AMBER Archive (2009) - Jul 2009 By Author

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

• Adrian Roitberg
  • Re: [AMBER] Protonated or not (Fri Jul 31 2009 - 12:32:50 CDT)
• AL Olson
  • [AMBER] vlimit error after heating restart (Fri Jul 17 2009 - 09:26:05 CDT)
• Alan
  • Re: [AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits (Thu Jul 30 2009 - 08:39:03 CDT)
  • [AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits (Wed Jul 29 2009 - 11:00:42 CDT)
  • [AMBER] Re: bugfix 10 failing for ambertools1.2 (Mon Jul 20 2009 - 03:25:55 CDT)
  • [AMBER] bugfix 10 failing for ambertools1.2 (Mon Jul 20 2009 - 03:14:16 CDT)
  • [AMBER] different results for antechamber/mopac for the same input (Wed Jul 15 2009 - 17:05:07 CDT)
  • Re: [AMBER] antechamber (Thu Jul 02 2009 - 05:16:55 CDT)
  • Re: [AMBER] antechamber (Wed Jul 01 2009 - 06:37:40 CDT)
• albert albert
  • Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) (Fri Jul 31 2009 - 14:27:02 CDT)
  • [AMBER] Removed proton in protein (Advanced Tutorials A1 old) (Mon Jul 27 2009 - 01:57:20 CDT)
  • Re: [AMBER] unsolved verbosity when running minimization (Wed Jul 08 2009 - 06:10:43 CDT)
  • [AMBER] unsolved verbosity when running minimization (Mon Jul 06 2009 - 14:09:02 CDT)
• Aldo Humberto Romero
  • [AMBER] Amber10, Serial compilation with ifort (Sun Jul 12 2009 - 15:57:40 CDT)
• Alison Saunders
  • [AMBER] Error in Sander Output File (Tue Jul 28 2009 - 12:00:12 CDT)
  • Re: [AMBER] Trouble saving amberparm files (Mon Jul 13 2009 - 16:43:40 CDT)
  • Re: [AMBER] Trouble saving amberparm files (Mon Jul 13 2009 - 16:06:12 CDT)
  • [AMBER] Trouble saving amberparm files (Mon Jul 13 2009 - 12:07:28 CDT)
  • Re: [AMBER] Acetylate and Amidate (Wed Jul 08 2009 - 17:47:59 CDT)
  • [AMBER] Acetylate and Amidate (Wed Jul 08 2009 - 17:19:44 CDT)
• amoreno_at_wesleyan.edu
  • [AMBER] Replacing DNA base with analog (Thu Jul 23 2009 - 09:20:08 CDT)
• Andrew Olson
  • Re: [AMBER] Holding ligand rigid for minimization (Tue Jul 14 2009 - 13:23:31 CDT)
  • [AMBER] Holding ligand rigid for minimization (Tue Jul 14 2009 - 10:23:01 CDT)
  • [AMBER] Holding ligand rigid for minimization (Tue Jul 14 2009 - 10:14:38 CDT)
  • Re: [AMBER] ligand/protein minimization (Mon Jul 13 2009 - 12:10:18 CDT)
  • Re: [AMBER] ligand/protein minimization (Mon Jul 13 2009 - 10:53:11 CDT)
  • [AMBER] ligand/protein minimization (Fri Jul 10 2009 - 16:00:26 CDT)
  • Re: [AMBER] Antechamber prep question (Fri Jul 10 2009 - 08:33:09 CDT)
  • Re: [AMBER] Antechamber prep question (Thu Jul 09 2009 - 12:00:19 CDT)
  • Re: [AMBER] Antechamber prep question (Thu Jul 09 2009 - 10:22:18 CDT)
  • [AMBER] Antechamber prep question (Thu Jul 09 2009 - 09:39:25 CDT)
• Andrew Voronkov
  • Re: [AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ? (Tue Jul 28 2009 - 23:19:41 CDT)
  • Re: [AMBER] only ff94 and ff99 for GBSA? (Tue Jul 28 2009 - 01:12:15 CDT)
  • Re: [AMBER] only ff94 and ff99 for GBSA? (Mon Jul 27 2009 - 11:41:27 CDT)
  • [AMBER] amino acids caps for truncated proteins (Thu Jul 16 2009 - 11:31:18 CDT)
  • Re: [AMBER] MPI process terminated unexpectedly forrtl: error (69): process interrupted (SIGINT) (Wed Jul 08 2009 - 05:05:52 CDT)
  • [AMBER] MPI process terminated unexpectedly forrtl: error (69): process interrupted (SIGINT) (Wed Jul 08 2009 - 04:39:03 CDT)
• aneesh cna
  • [AMBER] Regarding Hbond interactions (Wed Jul 22 2009 - 01:30:10 CDT)
• Ashish Runthala
  • Re: [AMBER] problem from xleap (Fri Jul 31 2009 - 22:33:10 CDT)
  • Re: [AMBER] Non-Standard Amino Acid Residue LEAP ERROR (Fri Jul 31 2009 - 20:39:54 CDT)
  • Re: [AMBER] ambpdb problem (Fri Jul 31 2009 - 20:28:42 CDT)
  • Re: [AMBER] query (Fri Jul 31 2009 - 20:23:07 CDT)
  • Re: [AMBER] Non-Standard Amino Acid Residue LEAP ERROR (Thu Jul 30 2009 - 22:40:45 CDT)
  • Re: [AMBER] ambpdb problem (Thu Jul 30 2009 - 22:44:10 CDT)
  • Re: [AMBER] Am I doing the right thing (Tue Jul 28 2009 - 22:44:59 CDT)
  • Re: [AMBER] Am I doing the right thing (Tue Jul 28 2009 - 20:35:09 CDT)
  • Re: [AMBER] Question on REST and VALUE1 keywords (Tue Jul 28 2009 - 20:26:19 CDT)
  • Re: [AMBER] Using idecomp=3 with igb=10 (PB) (Tue Jul 28 2009 - 09:33:02 CDT)
  • Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) (Tue Jul 28 2009 - 08:08:48 CDT)
  • Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) (Tue Jul 28 2009 - 05:28:40 CDT)
  • Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) (Mon Jul 27 2009 - 04:09:23 CDT)
  • Re: [AMBER] DNA + intercalator (Fri Jul 24 2009 - 22:12:27 CDT)
• Aust, Susanne
  • AW: [AMBER] Steered MD---more than one pair of atoms (Wed Jul 08 2009 - 01:47:56 CDT)
  • [AMBER] analysis of QM/MM - LCOD (Fri Jul 03 2009 - 04:51:34 CDT)
• Bala subramanian
  • Re: [AMBER] ouput trajectory of only CA atom (Wed Jul 08 2009 - 10:01:27 CDT)
  • [AMBER] ouput trajectory of only CA atom (Wed Jul 08 2009 - 08:24:56 CDT)
  • Re: [AMBER] amber9 in fedora10 (Thu Jul 02 2009 - 03:05:55 CDT)
  • Re: [AMBER] amber9 in fedora10 (Thu Jul 02 2009 - 02:02:54 CDT)
  • [AMBER] amber9 in fedora10 (Wed Jul 01 2009 - 09:09:15 CDT)
• balaji nagarajan
  • RE: [AMBER] rmsd_ptraj (Thu Jul 09 2009 - 00:50:10 CDT)
  • [AMBER] rmsd_ptraj (Wed Jul 08 2009 - 23:19:56 CDT)
  • RE: [AMBER] rmsd_dna (Wed Jul 08 2009 - 20:55:53 CDT)
  • [AMBER] rmsd_dna (Wed Jul 08 2009 - 11:15:02 CDT)
• Beale, John
  • [AMBER] (no subject) (Mon Jul 13 2009 - 12:35:46 CDT)
• Ben Roberts
  • Re: [AMBER] charge not zero on group: RESP (Sat Jul 18 2009 - 07:45:10 CDT)
• bharat lakhani
  • [AMBER] query (Fri Jul 31 2009 - 02:42:04 CDT)
  • [AMBER] Normal mode analysis of water (Thu Jul 30 2009 - 04:27:19 CDT)
  • Re: [AMBER] command for RESP fitting (Mon Jul 20 2009 - 02:01:23 CDT)
  • [AMBER] command for RESP fitting (Thu Jul 16 2009 - 02:10:33 CDT)
  • [AMBER] Please help me out (Wed Jul 15 2009 - 05:43:21 CDT)
• Bill Ross
  • Re: [AMBER] Am I doing the right thing (Tue Jul 28 2009 - 21:39:48 CDT)
  • Re: [AMBER] residues lacking connect0/connect1 (Mon Jul 27 2009 - 11:40:31 CDT)
  • Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) (Mon Jul 27 2009 - 11:17:29 CDT)
