AMBER Archive (2009) - Mar 2009 By Thread

Starting: Sun Mar 01 2009 - 05:52:43 CST
Ending: Tue Mar 31 2009 - 22:52:42 CDT

• Re: [AMBER] NAB md function prints strange output Scott Brozell (Thu Mar 12 2009 - 16:04:15 CDT)
• Re: [AMBER] IG not change at each restart of NPT simulation Hopkins, Robert (Wed Mar 18 2009 - 17:55:33 CDT)
  • RE: [AMBER] IG not change at each restart of NPT simulation Ross Walker (Wed Mar 18 2009 - 18:07:07 CDT)
    • RE: [AMBER] IG not change at each restart of NPT simulation Hopkins, Robert (Wed Mar 18 2009 - 18:15:54 CDT)
    • RE: [AMBER] IG not change at each restart of NPT simulation Rajesh Raju (Thu Mar 19 2009 - 07:54:26 CDT)
    • Re: [AMBER] IG not change at each restart of NPT simulation Robert Duke (Thu Mar 19 2009 - 08:24:02 CDT)
    • Re: [AMBER] IG not change at each restart of NPT simulation Adrian Roitberg (Thu Mar 19 2009 - 08:30:10 CDT)
    • Re: [AMBER] IG not change at each restart of NPT simulation Robert Duke (Thu Mar 19 2009 - 09:05:35 CDT)
    • Re: [AMBER] IG not change at each restart of NPT simulation Rajesh Raju (Fri Mar 20 2009 - 08:20:09 CDT)
    • Re: [AMBER] IG not change at each restart of NPT simulation Robert Duke (Fri Mar 20 2009 - 08:58:18 CDT)
• [AMBER] PMEMD error message neville forlemu (Sun Mar 08 2009 - 15:37:09 CDT)
• Re: [AMBER] PMEMD error message Robert Duke (Sun Mar 08 2009 - 15:47:16 CDT)
• RE: [AMBER] PMEMD error message Ross Walker (Sun Mar 08 2009 - 16:52:01 CDT)
• [AMBER] PMEMD error message neville forlemu (Tue Mar 10 2009 - 09:55:31 CDT)
• Re: [AMBER] PMEMD error message Robert Duke (Tue Mar 10 2009 - 10:39:38 CDT)
• Re: [AMBER] problem with amber installation nicholus bhattacharjee (Tue Mar 24 2009 - 12:14:10 CDT)
• Re: [AMBER] H-Bonds Thomas Cheatham III (Wed Mar 04 2009 - 15:00:30 CST)
  • [AMBER] What is the default position of the partial charges? Chih-Ying Lin (Wed Mar 04 2009 - 15:06:16 CST)
    • Re: [AMBER] What is the default position of the partial charges? Thomas Cheatham III (Wed Mar 04 2009 - 15:44:20 CST)
  • [AMBER] solvent and counter ions Taufik Al-Sarraj (Wed Mar 04 2009 - 15:36:36 CST)
    • Re: [AMBER] solvent and counter ions Thomas Cheatham III (Wed Mar 04 2009 - 15:49:35 CST)
    • Re: [AMBER] solvent and counter ions Taufik Al-Sarraj (Thu Mar 05 2009 - 17:16:24 CST)
    • Re: [AMBER] solvent and counter ions Bill Ross (Thu Mar 05 2009 - 17:29:50 CST)
• [AMBER] Re: using Gromacs for analysis oguz gurbulak (Mon Mar 02 2009 - 10:17:45 CST)
• Re: [AMBER] Question about NAB module David A. Case (Sun Mar 01 2009 - 07:52:19 CST)
  • RE: [AMBER] Question about NAB module Wei Huang (Sun Mar 01 2009 - 08:57:50 CST)
    • RE: [AMBER] Question about NAB module Andreas Svrcek-Seiler (Mon Mar 02 2009 - 03:23:52 CST)
• [AMBER] binding free energy Maryam Hamzehee (Sun Mar 01 2009 - 05:52:43 CST)
  • Re: [AMBER] binding free energy Barbault Florent (Sun Mar 01 2009 - 06:20:39 CST)
    • Re: [AMBER] binding free energy Don.Bashford_at_stjude.org (Sun Mar 01 2009 - 11:18:39 CST)
      • RE: [AMBER] binding free energy Ross Walker (Sun Mar 01 2009 - 11:29:35 CST)
      • RE: [AMBER] binding free energy Maryam Hamzehee (Mon Mar 02 2009 - 01:33:44 CST)
      • Re: [AMBER] binding free energy Robert Duke (Mon Mar 02 2009 - 07:22:22 CST)
      • RE: [AMBER] binding free energy Ross Walker (Mon Mar 02 2009 - 14:16:55 CST)
• [AMBER] Pseudoatoms waleed zalloum (Mon Mar 02 2009 - 06:12:33 CST)
  • Re: [AMBER] Pseudoatoms David A. Case (Mon Mar 02 2009 - 17:25:29 CST)
    • [AMBER] How to restart the umbrella sampling jobs? Catein Catherine (Mon Mar 02 2009 - 23:52:16 CST)
      • RE: [AMBER] How to restart the umbrella sampling jobs? Ross Walker (Tue Mar 03 2009 - 10:00:04 CST)
      • Re: [AMBER] How to restart the umbrella sampling jobs? Gustavo Seabra (Tue Mar 03 2009 - 14:41:25 CST)
• [AMBER] How can I use the charge I calculated (using mol2 file) ? ÀÌÀ±°æ (Mon Mar 02 2009 - 07:27:39 CST)
  • Re: [AMBER] How can I use the charge I calculated (using mol2 file) ? David A. Case (Mon Mar 02 2009 - 08:56:54 CST)
