49 CDT)
reference re. size of dt
- case (Mon Jul 13 2009 - 11:56:46 CDT)
Request to mailing list AMBER rejected
- E.M. (Mon Jul 13 2009 - 22:37:46 CDT)
Solved it thanks [AMBER] RED.III: Invalid Optimization OUTPUT
- s. Bill (Wed Jul 29 2009 - 07:14:02 CDT)
suggestions
- Cihan Aydin (Mon Jul 06 2009 - 20:29:22 CDT)
- Ross Walker (Mon Jul 06 2009 - 20:01:51 CDT)
the copper paramter
- Ross Walker (Mon Jul 20 2009 - 16:38:14 CDT)
´ð¸´: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished,
- Zhongjie Liang (Thu Jul 16 2009 - 04:16:02 CDT)
»Ø¸´£º [AMBER] antechamber
- ÁÎÇà»ª (Thu Jul 02 2009 - 19:45:41 CDT)
å›žå¤ï¼š [AMBER] amber10 parallel compiling error
- å»–é’åŽ (Thu Jul 16 2009 - 20:27:05 CDT)
å›žå¤ï¼š [AMBER] errors of PMEMD installation
- Qinghua Liao (Fri Jul 24 2009 - 20:24:10 CDT)
- Mengjuei Hsieh (Fri Jul 24 2009 - 13:12:00 CDT)
- Qinghua Liao (Fri Jul 24 2009 - 04:59:03 CDT)
- Qinghua Liao (Fri Jul 24 2009 - 04:18:44 CDT)
- Mengjuei Hsieh (Fri Jul 24 2009 - 03:41:05 CDT)
- å»–é’åŽ (Thu Jul 23 2009 - 20:27:51 CDT)
å›žå¤ï¼š [AMBER] missing Halogen parameters (radii) for PBSA/GBSA calculations - PB Bomb in pb_aaradi(): No radius assigned for atom
- å»–é’åŽ (Thu Jul 02 2009 - 23:53:09 CDT)
å›žå¤ï¼š [AMBER] question of mm_pbsa
- å»–é’åŽ (Sat Jul 11 2009 - 19:03:33 CDT)
- å»–é’åŽ (Fri Jul 10 2009 - 20:22:25 CDT)
- å»–é’åŽ (Fri Jul 10 2009 - 19:50:55 CDT)
å›žå¤ï¼š å›žå¤ï¼š [AMBER] antechamber
- å»–é’åŽ (Thu Jul 02 2009 - 19:53:06 CDT)

Last message date: Mon Nov 23 2009 - 13:51:08 CST
Archived on: Mon Nov 23 2009 - 13:51:12 CST

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