  • Re: [AMBER] DNA + intercalator (Fri Jul 24 2009 - 18:03:06 CDT)
  • Re: [AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S" (Wed Jul 15 2009 - 11:53:41 CDT)
  • Re: [AMBER] Acetylate and Amidate (Wed Jul 08 2009 - 18:13:09 CDT)
• Biswaranjan Meher
  • Re: [AMBER] Langevin Dynamics in AMBER10 (Thu Jul 23 2009 - 18:12:59 CDT)
  • [AMBER] Langevin Dynamics in AMBER10 (Thu Jul 23 2009 - 16:54:58 CDT)
• Bokun Cho
  • [AMBER] Re: Ambertools 1.2 installation error (Mon Jul 27 2009 - 01:51:49 CDT)
• Brothers, Michael Charles
  • RE: [AMBER] Non-Standard Amino Acid Residue LEAP ERROR (Fri Jul 31 2009 - 12:36:10 CDT)
  • [AMBER] Non-Standard Amino Acid Residue LEAP ERROR (Thu Jul 30 2009 - 17:28:43 CDT)
  • [AMBER] Syntax Bellymask (Fri Jul 10 2009 - 18:59:01 CDT)
  • RE: [AMBER] Tleap input error, atom not found in residue template (Tue Jul 07 2009 - 11:08:00 CDT)
  • [AMBER] Tleap input error, atom not found in residue template (Mon Jul 06 2009 - 20:25:00 CDT)
• Carlos Simmerling
  • Re: [AMBER] Question on REST and VALUE1 keywords (Tue Jul 28 2009 - 16:14:20 CDT)
  • Re: [AMBER] nonbon.f question (Mon Jul 27 2009 - 14:34:20 CDT)
  • Re: [AMBER] Langevin Dynamics in AMBER10 (Fri Jul 24 2009 - 07:01:28 CDT)
  • Re: [AMBER] Langevin Dynamics in AMBER10 (Thu Jul 23 2009 - 16:57:44 CDT)
  • Re: [AMBER] IGB=7 vs IGB=5 (Tue Jul 21 2009 - 08:51:22 CDT)
  • Re: [AMBER] Box shape change (Sun Jul 19 2009 - 08:51:44 CDT)
  • Re: [AMBER] Box shape change (Sun Jul 19 2009 - 06:40:03 CDT)
  • Re: [AMBER] Box shape change (Sat Jul 18 2009 - 20:35:41 CDT)
  • Re: [AMBER] unexplained blow-up at restart (Mon Jul 13 2009 - 05:24:23 CDT)
  • Re: [AMBER] problem with energy calculations (Sun Jul 12 2009 - 09:15:39 CDT)
  • Re: [AMBER] problem with energy calculations (Sun Jul 12 2009 - 08:42:35 CDT)
  • Re: [AMBER] unexplained blow-up at restart (Fri Jul 10 2009 - 12:58:15 CDT)
  • Re: [AMBER] problem with energy calculations (Fri Jul 10 2009 - 12:25:56 CDT)
  • Re: [AMBER] unexplained blow-up at restart (Fri Jul 10 2009 - 12:25:10 CDT)
  • Re: [AMBER] unexplained blow-up at restart (Fri Jul 10 2009 - 12:02:39 CDT)
  • TMD: was: Re: [AMBER] charges in topology file (Fri Jul 10 2009 - 11:36:30 CDT)
  • Re: [AMBER] implicit solvent (GB version2) MD simulation (Fri Jul 10 2009 - 10:57:57 CDT)
  • Re: [AMBER] EPtot for Alpha-L- methyl fucose (Fri Jul 10 2009 - 08:57:34 CDT)
  • Re: [AMBER] Restrained backbone conformation MD simulation" (Fri Jul 10 2009 - 06:47:20 CDT)
  • Re: [AMBER] unexplained blow-up at restart (Fri Jul 10 2009 - 05:55:51 CDT)
  • Re: [AMBER] Acetylate and Amidate (Thu Jul 09 2009 - 06:52:28 CDT)
  • Re: [AMBER] Acetylate and Amidate (Wed Jul 08 2009 - 17:22:58 CDT)
  • Re: [AMBER] rmsd_dna (Wed Jul 08 2009 - 13:21:29 CDT)
  • Re: [AMBER] ouput trajectory of only CA atom (Wed Jul 08 2009 - 09:41:25 CDT)
  • Re: [AMBER] unsolved verbosity when running minimization (Wed Jul 08 2009 - 06:34:20 CDT)
  • Re: [AMBER] unsolved verbosity when running minimization (Mon Jul 06 2009 - 14:28:08 CDT)
  • Re: [AMBER] The problem of restart file (Wed Jul 01 2009 - 07:49:32 CDT)
• case
  • Re: [AMBER] Normal mode analysis of water (Thu Jul 30 2009 - 09:11:23 CDT)
  • Re: [AMBER] error in antechamber (Mon Jul 27 2009 - 23:23:54 CDT)
  • Re: [AMBER] only ff94 and ff99 for GBSA? (Mon Jul 27 2009 - 12:05:48 CDT)
  • Re: [AMBER] Output forces in Sander (Mon Jul 27 2009 - 10:11:30 CDT)
  • Re: [AMBER] Re: bugfix 10 failing for ambertools1.2 (Mon Jul 27 2009 - 10:03:24 CDT)
  • Re: [AMBER] thymidine monophosphate parametrization (Mon Jul 27 2009 - 09:47:38 CDT)
  • Re: [AMBER] Re: Ambertools 1.2 installation error (Mon Jul 27 2009 - 09:38:28 CDT)
  • Re: [AMBER] cpin error (Fri Jul 24 2009 - 14:41:00 CDT)
  • Re: [AMBER] setting AMBERHOME (Wed Jul 22 2009 - 21:15:34 CDT)
  • Re: [AMBER] amber10 parallel compiling error (Wed Jul 22 2009 - 21:15:50 CDT)
  • Re: [AMBER] Steered MD.....SHAKE error!! (Fri Jul 17 2009 - 07:01:03 CDT)
  • Re: [AMBER] diffusion coeficients (Fri Jul 17 2009 - 06:59:41 CDT)
  • Re: [AMBER] File conversion for from Amber to Charmm (Fri Jul 17 2009 - 06:53:06 CDT)
  • Re: [AMBER] Disappearing common atoms in Amber 10 with TI (Fri Jul 17 2009 - 06:41:39 CDT)
  • Re: [AMBER] Umbrella Sampling (Thu Jul 16 2009 - 15:03:29 CDT)
  • Re: [AMBER] query regarding FE4S4 (Thu Jul 16 2009 - 06:45:06 CDT)
  • Re: [AMBER] carbonic anhydrase (CA) simulation (Thu Jul 16 2009 - 06:36:17 CDT)
  • Re: [AMBER] different results for antechamber/mopac for the same input (Thu Jul 16 2009 - 06:30:08 CDT)
  • Re: [AMBER] Please help me out (Wed Jul 15 2009 - 14:55:21 CDT)
  • Re: [AMBER] Equilibrium water density (Wed Jul 15 2009 - 14:53:54 CDT)
  • Re: [AMBER] Could not find bond parameter for O2 - ca (Tue Jul 14 2009 - 22:28:02 CDT)
  • Re: [AMBER] Counterion release and Free energy of binding ? (Tue Jul 14 2009 - 22:10:18 CDT)
  • Re: [AMBER] ptraj mask selection (Mon Jul 13 2009 - 13:10:46 CDT)
  • [AMBER] Re: reference re. size of dt (Mon Jul 13 2009 - 11:56:46 CDT)
  • Re: [AMBER] unexplained blow-up at restart (Mon Jul 13 2009 - 11:51:46 CDT)
  • Re: [AMBER] ligand/protein minimization (Mon Jul 13 2009 - 11:29:06 CDT)
  • Re: [AMBER] Peptide bond broken (Sun Jul 12 2009 - 21:35:35 CDT)
  • Re: [AMBER] ligand/protein minimization (Sun Jul 12 2009 - 21:32:29 CDT)
  • Re: [AMBER] amber dihedral format (Sun Jul 12 2009 - 16:49:12 CDT)
  • Re: [AMBER] Antechamber prep question (Thu Jul 09 2009 - 13:54:44 CDT)
  • Re: [AMBER] Antechamber prep question (Thu Jul 09 2009 - 11:48:44 CDT)
  • Re: [AMBER] Antechamber prep question (Thu Jul 09 2009 - 10:16:17 CDT)
  • Re: [AMBER] charged or not (Thu Jul 09 2009 - 10:10:14 CDT)
  • Re: [AMBER] ff parameters (Thu Jul 09 2009 - 08:23:31 CDT)
  • Re: [AMBER] amber10 installation problem (Thu Jul 09 2009 - 07:38:01 CDT)
  • Re: [AMBER] amber10 installation problem (Wed Jul 08 2009 - 06:56:19 CDT)
  • Re: [AMBER] Installing of amber10 (Wed Jul 08 2009 - 06:42:02 CDT)
  • Re: [AMBER] H-bond vs. VdW (Mon Jul 06 2009 - 12:29:49 CDT)
  • Re: [AMBER] need charges of FE-S cluster (Mon Jul 06 2009 - 07:35:19 CDT)