    • Re: Re: [AMBER] How can I use the charge I calculated (using mol2 file) ? ÀÌÀ±°æ (Mon Mar 02 2009 - 19:39:37 CST)
      • Re: Re: [AMBER] How can I use the charge I calculated (using mol2 file) ? David A. Case (Tue Mar 03 2009 - 07:39:26 CST)
      • Re: [AMBER] How can I use the charge I calculated (using mol2 file) ? FyD (Tue Mar 03 2009 - 08:12:18 CST)
• [AMBER] calculate shear viscosity oguz gurbulak (Mon Mar 02 2009 - 07:35:06 CST)
• [AMBER] assigning velocities to each atom without heating the system Parimal Kar (Mon Mar 02 2009 - 10:44:26 CST)
  • Re: [AMBER] assigning velocities to each atom without heating the system Gustavo Seabra (Mon Mar 02 2009 - 11:31:09 CST)
    • Re: [AMBER] assigning velocities to each atom without heating the system Parimal Kar (Mon Mar 02 2009 - 11:46:25 CST)
  • RE: [AMBER] assigning velocities to each atom without heating the system Ross Walker (Mon Mar 02 2009 - 14:23:22 CST)
• [AMBER] specification of antechamber AC file format? Nicholas Musolino (Tue Mar 03 2009 - 01:53:23 CST)
  • Re: [AMBER] specification of antechamber AC file format? David A. Case (Wed Mar 04 2009 - 16:39:44 CST)
    • [AMBER] AMBER installation : compilation error Catein Catherine (Wed Mar 04 2009 - 20:53:54 CST)
• [AMBER] inpcrd and prmtop m m (Tue Mar 03 2009 - 03:27:06 CST)
  • Re: [AMBER] inpcrd and prmtop Hannes Loeffler (Tue Mar 03 2009 - 03:37:16 CST)
    • RE: [AMBER] inpcrd and prmtop m m (Tue Mar 03 2009 - 04:08:51 CST)
    • Re: [AMBER] inpcrd and prmtop FyD (Tue Mar 03 2009 - 04:19:43 CST)
  • Re: [AMBER] inpcrd and prmtop Gustavo Seabra (Tue Mar 03 2009 - 14:20:38 CST)
• [AMBER] Fail to allocate ff Madhurima Jana (Tue Mar 03 2009 - 05:17:57 CST)
  • Re: [AMBER] Fail to allocate ff Nicholas Musolino (Tue Mar 03 2009 - 07:10:21 CST)
    • Re: [AMBER] Fail to allocate ff Madhurima Jana (Tue Mar 03 2009 - 08:27:41 CST)
  • Re: [AMBER] Fail to allocate ff Gustavo Seabra (Tue Mar 03 2009 - 14:36:53 CST)
• [AMBER] A good way to use an Amber force field with NAMD? Sasha Buzko (Tue Mar 03 2009 - 15:37:29 CST)
  • Re: [AMBER] A good way to use an Amber force field with NAMD? Gustavo Seabra (Tue Mar 03 2009 - 18:08:33 CST)
    • Re: [AMBER] A good way to use an Amber force field with NAMD? Adrian Roitberg (Tue Mar 03 2009 - 18:11:49 CST)
      • Re: [AMBER] A good way to use an Amber force field with NAMD? Sasha Buzko (Tue Mar 03 2009 - 18:26:44 CST)
      • RE: [AMBER] A good way to use an Amber force field with NAMD? Ross Walker (Tue Mar 03 2009 - 19:33:58 CST)
      • Re: [AMBER] A good way to use an Amber force field with NAMD? Sasha Buzko (Tue Mar 03 2009 - 20:55:56 CST)
      • Re: [AMBER] A good way to use an Amber force field with NAMD? Robert Duke (Tue Mar 03 2009 - 22:26:59 CST)
      • Re: [AMBER] A good way to use an Amber force field with NAMD? Sasha Buzko (Wed Mar 04 2009 - 11:58:09 CST)
• [AMBER] Amber: water-water hydrogen bonding analysis on a subset of waters in a trajectory Jeff Schwinefus (Tue Mar 03 2009 - 16:18:25 CST)
  • Re: [AMBER] Amber: water-water hydrogen bonding analysis on a subset of waters in a trajectory Thomas Cheatham III (Wed Mar 04 2009 - 13:59:30 CST)
    • Re: [AMBER] Amber: water-water hydrogen bonding analysis on a subset of waters in a trajectory Jeff Schwinefus (Wed Mar 04 2009 - 23:22:34 CST)
• [AMBER] angle between ligand ring plane and axis Jia Xu (Wed Mar 04 2009 - 05:00:08 CST)
• [AMBER] hydrogen bond . .. (Wed Mar 04 2009 - 05:12:33 CST)
  • Re: [AMBER] hydrogen bond Carlos Simmerling (Wed Mar 04 2009 - 05:20:53 CST)
  • RE: [AMBER] hydrogen bond Ross Walker (Wed Mar 04 2009 - 10:39:49 CST)
• [AMBER] Regarding leap aneesh cna (Wed Mar 04 2009 - 05:43:52 CST)
  • Re: [AMBER] Regarding leap Carlos Simmerling (Wed Mar 04 2009 - 05:48:30 CST)
  • Re: [AMBER] Regarding leap Gustavo Seabra (Wed Mar 04 2009 - 16:05:25 CST)
    • Re: [AMBER] Regarding leap aneesh cna (Wed Mar 04 2009 - 22:29:17 CST)
      • Re: [AMBER] Regarding leap Gustavo Seabra (Thu Mar 05 2009 - 09:32:56 CST)