  • Re: [AMBER] Boundary Condition Problem (Sat Jul 04 2009 - 08:45:45 CDT)
  • Re: [AMBER] default integration scheme in 7 vs. 10 (Thu Jul 02 2009 - 06:37:17 CDT)
  • Re: [AMBER] Steps for NMR structure minimization (Wed Jul 01 2009 - 07:48:13 CDT)
  • Re: [AMBER] antechamber (Wed Jul 01 2009 - 07:04:02 CDT)
• Catein Catherine
  • [AMBER] What is the meaning of "rms first *" (Thu Jul 30 2009 - 22:49:17 CDT)
  • RE: [AMBER] PCA analysis: the first vector is the movement of whole molecule. (Thu Jul 30 2009 - 22:46:49 CDT)
  • [AMBER] PCA analysis: the first vector is the movement of whole molecule. (Thu Jul 30 2009 - 05:37:49 CDT)
  • [AMBER] Re: MM-PBSA test jobs error messages (Can i fix the problem without recompile the amber?) (Wed Jul 29 2009 - 04:39:02 CDT)
  • [AMBER] RE: MM-PBSA test jobs error messages (with bugfix.all) (Wed Jul 29 2009 - 00:50:50 CDT)
  • [AMBER] How to visualize PCA results without IED? (Tue Jul 28 2009 - 04:30:22 CDT)
  • [AMBER] RE: MM-PBSA test jobs error messages (Tue Jul 28 2009 - 04:24:31 CDT)
  • [AMBER] MM-PBSA cannot finish without error message. (Thu Jul 23 2009 - 04:57:00 CDT)
  • [AMBER] Is rmsd ~ 3 A reasonable for a 4ns simulation? (Wed Jul 08 2009 - 04:45:41 CDT)
• Chris Whittleston
  • Re: [AMBER] Using idecomp=3 with igb=10 (PB) (Tue Jul 28 2009 - 05:54:09 CDT)
  • [AMBER] Using idecomp=3 with igb=10 (PB) (Mon Jul 27 2009 - 15:04:14 CDT)
• Christof Jaeger
  • Re: [AMBER] ptraj-radial distribution function (Thu Jul 16 2009 - 03:22:02 CDT)
• Chunliyan
  • [AMBER] Manganese bondi radii (Fri Jul 10 2009 - 08:39:51 CDT)
  • [AMBER] Manganese bondi radii for mm/pbsa calculation (Fri Jul 10 2009 - 08:39:51 CDT)
  • [AMBER] Manganese (Fri Jul 10 2009 - 08:39:51 CDT)
  • [AMBER] radius for Manganese ion (Fri Jul 10 2009 - 08:39:51 CDT)
  • [AMBER] manganese bondi radii for mm_pbsa calculation (Fri Jul 10 2009 - 08:39:51 CDT)
• Cihan Aydin
  • RE: [AMBER] ptraj - cluster (Fri Jul 17 2009 - 09:22:37 CDT)
  • [AMBER] ptraj - cluster (Thu Jul 16 2009 - 00:55:07 CDT)
  • Re: [AMBER] RE: suggestions (Mon Jul 06 2009 - 20:29:22 CDT)
  • Re: [AMBER] H-bond vs. VdW (Mon Jul 06 2009 - 10:13:39 CDT)
  • [AMBER] Leap Questions... (Sat Jul 04 2009 - 20:41:39 CDT)
• Clark, Tiffany D
  • [AMBER] vertex atom mismatch (Fri Jul 31 2009 - 08:14:15 CDT)
• David Dubins
  • [AMBER] Installing Amber10 on Ubuntu (Wed Jul 29 2009 - 13:50:12 CDT)
• David Mobley
  • [AMBER] Re: bug in antechamber (Mon Jul 13 2009 - 12:41:01 CDT)
  • [AMBER] bug in antechamber (Wed Jul 08 2009 - 11:19:12 CDT)
• David Watson
  • Re: [AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits (Thu Jul 30 2009 - 14:10:39 CDT)
  • Re: [AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits (Wed Jul 29 2009 - 11:21:50 CDT)
  • [AMBER] Compiling AMBER 10 (parallel, MPICH2) on Mac OS X Intel w/gcc, ifort, icc (Thu Jul 23 2009 - 15:03:59 CDT)
  • Re: [AMBER] how to launch XLEaP from SSH Secure Shell? (Wed Jul 22 2009 - 19:30:12 CDT)
  • [AMBER] Compiling Amber 10 (serial) on Mac OS X 10.5.7 w/ gcc, Intel Fortan 11.0 and MKL 10.0 (Tue Jul 21 2009 - 16:20:36 CDT)
• Duggan, Brendan M.
  • [AMBER] RE: DCCM (Mon Jul 20 2009 - 09:29:46 CDT)
  • RE: [AMBER] DCCM (Wed Jul 15 2009 - 11:06:57 CDT)
• E.M.
  • [AMBER] RESP fit (Fri Jul 17 2009 - 18:00:08 CDT)
  • [AMBER] Re: Request to mailing list AMBER rejected (Mon Jul 13 2009 - 22:37:46 CDT)
• felix
  • Re: [AMBER] diffusion coeficients (Fri Jul 17 2009 - 08:41:43 CDT)
  • [AMBER] diffusion coeficients (Fri Jul 17 2009 - 03:15:35 CDT)
• Frank X. Vázquez
  • [AMBER] Output forces in Sander (Tue Jul 21 2009 - 16:58:36 CDT)
• FyD
  • Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) (Tue Jul 28 2009 - 06:59:51 CDT)
  • Re: [AMBER] only ff94 and ff99 for GBSA? (Tue Jul 28 2009 - 02:32:52 CDT)
  • Re: [AMBER] loading a mol2 file in xleap (Mon Jul 27 2009 - 08:44:50 CDT)
  • Re: [AMBER] Could not find type: MG Parameter file was not saved. though it was loaded (Mon Jul 27 2009 - 00:03:00 CDT)
  • Re: [AMBER] loading a mol2 file in xleap (Fri Jul 24 2009 - 15:00:41 CDT)
  • Re: [AMBER] radical simulation (Fri Jul 24 2009 - 05:27:34 CDT)
  • Re: [AMBER] questions about RESP (Thu Jul 23 2009 - 12:49:23 CDT)
  • Re: [AMBER] saquinavir parameterization with antechamber (Thu Jul 23 2009 - 02:29:57 CDT)
  • Re: [AMBER] saquinavir parameterization with antechamber (Wed Jul 22 2009 - 13:41:21 CDT)
  • Re: [AMBER] questions about RESP (Mon Jul 20 2009 - 15:46:04 CDT)
  • Re: [AMBER] RE: charge not zero on group:''''.respin1 attached (Sun Jul 19 2009 - 02:41:17 CDT)
  • Re: [AMBER] RESP fit (Sat Jul 18 2009 - 01:29:56 CDT)
  • Re: [AMBER] amino acids caps for truncated proteins (Thu Jul 16 2009 - 11:58:32 CDT)
  • Re: [AMBER] command for RESP fitting (Thu Jul 16 2009 - 09:34:28 CDT)
  • Re: [AMBER] questions about RESP (Thu Jul 16 2009 - 09:27:44 CDT)
  • Re: [AMBER] GAFF and NME, ACE terminal res (Thu Jul 16 2009 - 01:25:03 CDT)
  • Re: [AMBER] R.E.D. help please (Wed Jul 15 2009 - 11:35:57 CDT)
  • Re: [AMBER] non standard residue (Tue Jul 14 2009 - 15:01:32 CDT)
  • Re: [AMBER] GAFF and NME, ACE terminal res (Tue Jul 14 2009 - 02:40:00 CDT)
  • Re: [AMBER] non standard residue (Tue Jul 14 2009 - 01:47:00 CDT)
  • Re: [AMBER] help needed for HID (Mon Jul 13 2009 - 15:27:13 CDT)
  • Re: [AMBER] R.E.D intra-mcc and reorientation (Sat Jul 11 2009 - 03:05:56 CDT)
  • Re: [AMBER] Peptide bond broken (Sat Jul 11 2009 - 01:58:06 CDT)
  • Re: [AMBER] Antechamber prep question (Fri Jul 10 2009 - 10:24:08 CDT)
  • Re: [AMBER] Antechamber prep question (Fri Jul 10 2009 - 00:52:12 CDT)
  • Re: [AMBER] Zinc ion, help (Wed Jul 08 2009 - 04:43:26 CDT)
  • Re: [AMBER] non standard residue (Tue Jul 07 2009 - 02:50:09 CDT)
  • Re: [AMBER] RED: Charge derivation of transtion state analogue (Mon Jul 06 2009 - 01:45:13 CDT)
  • Re: [AMBER] RED: Charge derivation of transtion state analogue (Mon Jul 06 2009 - 01:29:11 CDT)
  • Re: [AMBER] RED: Charge derivation of transtion state analogue (Sun Jul 05 2009 - 04:39:13 CDT)
  • [AMBER] Re: [q4md-fft] Charge calculation or non standard residue (Sun Jul 05 2009 - 03:30:50 CDT)
  • Re: [AMBER] H-bond vs. VdW (Sat Jul 04 2009 - 00:01:58 CDT)
  • [AMBER] Re: Error in REDIII (Fri Jul 03 2009 - 09:59:30 CDT)
  • Re: [AMBER] antechamber (Thu Jul 02 2009 - 01:33:46 CDT)
  • Re: [AMBER] antechamber (Wed Jul 01 2009 - 07:26:39 CDT)
• Ganesh Krishnan
  • Re: [AMBER] R.E.D intra-mcc and reorientation (Sat Jul 11 2009 - 17:56:18 CDT)
  • [AMBER] R.E.D intra-mcc and reorientation (Fri Jul 10 2009 - 17:00:35 CDT)
• gilbert_at_bluemarble.net
  • Re: [AMBER] Antechamber prep question (Fri Jul 10 2009 - 08:10:32 CDT)
  • Re: [AMBER] antechamber (Wed Jul 01 2009 - 07:11:17 CDT)
• Giorgos Lamprinidis
  • Re: [AMBER] Need help for PMEMD 10 installation (Tue Jul 14 2009 - 02:29:09 CDT)
  • Re: [AMBER] MM-PBSA problem (Mon Jul 06 2009 - 03:07:14 CDT)
  • [AMBER] MM-PBSA problem (Fri Jul 03 2009 - 08:50:36 CDT)
• Guillermo Mulliert Carlín
  • Re: [AMBER] vertex atom mismatch (Fri Jul 31 2009 - 09:33:46 CDT)
• gunajyoti das
  • [AMBER] (no subject) (Sun Jul 19 2009 - 10:13:01 CDT)
  • [AMBER] (no subject) (Sun Jul 19 2009 - 10:14:20 CDT)
• Gustavo Seabra
  • Re: [AMBER] reference re. determining size of timestep (Fri Jul 17 2009 - 11:53:46 CDT)
  • Re: Fw: [AMBER] Re: pls help and suggest (Fri Jul 17 2009 - 11:50:59 CDT)
  • Re: [AMBER] QMMM outupts (Thu Jul 09 2009 - 11:58:30 CDT)
  • [AMBER] Re: pls help and suggest (Thu Jul 09 2009 - 11:14:42 CDT)
• Hannes Kopitz
  • Re: [AMBER] Using idecomp=3 with igb=10 (PB) (Tue Jul 28 2009 - 07:47:15 CDT)
  • Re: [AMBER] Using idecomp=3 with igb=10 (PB) (Tue Jul 28 2009 - 05:09:01 CDT)
  • Re: [AMBER] question of mm_pbsa (Fri Jul 10 2009 - 04:36:44 CDT)
• Hannes Loeffler
  • RE: [AMBER] PCA analysis: the first vector is the movement of whole molecule. (Fri Jul 31 2009 - 02:27:54 CDT)
  • Re: [AMBER] PCA analysis: the first vector is the movement of whole molecule. (Thu Jul 30 2009 - 05:52:48 CDT)
  • Re: [AMBER] How to visualize PCA results without IED? (Tue Jul 28 2009 - 05:12:04 CDT)
  • [AMBER] nasty memory bug in calculatePrincipalAxis (Mon Jul 20 2009 - 03:30:38 CDT)
• Harald Lanig
  • [AMBER] Molecular Modeling Workshop and Model(l)ing'09 in Erlangen, Germany (Tue Jul 14 2009 - 09:02:16 CDT)
• Hemant Kumar
  • Re: [AMBER] Box shape change (Sun Jul 19 2009 - 12:38:43 CDT)
  • Re: [AMBER] Box shape change (Sun Jul 19 2009 - 07:05:04 CDT)
  • Re: [AMBER] Box shape change (Sun Jul 19 2009 - 06:00:18 CDT)
  • [AMBER] Box shape change (Sat Jul 18 2009 - 14:38:46 CDT)
  • RE: [AMBER] Umbrella Sampling (Sat Jul 18 2009 - 14:28:19 CDT)
  • [AMBER] Umbrella Sampling (Thu Jul 16 2009 - 13:01:40 CDT)
• Hlengisizwe Ndlovu
  • [AMBER] Steered MD.....SHAKE error!! (Fri Jul 17 2009 - 03:50:11 CDT)
  • [AMBER] vlimit exceeded....nscu_SMD!! (Thu Jul 16 2009 - 07:53:50 CDT)
  • [AMBER] Steered MD---more than one pair of atoms (Tue Jul 07 2009 - 08:27:59 CDT)
• Hopkins, Robert
  • RE: [Subject Filtered] Re: [AMBER] PMEMD in a Cygwin Environment 8% (Thu Jul 23 2009 - 15:37:12 CDT)
  • [AMBER] PMEMD in a Cygwin Environment (Tue Jul 14 2009 - 14:48:41 CDT)
• Hugh Heldenbrand
  • Re: [AMBER] Exclamation marks in trajectory (Mon Jul 13 2009 - 13:52:37 CDT)
  • [AMBER] Exclamation marks in trajectory (Mon Jul 13 2009 - 10:16:26 CDT)
• hwu_at_clarku.edu
  • [AMBER] Question on REST and VALUE1 keywords (Tue Jul 28 2009 - 16:06:34 CDT)
• Jeffrey
  • Re: [AMBER] radical simulation (Sun Jul 26 2009 - 07:28:39 CDT)
  • [AMBER] radical simulation (Fri Jul 24 2009 - 02:34:53 CDT)
  • Re: [AMBER] questions about RESP (Thu Jul 23 2009 - 07:51:34 CDT)
  • Re: [AMBER] questions about RESP (Mon Jul 20 2009 - 02:42:29 CDT)
  • [AMBER] questions about RESP (Thu Jul 16 2009 - 01:57:28 CDT)
  • [AMBER] TMD: solvation and equilibration questions (Fri Jul 10 2009 - 20:07:55 CDT)
  • Re: [AMBER] charges in topology file (Fri Jul 10 2009 - 11:20:01 CDT)
  • Re: [AMBER] The problem of restart file (Wed Jul 01 2009 - 09:07:08 CDT)
  • [AMBER] The problem of restart file (Wed Jul 01 2009 - 07:15:34 CDT)
• Jianyin Shao
  • Re: [AMBER] ptraj mask selection (Mon Jul 13 2009 - 14:02:03 CDT)
  • Re: [AMBER] ptraj mask selection (Mon Jul 13 2009 - 12:57:23 CDT)
• Jio M
  • Re: [AMBER] ambpdb problem (Fri Jul 31 2009 - 02:11:32 CDT)
  • [AMBER] ambpdb problem (Thu Jul 30 2009 - 14:12:10 CDT)
  • [AMBER] pdb file no bond and charges (Wed Jul 29 2009 - 01:28:48 CDT)
  • [AMBER] residues lacking connect0/connect1 (Mon Jul 27 2009 - 11:10:06 CDT)
  • [AMBER] -a flag :RESP (Sun Jul 19 2009 - 05:48:20 CDT)
  • [AMBER] RE: charge not zero on group:''''.respin1 attached (Sat Jul 18 2009 - 09:40:18 CDT)
  • [AMBER] charge not zero on group: RESP (Sat Jul 18 2009 - 00:14:58 CDT)
  • Re: [AMBER] GAFF and NME, ACE terminal res (Wed Jul 15 2009 - 23:29:08 CDT)
  • [AMBER] GAFF and NME, ACE terminal res (Mon Jul 13 2009 - 15:51:06 CDT)
  • [AMBER] suitable force field (Wed Jul 08 2009 - 02:14:12 CDT)
  • [AMBER] suitable force field (Wed Jul 08 2009 - 05:06:35 CDT)
• Jordan Monnet
  • Re: [AMBER] ambpdb problem (Fri Jul 31 2009 - 09:30:54 CDT)
  • Re: [AMBER] ambpdb problem (Thu Jul 30 2009 - 14:32:57 CDT)
  • Re: [AMBER] Can I get the torsion angle between base-pairs using ptraj ? (Wed Jul 15 2009 - 17:56:12 CDT)
  • Re: [AMBER] ouput trajectory of only CA atom (Wed Jul 08 2009 - 11:03:32 CDT)
• Jun Dong
  • Re: [AMBER] RE: pmemd parallel (Wed Jul 15 2009 - 10:00:49 CDT)
  • RE: [AMBER] Need help for PMEMD 10 installation (Mon Jul 13 2009 - 13:10:34 CDT)
  • RE: [AMBER] Need help for PMEMD 10 installation (Fri Jul 10 2009 - 12:25:03 CDT)
  • [AMBER] Need help for PMEMD 10 installation (Fri Jul 10 2009 - 11:05:49 CDT)
• Keith Van Nostrand
  • Re: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 (Wed Jul 22 2009 - 10:58:08 CDT)
  • Re: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 (Thu Jul 16 2009 - 16:08:04 CDT)
  • [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 (Fri Jul 10 2009 - 10:27:12 CDT)
• Khavrutskii, Ilja
  • Re: [AMBER] Disappearing common atoms in Amber 10 with TI (Mon Jul 20 2009 - 06:46:38 CDT)
  • Re: [AMBER] Disappearing common atoms in Amber 10 with TI (Thu Jul 16 2009 - 16:02:10 CDT)