• [AMBER] unning MMPBSA in CHCl3 environment SAFAK OZHAN (Wed Mar 04 2009 - 05:55:52 CST)
  • Re: [AMBER] unning MMPBSA in CHCl3 environment Ray Luo (Wed Mar 04 2009 - 11:15:55 CST)
• [AMBER] Thermodynamic Intergration problem Xiaohui Jiang [Contractor] (Wed Mar 04 2009 - 09:36:14 CST)
  • RE: [AMBER] Thermodynamic Intergration problem Ross Walker (Wed Mar 04 2009 - 10:45:24 CST)
    • RE: [AMBER] Thermodynamic Intergration problem Xiaohui Jiang [Contractor] (Wed Mar 04 2009 - 11:00:06 CST)
• [AMBER] Compilation and qmmm_div Benjamin Roberts (Wed Mar 04 2009 - 09:48:16 CST)
  • RE: [AMBER] Compilation and qmmm_div Ross Walker (Wed Mar 04 2009 - 10:36:07 CST)
    • Re: [AMBER] Compilation and qmmm_div Benjamin Roberts (Wed Mar 04 2009 - 18:15:37 CST)
• [AMBER] radial distribution function mask iccy liu (Wed Mar 04 2009 - 12:57:08 CST)
• [AMBER] Segmentation faults Benjamin Roberts (Wed Mar 04 2009 - 18:17:50 CST)
• Re: [AMBER] solvent and counter ions Bill Ross (Wed Mar 04 2009 - 18:20:45 CST)
• [AMBER] DNA simulation: Problem with RMSD BERGY (Wed Mar 04 2009 - 21:44:26 CST)
  • Re: [AMBER] DNA simulation: Problem with RMSD Thomas Cheatham (Wed Mar 04 2009 - 22:04:53 CST)
    • Re: [AMBER] DNA simulation: Problem with RMSD BERGY (Fri Mar 06 2009 - 00:20:00 CST)
• [AMBER] Fwd: please help me out bharat lakhani (Wed Mar 04 2009 - 22:42:06 CST)
• [AMBER] Re: Fw:How to creat .frcmod file FyD (Thu Mar 05 2009 - 00:22:56 CST)
• [AMBER] please help me out bharat lakhani (Thu Mar 05 2009 - 02:35:44 CST)
  • Re: [AMBER] please help me out FyD (Thu Mar 05 2009 - 03:22:20 CST)
    • Re: [AMBER] please help me out bharat lakhani (Thu Mar 05 2009 - 05:16:45 CST)
    • Re: [AMBER] please help me out bharat lakhani (Mon Mar 09 2009 - 00:04:45 CDT)
      • Re: [AMBER] please help me out FyD (Mon Mar 09 2009 - 03:10:08 CDT)
      • Re: [AMBER] please help me out bharat lakhani (Mon Mar 09 2009 - 03:43:08 CDT)
• [AMBER] chemical shift penalty Jacopo Sgrignani (Thu Mar 05 2009 - 03:47:03 CST)
  • Re: [AMBER] chemical shift penalty David A. Case (Thu Mar 05 2009 - 17:59:33 CST)
• [AMBER] divcon error during antechamber run, convergence problem drugdesign (Thu Mar 05 2009 - 07:53:59 CST)
  • Re: [AMBER] divcon error during antechamber run, convergence problem Martin Peters (Thu Mar 05 2009 - 08:21:19 CST)
  • Re: [AMBER] divcon error during antechamber run, convergence problem Andrew Voronkov (Fri Mar 06 2009 - 12:04:55 CST)
    • Re: [AMBER] divcon error during antechamber run, convergence problem David A. Case (Fri Mar 06 2009 - 12:33:24 CST)
      • Re: [AMBER] divcon error during antechamber run, convergence problem Andrew Voronkov (Sat Mar 07 2009 - 09:58:19 CST)
• [AMBER] secstruct Beale, John (Thu Mar 05 2009 - 07:54:20 CST)
  • Re: [AMBER] secstruct Carlos Simmerling (Thu Mar 05 2009 - 08:27:18 CST)
• [AMBER] MM-PBSA decomp by residue and snapshot? Bradshaw, Richard (Thu Mar 05 2009 - 11:55:05 CST)
• [AMBER] Warning: name change in pdb file residue Donald Keidel (Thu Mar 05 2009 - 13:25:38 CST)
  • RE: [AMBER] Warning: name change in pdb file residue Duggan, Brendan M. (Thu Mar 05 2009 - 14:42:21 CST)
• [AMBER] GBSA: dielectric symmetry Giacomo Bastianelli (Thu Mar 05 2009 - 17:29:50 CST)
  • Re: [AMBER] GBSA: dielectric symmetry David A. Case (Thu Mar 05 2009 - 18:05:51 CST)
• [AMBER] High RMSD for DNA: A to B transition study BERGY (Fri Mar 06 2009 - 01:26:57 CST)
  • Re: [AMBER] High RMSD for DNA: A to B transition study David A. Case (Fri Mar 06 2009 - 08:57:02 CST)
    • Re: [AMBER] High RMSD for DNA: A to B transition study SENTHIL KUMAR (Fri Mar 13 2009 - 01:36:43 CDT)
      • Re: [AMBER] High RMSD for DNA: A to B transition study David A. Case (Fri Mar 13 2009 - 07:00:40 CDT)
• [AMBER] Quality/size of HDD for Amber Francesco Pietra (Fri Mar 06 2009 - 03:26:03 CST)
  • Re: [AMBER] Quality/size of HDD for Amber M. L. Dodson (Fri Mar 06 2009 - 09:44:45 CST)
    • Re: [AMBER] Quality/size of HDD for Amber Gustavo Seabra (Mon Mar 09 2009 - 12:44:54 CDT)
• [AMBER] Solvate Box od amoeba water Hemant Gangwar (Fri Mar 06 2009 - 03:50:01 CST)