  • [AMBER] Disappearing common atoms in Amber 10 with TI (Thu Jul 16 2009 - 08:38:43 CDT)
• Kristina Furse
  • RE: [AMBER] Replacing DNA base with analog (Thu Jul 23 2009 - 09:36:26 CDT)
  • RE: [AMBER] question of ibelly used in pmemd (Tue Jul 21 2009 - 11:27:29 CDT)
  • RE: [AMBER] question of ibelly used in pmemd (Tue Jul 21 2009 - 08:53:21 CDT)
  • RE: [AMBER] question of ibelly used in pmemd (Mon Jul 20 2009 - 11:56:26 CDT)
  • RE: [AMBER] ntt=3 and ibelly=1 (Fri Jul 17 2009 - 11:41:29 CDT)
  • [AMBER] ntt=3 and ibelly=1 (Thu Jul 16 2009 - 11:07:23 CDT)
• Lake, Thomas
  • RE: [AMBER] problem with energy calculations (Sun Jul 12 2009 - 08:35:33 CDT)
• Lan JIN
  • Re: [AMBER] amber10 installation problem (Fri Jul 10 2009 - 02:41:34 CDT)
  • Re: [AMBER] amber10 installation problem (Wed Jul 08 2009 - 21:46:22 CDT)
  • [AMBER] amber10 installation problem (Wed Jul 08 2009 - 01:49:05 CDT)
• Mahmoud A. A. Ibrahim
  • Re: [AMBER] problem with the energetics of the system (Sun Jul 12 2009 - 05:37:37 CDT)
  • [AMBER] problem with the energetics of the system (Sat Jul 11 2009 - 18:23:13 CDT)
  • [AMBER] Zinc ion, help (Tue Jul 07 2009 - 09:26:48 CDT)
• Manish Kumar
  • Re: [AMBER] Simulation with United atom force field in Implicit solvent. (Sun Jul 26 2009 - 13:22:40 CDT)
  • [AMBER] Simulation with United atom force field in Implicit solvent. (Sat Jul 25 2009 - 22:55:42 CDT)
  • Re: [AMBER] radical simulation (Fri Jul 24 2009 - 02:48:01 CDT)
  • Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz (Thu Jul 23 2009 - 02:10:51 CDT)
  • [AMBER] Patching terminal (Tue Jul 21 2009 - 18:53:54 CDT)
  • Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz (Mon Jul 20 2009 - 16:11:20 CDT)
  • Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz (Sun Jul 19 2009 - 14:36:35 CDT)
  • [AMBER] Re: MM-PBSA delphi.crg and delphi.siz (Thu Jul 09 2009 - 22:33:01 CDT)
  • [AMBER] MM-PBSA delphi.crg and delphi.siz (Wed Jul 08 2009 - 16:29:40 CDT)
• Mannan
  • [AMBER] Could not find type: MG Parameter file was not saved. though it was loaded (Sun Jul 26 2009 - 22:49:54 CDT)
  • [AMBER] Could not find type: MG Parameter file was not saved. (Sat Jul 25 2009 - 22:41:24 CDT)
• manoj singh
  • Re: [AMBER] RED: Charge derivation of transtion state analogue (Mon Jul 06 2009 - 00:03:27 CDT)
  • [AMBER] RED: Charge derivation of transtion state analogue (Sun Jul 05 2009 - 01:10:57 CDT)
• Marek Maly
  • Re: [AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ? (Fri Jul 17 2009 - 13:37:02 CDT)
  • [AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ? (Fri Jul 17 2009 - 11:34:44 CDT)
  • Re: [AMBER] Counterion release and Free energy of binding ? (Fri Jul 17 2009 - 06:10:40 CDT)
  • [AMBER] Counterion release and Free energy of binding ? (Tue Jul 14 2009 - 17:27:18 CDT)
  • Re: [AMBER] Nonstandard molecules simulated with parm99EP ? (Wed Jul 01 2009 - 11:02:29 CDT)
  • Re: [AMBER] Nonstandard molecules simulated with parm99EP ? (Wed Jul 01 2009 - 10:47:04 CDT)
• Marius Retegan
  • Re: [AMBER] help needed for HID (Sun Jul 12 2009 - 13:24:40 CDT)
• Markus Kaukonen
  • Re: [AMBER] need charges of FE-S cluster (Tue Jul 21 2009 - 13:50:39 CDT)
• Massimiliano Bonomi
  • [AMBER] PLUMED release 1.1.0 available (Tue Jul 28 2009 - 03:10:39 CDT)
• Matthias Negri
  • [AMBER] MM/PBSA, MM/GBSA and NMODE Analysis (Wed Jul 29 2009 - 05:55:46 CDT)
• Mengjuei Hsieh
  • [AMBER] Re: problem of installation of amber10 (Wed Jul 29 2009 - 14:41:52 CDT)
  • Re: [AMBER] error in antechamber (Mon Jul 27 2009 - 17:29:06 CDT)
  • Re: [AMBER] errors of PMEMD installation (Sat Jul 25 2009 - 22:10:11 CDT)
  • Re: 回å¤�： [AMBER] errors of PMEMD installation (Fri Jul 24 2009 - 13:12:00 CDT)
  • Re: 回å¤�： [AMBER] errors of PMEMD installation (Fri Jul 24 2009 - 03:41:05 CDT)
  • Re: [AMBER] errors of PMEMD installation (Thu Jul 23 2009 - 14:25:27 CDT)
• moitrayee_at_mbu.iisc.ernet.in
  • RE: [AMBER] Problem with amber9 installation (Tue Jul 14 2009 - 02:02:39 CDT)
  • [AMBER] Problem with amber9 installation (Mon Jul 13 2009 - 15:31:18 CDT)
• Myeong Lee
  • [AMBER] How to read md trajectory for each time slice as an input coordinate (Mon Jul 27 2009 - 03:16:47 CDT)
  • [AMBER] Can I get the torsion angle between base-pairs using ptraj ? (Wed Jul 15 2009 - 16:51:02 CDT)
  • [AMBER] Equilibrium water density (Wed Jul 15 2009 - 03:58:52 CDT)
  • [AMBER] How to fix specific atoms? (not residue) (Sat Jul 11 2009 - 06:46:06 CDT)
  • [AMBER] QMMM outupts (Tue Jul 07 2009 - 12:13:27 CDT)
• nam kim
  • Re: [AMBER] amber10 parallel compiling error (Thu Jul 23 2009 - 23:32:14 CDT)
  • Re: [AMBER] amber10 parallel compiling error (Tue Jul 21 2009 - 12:06:32 CDT)
  • Re: [AMBER] amber10 parallel compiling error (Mon Jul 20 2009 - 17:53:24 CDT)
  • Re: [AMBER] amber10 parallel compiling error (Mon Jul 20 2009 - 13:34:41 CDT)
  • Re: [AMBER] amber10 parallel compiling error (Mon Jul 20 2009 - 13:15:16 CDT)
  • Re: [AMBER] amber10 parallel compiling error (Mon Jul 20 2009 - 12:24:14 CDT)
  • [AMBER] amber10 parallel compiling error (Sat Jul 18 2009 - 12:19:39 CDT)
  • [AMBER] amber10 parallel compiling error (Thu Jul 16 2009 - 19:50:57 CDT)
• Nancy
  • [AMBER] ptraj-radial distribution function (Thu Jul 16 2009 - 01:34:12 CDT)
• Naser Alijabbari
  • Re: [AMBER] Re: mpirun noticed that process rank 1 ... on signal 1 (Hangup). (Tue Jul 14 2009 - 11:30:55 CDT)
  • [AMBER] Re: mpirun noticed that process rank 1 ... on signal 1 (Hangup). (Tue Jul 14 2009 - 05:49:14 CDT)
  • [AMBER] mpirun noticed that process rank 1 ... on signal 1 (Hangup). (Tue Jul 14 2009 - 05:41:39 CDT)
• Neha Gandhi
  • [AMBER] Re: non aminoacid Residue (Mon Jul 06 2009 - 03:43:56 CDT)
  • [AMBER] non standard residue (Mon Jul 06 2009 - 03:07:35 CDT)
• nicholus bhattacharjee
  • Re: [AMBER] Am I doing the right thing (Tue Jul 28 2009 - 23:36:31 CDT)
  • [AMBER] Am I doing the right thing (Tue Jul 28 2009 - 12:20:57 CDT)
• Nicolas SAPAY
  • Re: [AMBER] Compilation error with pmemd (amber10) on fedora9 64 bits (Fri Jul 31 2009 - 07:55:18 CDT)
  • [AMBER] Compilation error with pmemd (amber10) on fedora9 64 bits (Fri Jul 31 2009 - 04:41:21 CDT)
• Niel Henriksen
  • [AMBER] RE: Average structure over simulation (Mon Jul 27 2009 - 09:56:40 CDT)
• oguz gurbulak
  • [AMBER] ff parameters (Wed Jul 08 2009 - 09:35:40 CDT)
• Oliver Kuhn
  • Re: [AMBER] saquinavir parameterization with antechamber (Thu Jul 23 2009 - 03:06:00 CDT)
  • Re: [AMBER] saquinavir parameterization with antechamber (Thu Jul 23 2009 - 02:02:49 CDT)
  • [AMBER] saquinavir parameterization with antechamber (Wed Jul 22 2009 - 10:42:49 CDT)
• Olotu Odunayo
  • RE: [AMBER] RE: Average structure over simulation (Mon Jul 27 2009 - 10:47:20 CDT)
  • [AMBER] Average structure over simulation (Mon Jul 27 2009 - 08:38:59 CDT)
  • RE: [AMBER] Equilibration step (Thu Jul 23 2009 - 01:52:50 CDT)
  • RE: [AMBER] Equilibration step (Wed Jul 22 2009 - 11:46:12 CDT)
  • RE: [AMBER] Equilibration step (Wed Jul 22 2009 - 11:41:13 CDT)
  • [AMBER] Equilibration step (Wed Jul 22 2009 - 04:47:37 CDT)
• Organization
  • [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. (Wed Jul 22 2009 - 14:13:37 CDT)
• Pansy Patel
  • Re: [AMBER] query (Fri Jul 31 2009 - 09:41:05 CDT)
• Patrick Gedeon
  • Re: [AMBER] ptraj mask selection (Mon Jul 13 2009 - 14:58:18 CDT)
  • [AMBER] ptraj mask selection (Sun Jul 12 2009 - 22:45:56 CDT)
  • [AMBER] Re: Directory - GAFF Parameter File? (Mon Jul 06 2009 - 18:38:57 CDT)
  • [AMBER] Directory - GAFF Parameter File? (Mon Jul 06 2009 - 18:31:49 CDT)
• Paul Brandt
  • [AMBER] reference re. determining size of timestep (Thu Jul 09 2009 - 13:07:50 CDT)
  • [AMBER] default integration scheme in 7 vs. 10 (Wed Jul 01 2009 - 15:48:46 CDT)
• Paul Mortenson
  • [AMBER] rdparm bug? (Tue Jul 07 2009 - 11:29:44 CDT)
• Pepe` Falahat
  • [AMBER] Boundary Condition Problem (Sat Jul 04 2009 - 07:10:59 CDT)
• Peter Varnai
  • [AMBER] pmemd/bintraj and ifort 10.1.0.21 (Wed Jul 01 2009 - 13:28:30 CDT)
• Prem Prakash Pathak
  • [AMBER] Restrained backbone conformation MD simulation" (Fri Jul 10 2009 - 06:27:38 CDT)
• Qinghua Liao
  • Re: [AMBER] problem from xleap (Fri Jul 31 2009 - 20:38:19 CDT)
  • [AMBER] problem from xleap (Fri Jul 31 2009 - 09:38:18 CDT)
  • Re: [AMBER] error in antechamber (Tue Jul 28 2009 - 00:13:49 CDT)
  • Re: [AMBER] error in antechamber (Mon Jul 27 2009 - 20:02:26 CDT)
  • [AMBER] error in antechamber (Mon Jul 27 2009 - 06:57:50 CDT)
  • Re: 回å¤�： [AMBER] errors of PMEMD installation (Fri Jul 24 2009 - 20:24:10 CDT)
  • Re: 回å¤�： [AMBER] errors of PMEMD installation (Fri Jul 24 2009 - 04:59:03 CDT)
  • Re: 回å¤�： [AMBER] errors of PMEMD installation (Fri Jul 24 2009 - 04:18:44 CDT)
  • [AMBER] mailing list (Thu Jul 23 2009 - 20:45:50 CDT)
• R. A.
  • Re: [AMBER] antechamber (Thu Jul 02 2009 - 19:35:42 CDT)
  • Re: [AMBER] antechamber (Wed Jul 01 2009 - 19:46:19 CDT)
  • [AMBER] antechamber (Wed Jul 01 2009 - 04:19:54 CDT)
  • [AMBER] antechamber (Wed Jul 01 2009 - 04:17:51 CDT)
• Raja Pandian
  • [AMBER] DCCM (Tue Jul 07 2009 - 06:05:20 CDT)
• Ray Luo
  • Re: [AMBER] MM/PBSA, MM/GBSA and NMODE Analysis (Wed Jul 29 2009 - 19:25:14 CDT)
  • Re: [AMBER] Simulation with United atom force field in Implicit solvent. (Sun Jul 26 2009 - 02:09:07 CDT)
  • Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz (Tue Jul 21 2009 - 09:24:40 CDT)
  • Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz (Sun Jul 19 2009 - 17:45:29 CDT)
  • Re: [AMBER] question of mm_pbsa (Fri Jul 10 2009 - 11:47:12 CDT)
  • Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz (Fri Jul 10 2009 - 11:32:18 CDT)
• Rilei Yu
  • [AMBER] installing of amber10 problem (Wed Jul 08 2009 - 03:47:13 CDT)
  • [AMBER] Installing of amber10 (Wed Jul 08 2009 - 03:34:24 CDT)
  • [AMBER] calculation of the solvent accessibility (Sat Jul 04 2009 - 03:54:23 CDT)
• Rizwan Tai
  • [AMBER] nonbon.f question (Mon Jul 27 2009 - 14:30:12 CDT)
  • [AMBER] nonbon.f question (Mon Jul 20 2009 - 14:31:17 CDT)
• Robert Duke
  • Re: [AMBER] Compilation error with pmemd (amber10) on fedora9 64 bits (Fri Jul 31 2009 - 07:33:52 CDT)
  • Re: [AMBER] MPI error (Wed Jul 29 2009 - 07:05:57 CDT)
  • Re: [AMBER] how to launch XLEaP from SSH Secure Shell? (Wed Jul 22 2009 - 18:07:24 CDT)
  • Re: [AMBER] question of ibelly used in pmemd (Tue Jul 21 2009 - 09:16:21 CDT)
  • Re: [AMBER] question of ibelly used in pmemd (Tue Jul 21 2009 - 08:15:20 CDT)
  • Re: [AMBER] question of ibelly used in pmemd (Mon Jul 20 2009 - 12:55:23 CDT)
  • Re: [AMBER] question of ibelly used in pmemd (Mon Jul 20 2009 - 12:10:03 CDT)
  • Re: [AMBER] question of ibelly used in pmemd (Mon Jul 20 2009 - 11:42:08 CDT)
  • Re: [AMBER] question of ibelly used in pmemd (Mon Jul 20 2009 - 10:53:50 CDT)
  • Re: [AMBER] question of ibelly used in pmemd (Mon Jul 20 2009 - 09:42:15 CDT)
  • Re: [AMBER] question of ibelly used in pmemd (Fri Jul 17 2009 - 10:48:41 CDT)
  • Re: [AMBER] question of ibelly used in pmemd (Wed Jul 15 2009 - 16:56:00 CDT)
  • Re: [AMBER] question of ibelly used in pmemd (Wed Jul 15 2009 - 13:22:23 CDT)
  • Re: [AMBER] PMEMD in a Cygwin Environment (Tue Jul 14 2009 - 15:16:46 CDT)
  • Re: [AMBER] Need help for PMEMD 10 installation (Tue Jul 14 2009 - 06:50:26 CDT)
  • Re: [AMBER] pmemd/bintraj and ifort 10.1.0.21 (Wed Jul 01 2009 - 13:54:52 CDT)
• Rodrigo Galindo
  • Re: [AMBER] Installing Amber10 on Ubuntu (Wed Jul 29 2009 - 14:49:33 CDT)
  • [AMBER] DNA + intercalator (Fri Jul 24 2009 - 17:22:35 CDT)
• Ross Walker
  • [AMBER] RE: Questions about QMMM (Tue Jul 21 2009 - 17:47:49 CDT)
  • [AMBER] RE: the copper paramter (Mon Jul 20 2009 - 16:38:14 CDT)
  • RE: [AMBER] Tutorial A3 (Mon Jul 20 2009 - 14:03:44 CDT)
  • RE: [AMBER] amber10 parallel compiling error (Mon Jul 20 2009 - 12:33:08 CDT)
  • RE: [AMBER] question of ibelly used in pmemd (Mon Jul 20 2009 - 12:32:08 CDT)
  • RE: [AMBER] Different machines (Sun Jul 19 2009 - 11:28:52 CDT)
  • RE: [AMBER] production phase (Thu Jul 16 2009 - 22:56:13 CDT)
  • RE: [AMBER] ntt=3 and ibelly=1 (Thu Jul 16 2009 - 22:44:47 CDT)
  • RE: [AMBER] amber10 parallel compiling error (Thu Jul 16 2009 - 22:43:15 CDT)
  • RE: [AMBER] IDIVF and PN (Thu Jul 16 2009 - 22:40:11 CDT)
  • RE: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 (Thu Jul 16 2009 - 22:34:13 CDT)