  • Re: [AMBER] Solvate Box od amoeba water Wei Zhang (Fri Mar 06 2009 - 08:20:09 CST)
    • Re: [AMBER] Solvate Box od amoeba water Hemant Kumar (Sun Mar 22 2009 - 11:06:01 CDT)
• [AMBER] catenan simulation problems Cristina Sisu (Fri Mar 06 2009 - 07:16:08 CST)
  • Re: [AMBER] catenan simulation problems David A. Case (Fri Mar 06 2009 - 08:59:24 CST)
    • Re: [AMBER] catenan simulation problems Cristina Sisu (Fri Mar 06 2009 - 09:28:00 CST)
      • Re: [AMBER] catenan simulation problems David A. Case (Sat Mar 07 2009 - 17:25:07 CST)
      • Re: [AMBER] catenan simulation problems David A. Case (Wed Mar 18 2009 - 06:47:32 CDT)
    • Re: [AMBER] catenan simulation problems Cristina S.D. Sisu (Fri Mar 06 2009 - 09:35:46 CST)
• [AMBER] Help with torsions in parm99.dat file Gregersen, Brent (Fri Mar 06 2009 - 16:44:17 CST)
  • RE: [AMBER] Help with torsions in parm99.dat file Ross Walker (Fri Mar 06 2009 - 18:52:05 CST)
    • RE: [AMBER] Help with torsions in parm99.dat file Gregersen, Brent (Fri Mar 06 2009 - 20:15:11 CST)
      • RE: [AMBER] Help with torsions in parm99.dat file Ross Walker (Sat Mar 07 2009 - 00:32:23 CST)
    • Re: [AMBER] Help with torsions in parm99.dat file Astrid Maaß (Mon Mar 09 2009 - 08:27:30 CDT)
      • Re: [AMBER] Help with torsions in parm99.dat file Wei Zhang (Mon Mar 09 2009 - 09:38:56 CDT)
• [AMBER] Problem with particle-mesh Ewald method Yunjie Zhao (Fri Mar 06 2009 - 21:29:02 CST)
  • Re: [AMBER] Problem with particle-mesh Ewald method steinbrt_at_rci.rutgers.edu (Fri Mar 06 2009 - 21:42:26 CST)
  • RE: [AMBER] Problem with particle-mesh Ewald method Ross Walker (Sat Mar 07 2009 - 00:10:34 CST)
• [AMBER] analysis on Amber oguz gurbulak (Sat Mar 07 2009 - 12:04:19 CST)
  • Re: [AMBER] analysis on Amber Thomas Cheatham (Sat Mar 07 2009 - 12:18:58 CST)
• [AMBER] Fw:how to select force field Nancy (Sun Mar 08 2009 - 09:07:48 CDT)
  • RE: [AMBER] Fw:how to select force field Ross Walker (Sun Mar 08 2009 - 12:52:56 CDT)
• [AMBER] nmoldyn2 with Amber Adrien Delmont (Sun Mar 08 2009 - 09:37:40 CDT)
  • Re: [AMBER] nmoldyn2 with Amber David Watson (Sun Mar 08 2009 - 09:54:57 CDT)
    • Re: [AMBER] nmoldyn2 with Amber M. L. Dodson (Sun Mar 08 2009 - 13:32:22 CDT)
      • Re: [AMBER] nmoldyn2 with Amber David Watson (Sun Mar 08 2009 - 15:00:39 CDT)
      • Re: [AMBER] nmoldyn2 with Amber Thomas Cheatham (Sun Mar 08 2009 - 15:10:17 CDT)
  • Re: [AMBER] nmoldyn2 with Amber David Watson (Sun Mar 08 2009 - 10:02:55 CDT)
    • Re: [AMBER] nmoldyn2 with Amber M. L. Dodson (Sun Mar 08 2009 - 13:34:03 CDT)
• [AMBER] addles segmentation fault gmail (Mon Mar 09 2009 - 03:28:56 CDT)
  • Re: [AMBER] addles segmentation fault Carlos Simmerling (Mon Mar 09 2009 - 06:45:24 CDT)
    • Re: [AMBER] addles segmentation fault xiaonan zhang (Mon Mar 09 2009 - 08:08:47 CDT)
• [AMBER] Particle-mesh Ewald method Yunjie Zhao (Mon Mar 09 2009 - 04:46:15 CDT)
  • RE: [AMBER] Particle-mesh Ewald method Ross Walker (Mon Mar 09 2009 - 14:53:52 CDT)
• [AMBER] 8Mureabox anna berteotti (Mon Mar 09 2009 - 05:07:52 CDT)
  • Re: [AMBER] 8Mureabox David A. Case (Tue Mar 10 2009 - 07:51:08 CDT)
    • RE: [AMBER] 8Mureabox anna berteotti (Wed Mar 11 2009 - 03:45:03 CDT)
• [AMBER] Restraint Mask length restriction !! Sampath Koppole (Mon Mar 09 2009 - 08:32:35 CDT)
  • Re: [AMBER] Restraint Mask length restriction !! David A. Case (Mon Mar 09 2009 - 08:43:34 CDT)
  • Re: [AMBER] Restraint Mask length restriction !! Sampath Koppole (Mon Mar 09 2009 - 09:06:23 CDT)
    • Re: [AMBER] Restraint Mask length restriction !! David A. Case (Mon Mar 09 2009 - 09:30:16 CDT)
  • Re: [AMBER] Restraint Mask length restriction !! Sampath Koppole (Mon Mar 09 2009 - 09:39:38 CDT)
    • RE: [AMBER] Restraint Mask length restriction !! Ross Walker (Mon Mar 09 2009 - 14:50:08 CDT)
• [AMBER] generalized distance restraint Rausch, Felix (Mon Mar 09 2009 - 08:48:01 CDT)
  • Re: [AMBER] generalized distance restraint Carlos Simmerling (Mon Mar 09 2009 - 10:13:50 CDT)