  • RE: [AMBER] question of ibelly used in pmemd (Wed Jul 15 2009 - 20:32:07 CDT)
  • RE: [AMBER] Re: mpirun noticed that process rank 1 ... on signal 1 (Hangup). (Tue Jul 14 2009 - 07:33:49 CDT)
  • [AMBER] RE: pmemd parallel (Tue Jul 14 2009 - 07:24:06 CDT)
  • RE: [AMBER] Problem with amber9 installation (Mon Jul 13 2009 - 22:34:54 CDT)
  • RE: [AMBER] Exclamation marks in trajectory (Mon Jul 13 2009 - 14:20:37 CDT)
  • RE: [AMBER] Need help for PMEMD 10 installation (Mon Jul 13 2009 - 14:18:26 CDT)
  • RE: [AMBER] Exclamation marks in trajectory (Mon Jul 13 2009 - 13:13:17 CDT)
  • RE: [AMBER] Amber10, Serial compilation with ifort (Sun Jul 12 2009 - 16:41:07 CDT)
  • Re: [AMBER] problem with the energetics of the system (Sat Jul 11 2009 - 18:52:42 CDT)
  • RE: [AMBER] Need help for PMEMD 10 installation (Fri Jul 10 2009 - 13:52:13 CDT)
  • RE: [AMBER] Need help for PMEMD 10 installation (Fri Jul 10 2009 - 11:26:29 CDT)
  • RE: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 (Fri Jul 10 2009 - 11:21:11 CDT)
  • RE: [AMBER] AMBER windows version ? (Thu Jul 09 2009 - 17:45:49 CDT)
  • RE: [AMBER] rmsd_ptraj (Wed Jul 08 2009 - 23:35:59 CDT)
  • RE: [AMBER] MPI process terminated unexpectedly forrtl: error (69): process interrupted (SIGINT) (Wed Jul 08 2009 - 10:01:24 CDT)
  • RE: [AMBER] Principle Questions (Tue Jul 07 2009 - 18:42:42 CDT)
  • RE: [AMBER] Tleap input error, atom not found in residue template (Mon Jul 06 2009 - 23:28:46 CDT)
  • [AMBER] RE: suggestions (Mon Jul 06 2009 - 20:01:51 CDT)
  • [AMBER] RE: question about TUTORIAL A1 (Mon Jul 06 2009 - 11:58:47 CDT)
  • RE: [AMBER] Re: non aminoacid Residue (Mon Jul 06 2009 - 11:21:44 CDT)
  • RE: [AMBER] Leap Questions... (Sun Jul 05 2009 - 23:01:34 CDT)
  • [AMBER] RE: ask for help (zn parameters) (Sun Jul 05 2009 - 21:56:50 CDT)
  • [AMBER] RE: question about TUTORIAL A1 (Sun Jul 05 2009 - 21:29:38 CDT)
  • RE: [AMBER] default integration scheme in 7 vs. 10 (Wed Jul 01 2009 - 16:29:12 CDT)
  • RE: [AMBER] amber9 in fedora10 (Wed Jul 01 2009 - 11:36:33 CDT)
• Rubben Torella
  • Re: [AMBER] MM-PBSA problem (Fri Jul 03 2009 - 08:57:09 CDT)
• Rukman Hertadi
  • RE: [AMBER] cpin error (Tue Jul 28 2009 - 00:22:18 CDT)
  • [AMBER] cpin error (Fri Jul 24 2009 - 02:18:52 CDT)
• s. Bill
  • [AMBER] Metalloproteins - Ligand Protonation (Fri Jul 31 2009 - 13:01:42 CDT)
  • [AMBER] Protonated or not (Fri Jul 31 2009 - 12:15:32 CDT)
  • Re: Solved it thanks [AMBER] RED.III: Invalid Optimization OUTPUT (Wed Jul 29 2009 - 07:14:02 CDT)
  • [AMBER] RED.III: Invalid Optimization OUTPUT (Wed Jul 29 2009 - 03:37:27 CDT)
  • [AMBER] QM/MM (Tue Jul 28 2009 - 01:44:15 CDT)
  • [AMBER] Tutorial A3 (Sun Jul 19 2009 - 14:33:58 CDT)
  • [AMBER] which keyword (Sun Jul 19 2009 - 07:21:23 CDT)
  • [AMBER] Different machines (Sun Jul 19 2009 - 04:55:48 CDT)
  • [AMBER] production phase (Thu Jul 16 2009 - 07:18:25 CDT)
  • [AMBER] IDIVF and PN (Thu Jul 16 2009 - 07:11:27 CDT)
  • [AMBER] R.E.D. help please (Wed Jul 15 2009 - 09:11:46 CDT)
  • [AMBER] help needed for HID (Sun Jul 12 2009 - 13:16:08 CDT)
  • [AMBER] amber dihedral format (Sun Jul 12 2009 - 09:05:23 CDT)
  • [AMBER] charged or not (Thu Jul 09 2009 - 07:33:05 CDT)
• s_bill36_at_yahoo.co.uk
  • [AMBER] Principle Questions (Tue Jul 07 2009 - 02:50:53 CDT)
• Sally Pias
  • Re: [AMBER] unexplained blow-up at restart (Mon Jul 13 2009 - 11:11:08 CDT)
  • Re: [AMBER] unexplained blow-up at restart (Mon Jul 13 2009 - 02:01:29 CDT)
  • Re: [AMBER] unexplained blow-up at restart (Fri Jul 10 2009 - 13:59:24 CDT)
  • Re: [AMBER] unexplained blow-up at restart (Fri Jul 10 2009 - 12:20:27 CDT)
  • Re: [AMBER] unexplained blow-up at restart (Fri Jul 10 2009 - 11:31:59 CDT)
  • Re: [AMBER] unexplained blow-up at restart (Fri Jul 10 2009 - 10:29:01 CDT)
  • [AMBER] unexplained blow-up at restart (Fri Jul 10 2009 - 03:02:42 CDT)
• Santosh Mogurampelly
  • [AMBER] pulling two atoms in SMD (Tue Jul 28 2009 - 07:10:12 CDT)
• Scott Brozell
  • Re: [AMBER] Compiling Amber 10 (serial) on Mac OS X 10.5.7 w/ gcc, Intel Fortan 11.0 and MKL 10.0 (Wed Jul 22 2009 - 14:52:59 CDT)
• Seetin, Matthew
  • RE: [AMBER] Umbrella Sampling (Thu Jul 16 2009 - 15:13:59 CDT)
• Sergey Samsonov
  • [AMBER] xleap facility to insert a residue (Fri Jul 24 2009 - 08:07:27 CDT)
• Shozeb Haider
  • Re: [AMBER] How to visualize PCA results without IED? (Tue Jul 28 2009 - 06:02:22 CDT)
  • [AMBER] position v time graph (Wed Jul 15 2009 - 13:21:35 CDT)
• Shubhra Gupta
  • Re: [AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S" (Wed Jul 15 2009 - 07:38:34 CDT)
  • Re: [AMBER] Peptide bond broken (Sun Jul 12 2009 - 23:17:31 CDT)
• Siddharth Rastogi
  • Re: [AMBER] AMBER windows version ? (Thu Jul 09 2009 - 18:17:33 CDT)
  • [AMBER] AMBER windows version ? (Thu Jul 09 2009 - 16:14:05 CDT)
• Simon Becker
  • Re: [AMBER] unexplained blow-up at restart (Fri Jul 10 2009 - 08:24:13 CDT)
• steinbrt_at_rci.rutgers.edu
  • Re: [AMBER] QM/MM (Tue Jul 28 2009 - 02:19:32 CDT)
  • Re: [AMBER] Disappearing common atoms in Amber 10 with TI (Mon Jul 20 2009 - 07:05:24 CDT)
  • Re: [AMBER] Disappearing common atoms in Amber 10 with TI (Fri Jul 17 2009 - 03:53:19 CDT)
  • Re: [AMBER] Disappearing common atoms in Amber 10 with TI (Thu Jul 16 2009 - 09:09:39 CDT)
  • Re: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished, (Thu Jul 16 2009 - 04:01:15 CDT)
• subarna thakur
  • [AMBER] ESP charges of Fe4S4 (Wed Jul 22 2009 - 00:19:48 CDT)
  • [AMBER] query regarding FE4S4 (Thu Jul 16 2009 - 02:14:27 CDT)
  • [AMBER] need charges of FE-S cluster (Mon Jul 06 2009 - 05:44:05 CDT)
• suhaib sh
  • Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz (Fri Jul 10 2009 - 09:17:52 CDT)
  • [AMBER] missing Halogen parameters (radii) for PBSA/GBSA calculations - PB Bomb in pb_aaradi(): No radius assigned for atom (Thu Jul 02 2009 - 08:18:05 CDT)
• Sushil Mishra
  • [AMBER] file truncated : Output file truncated during equilibration of salivated complex in MM-PBSA (Mon Jul 20 2009 - 07:26:27 CDT)
  • [AMBER] Output file truncated during equilibration of salivated complex in MM-PBSA (Mon Jul 20 2009 - 05:40:51 CDT)
  • [AMBER] MM-PBSA tail: equil.out: file truncated during equilibration of salivated complex (Mon Jul 20 2009 - 03:32:32 CDT)
  • Re: [AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S" (Wed Jul 15 2009 - 08:58:13 CDT)
  • [AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S" (Wed Jul 15 2009 - 05:36:26 CDT)
  • [AMBER] calculation of binding energy for lectin and fucuse.. (Fri Jul 10 2009 - 13:26:20 CDT)
  • Re: [AMBER] EPtot for Alpha-L- methyl fucose (Fri Jul 10 2009 - 09:12:28 CDT)
  • [AMBER] EPtot for Alpha-L- methyl fucose (Fri Jul 10 2009 - 08:47:26 CDT)
• Syed Tarique Moin
  • Re: [AMBER] Peptide bond broken (Mon Jul 13 2009 - 08:20:02 CDT)
  • [AMBER] Peptide bond broken (Fri Jul 10 2009 - 13:19:02 CDT)
• Taufik Al-Sarraj
  • [AMBER] H-bond vs. VdW (Fri Jul 03 2009 - 13:48:12 CDT)
• Thomas Cheatham
  • Re: [AMBER] Regarding Hbond interactions (Thu Jul 23 2009 - 17:57:57 CDT)
  • RE: [AMBER] rmsd_ptraj (Thu Jul 09 2009 - 02:08:53 CDT)
• Thomas Cheatham III
  • Re: [AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ? (Fri Jul 17 2009 - 11:50:15 CDT)
• Thomas Lake
  • Re: [AMBER] problem with energy calculations (Sun Jul 12 2009 - 09:10:58 CDT)
  • [AMBER] problem with energy calculations (Fri Jul 10 2009 - 11:13:55 CDT)
• Thomas Patko
  • Re: [AMBER] how to launch XLEaP from SSH Secure Shell? (Wed Jul 22 2009 - 19:47:51 CDT)
• Tom Joseph
  • Re: [AMBER] problem from xleap (Fri Jul 31 2009 - 11:41:49 CDT)
  • Re: [AMBER] how to launch XLEaP from SSH Secure Shell? (Wed Jul 22 2009 - 18:24:56 CDT)
  • Re: [AMBER] Equilibration step (Wed Jul 22 2009 - 14:05:58 CDT)
  • Re: [AMBER] Equilibration step (Wed Jul 22 2009 - 07:35:15 CDT)
  • Re: [AMBER] Trouble saving amberparm files (Mon Jul 13 2009 - 16:14:39 CDT)
  • Re: [AMBER] Trouble saving amberparm files (Mon Jul 13 2009 - 16:13:14 CDT)
  • Re: [AMBER] Trouble saving amberparm files (Mon Jul 13 2009 - 15:16:27 CDT)
  • Re: [AMBER] How to fix specific atoms? (not residue) (Sat Jul 11 2009 - 17:01:04 CDT)
• Toshifumi Yui
  • Re: [AMBER] amber10 parallel compiling error (Tue Jul 21 2009 - 00:46:11 CDT)
• vallespardojl_at_chem.leidenuniv.nl
  • Re: [AMBER] loading a mol2 file in xleap (Mon Jul 27 2009 - 07:40:13 CDT)
  • [AMBER] loading a mol2 file in xleap (Fri Jul 24 2009 - 12:40:13 CDT)
• vhakkim boy
  • [AMBER] MPI error (Wed Jul 29 2009 - 04:44:35 CDT)
  • [AMBER] carbonic anhydrase (CA) simulation (Thu Jul 16 2009 - 02:03:23 CDT)
• Vishal Maingi
  • Fw: [AMBER] Re: pls help and suggest (Thu Jul 09 2009 - 13:45:21 CDT)
  • [AMBER] unable to read MM charges (no reply yet) (Mon Jul 06 2009 - 22:32:07 CDT)
  • [AMBER] unable to read MM charges (Mon Jul 06 2009 - 04:32:29 CDT)
• vitor.felix
  • =?utf-8?B?UmU6IFtBTUJFUl0gQ29tcGlsaW5nIEFtYmVyIDEwIChzZXJpYWwpIG9uIE1hYyBPUyBYIDEwLjUuNyB3LyBnY2MsCUludGVsIEZvcnRhbiAxMS4wIGFuZCBNS0wgMTAuMA==?= (Tue Jul 21 2009 - 22:15:06 CDT)
• Vlad Cojocaru
  • Re: [AMBER] How to visualize PCA results without IED? (Tue Jul 28 2009 - 05:42:05 CDT)
  • Re: [AMBER] How to visualize PCA results without IED? (Tue Jul 28 2009 - 04:58:50 CDT)
  • Re: [AMBER] ouput trajectory of only CA atom (Wed Jul 08 2009 - 10:07:30 CDT)
• Wei Huang
  • RE: [AMBER] ptraj - cluster (Fri Jul 17 2009 - 07:34:00 CDT)
• workalemahu berhanu
  • [AMBER] implicit solvent (GB version2) MD simulation (Fri Jul 10 2009 - 10:53:47 CDT)
• xiaoqin huang
  • RE: [AMBER] question of ibelly used in pmemd (Mon Jul 20 2009 - 12:39:16 CDT)
  • RE: [AMBER] question of ibelly used in pmemd (Mon Jul 20 2009 - 12:20:36 CDT)
  • RE: [AMBER] question of ibelly used in pmemd (Mon Jul 20 2009 - 11:28:42 CDT)
  • RE: [AMBER] question of ibelly used in pmemd (Mon Jul 20 2009 - 10:20:32 CDT)
  • RE: [AMBER] question of ibelly used in pmemd (Mon Jul 20 2009 - 09:21:20 CDT)
  • RE: [AMBER] question of ibelly used in pmemd (Fri Jul 17 2009 - 09:54:55 CDT)
  • RE: [AMBER] question of ibelly used in pmemd (Fri Jul 17 2009 - 09:36:06 CDT)
  • RE: [AMBER] question of ibelly used in pmemd (Wed Jul 15 2009 - 16:28:52 CDT)
  • [AMBER] question of ibelly used in pmemd (Wed Jul 15 2009 - 12:34:20 CDT)
• xueqin pang
  • [AMBER] how to choose exclusion policy for GPCR (Tue Jul 28 2009 - 21:12:33 CDT)
• Yana Berezovskaya
  • [AMBER] how to launch XLEaP from SSH Secure Shell? (Wed Jul 22 2009 - 17:44:45 CDT)
• Ye MEI
  • [AMBER] equivalent atoms (Mon Jul 20 2009 - 23:56:52 CDT)
• Yogesh Aher
  • [AMBER] File conversion for from Amber to Charmm (Fri Jul 17 2009 - 01:45:11 CDT)
  • Re: [AMBER] Could not find bond parameter for O2 - ca (Fri Jul 17 2009 - 01:37:52 CDT)
  • [AMBER] Could not find bond parameter for O2 - ca (Tue Jul 14 2009 - 07:53:35 CDT)
• Youn Kyeung Lee
  • [AMBER] ptraj grid option (Tue Jul 21 2009 - 02:15:11 CDT)
• Yvonne.Westermaier_at_unige.ch
  • Re: [AMBER] thymidine monophosphate parametrization (Tue Jul 28 2009 - 07:10:43 CDT)
  • [AMBER] thymidine monophosphate parametrization (Fri Jul 24 2009 - 10:18:18 CDT)
• Zhongjie Liang
  • ´ð¸´: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished, (Thu Jul 16 2009 - 04:16:02 CDT)
  • [AMBER] Coordinate resetting (SHAKE) cannot be accomplished, (Thu Jul 16 2009 - 03:37:29 CDT)
• ÁÎÇ໪
  • »Ø¸´£º [AMBER] antechamber (Thu Jul 02 2009 - 19:45:41 CDT)
• å»–é�’å�Ž
  • 回å¤�： [AMBER] errors of PMEMD installation (Thu Jul 23 2009 - 20:27:51 CDT)
  • [AMBER] errors of PMEMD installation (Wed Jul 22 2009 - 09:28:45 CDT)
  • 回å¤�： [AMBER] amber10 parallel compiling error (Thu Jul 16 2009 - 20:27:05 CDT)
  • 回å¤�： [AMBER] question of mm_pbsa (Sat Jul 11 2009 - 19:03:33 CDT)
  • 回å¤�： [AMBER] question of mm_pbsa (Fri Jul 10 2009 - 20:22:25 CDT)
  • 回å¤�： [AMBER] question of mm_pbsa (Fri Jul 10 2009 - 19:50:55 CDT)
  • [AMBER] question of mm_pbsa (Thu Jul 09 2009 - 20:49:40 CDT)
  • 回å¤�： [AMBER] missing Halogen parameters (radii) for PBSA/GBSA calculations - PB Bomb in pb_aaradi(): No radius assigned for atom (Thu Jul 02 2009 - 23:53:09 CDT)
  • 回å¤�： 回å¤�： [AMBER] antechamber (Thu Jul 02 2009 - 19:53:06 CDT)

Last message date: Thu Dec 31 2009 - 22:57:46 CST
Archived on: Thu Dec 31 2009 - 22:58:33 CST