    • RE: [AMBER] generalized distance restraint Rausch, Felix (Mon Mar 09 2009 - 11:15:11 CDT)
      • Re: [AMBER] generalized distance restraint Carlos Simmerling (Mon Mar 09 2009 - 11:39:43 CDT)
      • Re: [AMBER] generalized distance restraint M. L. Dodson (Mon Mar 09 2009 - 11:51:19 CDT)
  • RE: [AMBER] generalized distance restraint Rausch, Felix (Wed Mar 11 2009 - 02:39:05 CDT)
• [AMBER] Free Energy Decomposition Problem ozlem ulucan (Mon Mar 09 2009 - 08:55:45 CDT)
• [AMBER] Changing Force Fields in "Midstream" Hopkins, Robert (Mon Mar 09 2009 - 19:12:27 CDT)
  • RE: [AMBER] Changing Force Fields in "Midstream" Ross Walker (Mon Mar 09 2009 - 19:21:15 CDT)
    • RE: [AMBER] Changing Force Fields in "Midstream" Hopkins, Robert (Tue Mar 10 2009 - 18:29:44 CDT)
    • RE: [AMBER] Changing Force Fields in "Midstream" Hopkins, Robert (Wed Mar 11 2009 - 16:36:12 CDT)
      • Re: [AMBER] Changing Force Fields in "Midstream" Wei Zhang (Wed Mar 11 2009 - 16:42:52 CDT)
      • Re: [AMBER] Changing Force Fields in "Midstream" David A. Case (Wed Mar 11 2009 - 17:36:56 CDT)
      • RE: [AMBER] Changing Force Fields in "Midstream" Hopkins, Robert (Thu Mar 12 2009 - 15:45:46 CDT)
      • RE: [AMBER] Changing Force Fields in "Midstream" Kristina Furse (Wed Mar 11 2009 - 16:58:06 CDT)
• [AMBER] problem in rmsd Parimal Kar (Mon Mar 09 2009 - 22:18:48 CDT)
  • Re: [AMBER] problem in rmsd Thomas Cheatham (Mon Mar 09 2009 - 22:25:18 CDT)
    • Re: [AMBER] problem in rmsd Parimal Kar (Mon Mar 09 2009 - 22:36:13 CDT)
      • Re: [AMBER] problem in rmsd Thomas Cheatham (Mon Mar 09 2009 - 22:48:53 CDT)
      • Re: [AMBER] problem in rmsd Hannes Loeffler (Tue Mar 10 2009 - 03:30:16 CDT)
      • Re: [AMBER] problem in rmsd Carlos Simmerling (Tue Mar 10 2009 - 05:29:20 CDT)
      • [AMBER] mol2 - pdb conversion Taufik Al-Sarraj (Mon Mar 16 2009 - 16:38:09 CDT)
      • Re: [AMBER] mol2 - pdb conversion David A. Case (Tue Mar 17 2009 - 10:47:53 CDT)
      • Re: [AMBER] mol2 - pdb conversion Taufik Al-Sarraj (Wed Mar 18 2009 - 14:20:54 CDT)
      • Re: [AMBER] mol2 - pdb conversion David A. Case (Wed Mar 18 2009 - 16:53:06 CDT)
• [AMBER] PB Bomb from MM-PBSA of Amber 10 Zhu, Yong-Liang (Mon Mar 09 2009 - 23:30:33 CDT)
  • RE: [AMBER] PB Bomb from MM-PBSA of Amber 10 Wei Huang (Tue Mar 10 2009 - 05:30:50 CDT)
    • RE: [AMBER] PB Bomb from MM-PBSA of Amber 10 Zhu, Yong-Liang (Tue Mar 10 2009 - 11:06:43 CDT)
      • RE: [AMBER] PB Bomb from MM-PBSA of Amber 10 Wei Huang (Tue Mar 10 2009 - 11:20:29 CDT)
  • RE: [AMBER] PB Bomb from MM-PBSA of Amber 10 Ray Luo (Tue Mar 10 2009 - 11:28:15 CDT)
• [AMBER] sulfotyrosine parameters Ryan Pavlovicz (Tue Mar 10 2009 - 10:05:59 CDT)
• [AMBER] wrong estimation of hydrogen velocities when using SHAKE? Jose Borreguero (Tue Mar 10 2009 - 11:09:48 CDT)
  • Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? David A. Case (Wed Mar 11 2009 - 06:08:17 CDT)
    • Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? Jose Borreguero (Wed Mar 11 2009 - 12:28:21 CDT)
      • Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? steinbrt_at_rci.rutgers.edu (Wed Mar 11 2009 - 12:45:56 CDT)
      • Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? Jose Borreguero (Wed Mar 11 2009 - 13:46:29 CDT)
      • Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? steinbrt_at_rci.rutgers.edu (Wed Mar 11 2009 - 13:56:15 CDT)
      • Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? Jose Borreguero (Wed Mar 11 2009 - 16:56:03 CDT)
• [AMBER] about MD simulation ÁÎÇ໪ (Wed Mar 11 2009 - 04:19:28 CDT)
  • Re: [AMBER] about MD simulation Carlos Simmerling (Wed Mar 11 2009 - 05:56:43 CDT)
    • 回å¤�： [AMBER] about MD simulation å»–é�’å�Ž (Wed Mar 11 2009 - 11:25:05 CDT)
• [AMBER] Seeking for suggestion related to plot the cluster out file S.Sundar Raman (Wed Mar 11 2009 - 07:44:17 CDT)
  • RE: [AMBER] Seeking for suggestion related to plot the cluster out file Ross Walker (Wed Mar 11 2009 - 09:33:38 CDT)
    • Re: [AMBER] Seeking for suggestion related to plot the cluster out file S.Sundar Raman (Wed Mar 11 2009 - 09:57:40 CDT)
      • RE: [AMBER] Seeking for suggestion related to plot the cluster out file Ross Walker (Wed Mar 11 2009 - 10:55:38 CDT)
      • Re: [AMBER] Seeking for suggestion related to plot the cluster out file S.Sundar Raman (Wed Mar 11 2009 - 11:07:25 CDT)
• [AMBER] installing AmberTools on Windows machines David A. Case (Wed Mar 11 2009 - 15:27:07 CDT)
• [AMBER] polarizable force field and solvent zeinab bagheri (Wed Mar 11 2009 - 17:02:06 CDT)
• [AMBER] Understanding the all.out file in the MM-PBSA output gmail (Wed Mar 11 2009 - 20:39:10 CDT)
  • Re: [AMBER] Understanding the all.out file in the MM-PBSA output Hannes Kopitz (Thu Mar 12 2009 - 05:54:27 CDT)
    • RE: [AMBER] Understanding the all.out file in the MM-PBSA output Ray Luo (Thu Mar 12 2009 - 11:29:22 CDT)
• [AMBER] polarizable force field and solvent zeinab bagheri (Thu Mar 12 2009 - 00:40:33 CDT)
• [AMBER] Problem with REMD parul sharma (Thu Mar 12 2009 - 02:45:09 CDT)
  • Re: [AMBER] Problem with REMD Carlos Simmerling (Thu Mar 12 2009 - 06:00:07 CDT)
• [AMBER] Problems with MM-PBSA Calculation after MD German Erlenkamp (Thu Mar 12 2009 - 04:28:23 CDT)
  • Re: [AMBER] Problems with MM-PBSA Calculation after MD Hannes Kopitz (Thu Mar 12 2009 - 06:06:54 CDT)
• [AMBER] SMD in Amber10 Dmitri Nilov (Thu Mar 12 2009 - 13:12:13 CDT)
  • Re: [AMBER] SMD in Amber10 Adrian Roitberg (Thu Mar 12 2009 - 13:46:14 CDT)
    • Re: [AMBER] SMD in Amber10 Dmitri Nilov (Fri Mar 13 2009 - 03:52:26 CDT)
      • Re: [AMBER] SMD in Amber10 Adrian Roitberg (Fri Mar 13 2009 - 08:45:39 CDT)
      • Re: [AMBER] SMD in Amber10 Dmitri Nilov (Fri Mar 13 2009 - 09:54:07 CDT)
      • Re: [AMBER] SMD in Amber10 Adrian Roitberg (Fri Mar 13 2009 - 10:01:31 CDT)
      • Re: [AMBER] SMD in Amber10 Dmitri Nilov (Fri Mar 13 2009 - 10:17:44 CDT)
• [AMBER] Thermodynamic Integration at higher values of clambda using AMBER 9 PRADEEP VENKATARAMAN (Thu Mar 12 2009 - 16:56:59 CDT)
  • Re: [AMBER] Thermodynamic Integration at higher values of clambda using AMBER 9 steinbrt_at_rci.rutgers.edu (Thu Mar 12 2009 - 19:37:08 CDT)
• [AMBER] Problem running test.pmemd.AMOEBA mloureiro_at_cesga.es (Fri Mar 13 2009 - 06:45:30 CDT)
  • [AMBER] Problem build pmemd Yiannis Georgiadis (Fri Mar 13 2009 - 19:14:49 CDT)
    • Re: [AMBER] Problem build pmemd Robert Duke (Fri Mar 13 2009 - 07:40:09 CDT)
      • Re: [AMBER] Problem build pmemd Yiannis Georgiadis (Wed Mar 18 2009 - 19:57:44 CDT)
      • Re: [AMBER] Problem build pmemd Giorgos Lamprinidis (Wed Mar 18 2009 - 08:28:06 CDT)
      • Re: [AMBER] Problem build pmemd Robert Duke (Wed Mar 18 2009 - 08:53:17 CDT)
    • Re: [AMBER] Problem build pmemd Atro Tossavainen (Sat Mar 14 2009 - 14:10:53 CDT)
  • Re: [AMBER] Problem running test.pmemd.AMOEBA Robert Duke (Fri Mar 13 2009 - 09:33:55 CDT)
• [AMBER] to understand multiplicity in antechamber Alan (Fri Mar 13 2009 - 07:06:45 CDT)
• [AMBER] to understand multiplicity in antechamber Alan (Fri Mar 13 2009 - 09:43:45 CDT)
  • Re: [AMBER] to understand multiplicity in antechamber Scott Brozell (Fri Mar 13 2009 - 14:05:06 CDT)
    • Re: [AMBER] to understand multiplicity in antechamber Alan (Fri Mar 13 2009 - 17:43:28 CDT)
• [AMBER] doubt-reg_ Targeted molecular dynamics balaji nagarajan (Fri Mar 13 2009 - 11:20:41 CDT)
• [AMBER] problems compiling ambertool Per Jr. Greisen (Fri Mar 13 2009 - 14:08:36 CDT)
  • Re: [AMBER] problems compiling ambertool David A. Case (Fri Mar 13 2009 - 14:54:56 CDT)
    • Re: [AMBER] problems compiling ambertool Per Jr. Greisen (Fri Mar 13 2009 - 17:01:35 CDT)
    • Re: [AMBER] problems compiling ambertool Atro Tossavainen (Sat Mar 14 2009 - 14:09:36 CDT)
    • Re: [AMBER] problems compiling ambertool Atro Tossavainen (Mon Mar 16 2009 - 05:18:58 CDT)
      • Re: [AMBER] problems compiling ambertool David A. Case (Mon Mar 16 2009 - 07:13:23 CDT)
      • Re: [AMBER] problems compiling ambertool Per Jr. Greisen (Mon Mar 16 2009 - 08:29:37 CDT)
      • Re: [AMBER] problems compiling ambertool David A. Case (Mon Mar 16 2009 - 08:50:24 CDT)
      • Re: [AMBER] problems compiling ambertool Per Jr. Greisen (Mon Mar 16 2009 - 09:00:14 CDT)
      • Re: [AMBER] problems compiling ambertool David A. Case (Mon Mar 16 2009 - 09:27:26 CDT)
      • Re: [AMBER] problems compiling ambertool Per Jr. Greisen (Mon Mar 16 2009 - 09:41:26 CDT)
      • Re: [AMBER] problems compiling ambertool David A. Case (Mon Mar 16 2009 - 10:12:40 CDT)
      • Re: [AMBER] problems compiling ambertool Per Jr. Greisen (Mon Mar 16 2009 - 17:35:38 CDT)
  • Re: [AMBER] problems compiling ambertool Bill Ross (Mon Mar 16 2009 - 17:50:44 CDT)
    • Re: [AMBER] problems compiling ambertool Per Jr. Greisen (Tue Mar 17 2009 - 03:10:20 CDT)
      • Re: [AMBER] problems compiling ambertool David A. Case (Tue Mar 17 2009 - 07:49:20 CDT)
      • Re: [AMBER] problems compiling ambertool Per Jr. Greisen (Tue Mar 17 2009 - 11:06:00 CDT)
      • Re: [AMBER] problems compiling ambertool David A. Case (Tue Mar 17 2009 - 11:13:30 CDT)
  • Re: [AMBER] problems compiling ambertool Bill Ross (Tue Mar 17 2009 - 12:10:01 CDT)
  • Re: [AMBER] problems compiling ambertool Bill Ross (Tue Mar 17 2009 - 12:24:48 CDT)
    • Re: [AMBER] problems compiling ambertool Per Jr. Greisen (Wed Mar 18 2009 - 06:49:57 CDT)
      • Re: [AMBER] problems compiling ambertool David A. Case (Wed Mar 18 2009 - 07:39:38 CDT)
      • Re: [AMBER] problems compiling ambertool Per Jr. Greisen (Wed Mar 18 2009 - 07:45:53 CDT)
      • [AMBER] lipid bliayers Urszula Uciechowska (Wed Mar 18 2009 - 08:00:32 CDT)
      • Re: [AMBER] lipid bliayers Hannes Loeffler (Wed Mar 18 2009 - 08:17:04 CDT)
      • Re: [AMBER] problem in running sander Carlos Simmerling (Wed Mar 18 2009 - 09:58:04 CDT)
      • Re: [AMBER] problem in running sander Carlos Simmerling (Wed Mar 18 2009 - 10:51:07 CDT)
      • Re: [AMBER] problem in running sander Kshatresh Dutta Dubey (Thu Mar 19 2009 - 02:17:21 CDT)
      • Re: [AMBER] problem in running sander David A. Case (Thu Mar 19 2009 - 07:13:11 CDT)
• [AMBER] suggestions for PB simulation Bala subramanian (Sat Mar 14 2009 - 11:41:19 CDT)
• [AMBER] sander.MPI and pmemd.MPI in Fedora 8 John Bennett (Sun Mar 15 2009 - 16:23:16 CDT)
• [AMBER] Unit 5 Error on OPEN: nan.in Nancy (Mon Mar 16 2009 - 07:49:31 CDT)
• [AMBER] about mm-pbsa å»–é�’å�Ž (Mon Mar 16 2009 - 09:59:40 CDT)
• [AMBER] about mm-pbsa å»–é�’å�Ž (Mon Mar 16 2009 - 10:02:49 CDT)
  • RE: [AMBER] about mm-pbsa Wei Huang (Mon Mar 16 2009 - 10:17:30 CDT)
• [AMBER] minimisation with igb=10 Bala subramanian (Mon Mar 16 2009 - 10:43:10 CDT)
  • Re: [AMBER] minimisation with igb=10 Carlos Simmerling (Mon Mar 16 2009 - 10:45:47 CDT)
    • Re: [AMBER] minimisation with igb=10 Bala subramanian (Mon Mar 16 2009 - 10:56:48 CDT)
      • Re: [AMBER] minimisation with igb=10 Carlos Simmerling (Mon Mar 16 2009 - 11:04:37 CDT)
      • RE: [AMBER] minimisation with igb=10 Ray Luo (Mon Mar 16 2009 - 11:34:21 CDT)
• [AMBER] Actual force constant in SMD Dmitri Nilov (Mon Mar 16 2009 - 13:07:09 CDT)
• [AMBER] Re: join two units in amber9 or amber10 Taufik Al-Sarraj (Mon Mar 16 2009 - 16:11:30 CDT)
• Re: [AMBER] Re: join two units in amber9 or amber10 Bill Ross (Mon Mar 16 2009 - 17:56:01 CDT)
• [AMBER] Unit 5 Error on OPEN: nan.in Nancy (Mon Mar 16 2009 - 20:02:09 CDT)
• [AMBER] Input file of the second stage RESP fitting Cen Gao (Mon Mar 16 2009 - 23:29:17 CDT)
  • Re: [AMBER] Input file of the second stage RESP fitting FyD (Tue Mar 17 2009 - 08:32:58 CDT)
    • Re: [AMBER] Input file of the second stage RESP fitting Cen Gao (Tue Mar 17 2009 - 16:24:24 CDT)
• [AMBER] regarding tutorial on united atom force field jani sahil (Mon Mar 16 2009 - 23:51:16 CDT)
  • Re: [AMBER] regarding tutorial on united atom force field Ray Luo (Tue Mar 17 2009 - 11:22:01 CDT)
• [AMBER] need- help-for TMD balaji nagarajan (Tue Mar 17 2009 - 00:16:34 CDT)
• [AMBER] Unit 5 Error on OPEN: nan.in Nancy (Tue Mar 17 2009 - 04:11:10 CDT)
  • Re: [AMBER] Unit 5 Error on OPEN: nan.in mathew k varghese (Mon Mar 16 2009 - 08:36:57 CDT)
    • Re:Re: [AMBER] Unit 5 Error on OPEN: nan.in Nancy (Mon Mar 16 2009 - 09:01:14 CDT)
      • Re: Re: [AMBER] Unit 5 Error on OPEN: nan.in Carlos Simmerling (Mon Mar 16 2009 - 09:32:02 CDT)
  • Re: [AMBER] Unit 5 Error on OPEN: nan.in mathew k varghese (Tue Mar 17 2009 - 06:22:08 CDT)
    • Re: [AMBER] Unit 5 Error on OPEN: nan.in Jenny Iskrenova (Tue Mar 17 2009 - 07:34:00 CDT)
    • Re:Re: [AMBER] Unit 5 Error on OPEN: nan.in Nancy (Tue Mar 17 2009 - 08:37:44 CDT)
• [AMBER] removing center of mass Bala subramanian (Tue Mar 17 2009 - 10:21:28 CDT)
• [AMBER] convert .mol2 file to .pdb with atomtype definitions Pansy Patel (Tue Mar 17 2009 - 10:50:57 CDT)
  • Re: [AMBER] convert .mol2 file to .pdb with atomtype definitions David A. Case (Tue Mar 17 2009 - 11:00:19 CDT)
    • Re: [AMBER] convert .mol2 file to .pdb with atomtype definitions Pansy Patel (Tue Mar 17 2009 - 11:09:10 CDT)
      • Re: [AMBER] convert .mol2 file to .pdb with atomtype definitions Wei Zhang (Tue Mar 17 2009 - 11:33:27 CDT)
      • RE: [AMBER] convert .mol2 file to .pdb with atomtype definitions Pankaj R. Daga (Tue Mar 17 2009 - 11:41:20 CDT)
• [AMBER] temperature rises with igb=1 Bala subramanian (Tue Mar 17 2009 - 11:35:41 CDT)
  • Re: [AMBER] temperature rises with igb=1 Carlos Simmerling (Tue Mar 17 2009 - 11:44:32 CDT)
  • RE: [AMBER] temperature rises with igb=1 Ross Walker (Tue Mar 17 2009 - 11:53:04 CDT)
    • Re: [AMBER] temperature rises with igb=1 Carlos Simmerling (Tue Mar 17 2009 - 11:58:05 CDT)
      • Re: [AMBER] temperature rises with igb=1 Bala subramanian (Thu Mar 19 2009 - 06:24:45 CDT)
      • Re: [AMBER] temperature rises with igb=1 David A. Case (Thu Mar 19 2009 - 07:04:54 CDT)
• Re: [AMBER] Unit 5 Error on OPEN: nan.in Bill Ross (Tue Mar 17 2009 - 12:12:07 CDT)
• [AMBER] CCL4 simulation sudipta (Tue Mar 17 2009 - 13:18:07 CDT)
  • Re: [AMBER] CCL4 simulation David A. Case (Tue Mar 17 2009 - 21:14:51 CDT)
    • Re: [AMBER] CCL4 simulation sudipta (Wed Mar 18 2009 - 02:47:48 CDT)
      • Re: [AMBER] CCL4 simulation David A. Case (Wed Mar 18 2009 - 06:06:30 CDT)
• [AMBER] error in constructing DNA from nucgen Pansy Patel (Tue Mar 17 2009 - 13:43:49 CDT)
  • Re: [AMBER] error in constructing DNA from nucgen Carlos Simmerling (Tue Mar 17 2009 - 13:53:05 CDT)
    • Re: [AMBER] error in constructing DNA from nucgen Pansy Patel (Tue Mar 17 2009 - 14:24:58 CDT)
      • RE: [AMBER] error in constructing DNA from nucgen Ross Walker (Tue Mar 17 2009 - 14:31:16 CDT)
  • Re: [AMBER] error in constructing DNA from nucgen Carlos Simmerling (Tue Mar 17 2009 - 13:53:05 CDT)
  • Re: [AMBER] error in constructing DNA from nucgen Carlos Simmerling (Tue Mar 17 2009 - 13:53:05 CDT)
  • Re: [AMBER] error in constructing DNA from nucgen Bill Ross (Tue Mar 17 2009 - 17:47:07 CDT)
• [AMBER] TMD balaji nagarajan (Tue Mar 17 2009 - 23:58:37 CDT)
  • Re: [AMBER] TMD Carlos Simmerling (Wed Mar 18 2009 - 05:32:14 CDT)
    • RE: [AMBER] TMD balaji nagarajan (Wed Mar 18 2009 - 06:15:55 CDT)
• [AMBER] About error of "vertex atom mismatch" å»–é�’å�Ž (Wed Mar 18 2009 - 03:30:29 CDT)
• [AMBER] errors about install amber9 on MAC OS zgong.hust (Wed Mar 18 2009 - 03:41:19 CDT)
  • Re: [AMBER] errors about install amber9 on MAC OS David A. Case (Wed Mar 18 2009 - 06:08:44 CDT)
• [AMBER] protein protrudes from unit cell Jeffrey (Wed Mar 18 2009 - 03:59:06 CDT)
  • Re: [AMBER] protein protrudes from unit cell Hannes Loeffler (Wed Mar 18 2009 - 04:08:41 CDT)
  • RE: [AMBER] protein protrudes from unit cell Ross Walker (Wed Mar 18 2009 - 10:39:23 CDT)
    • Re: [AMBER] protein protrudes from unit cell Carlos Simmerling (Wed Mar 18 2009 - 10:49:43 CDT)
• [AMBER] sleap and check Alan (Wed Mar 18 2009 - 06:18:27 CDT)
  • Re: [AMBER] sleap and check Wei Zhang (Wed Mar 18 2009 - 09:40:57 CDT)
    • Re: [AMBER] sleap and check Alan (Wed Mar 18 2009 - 16:23:51 CDT)
• [AMBER] Mass of LP PRADEEP VENKATARAMAN (Wed Mar 18 2009 - 22:27:24 CDT)
  • Re: [AMBER] Mass of LP David A. Case (Thu Mar 19 2009 - 06:27:48 CDT)
• [AMBER] simulation in water-oil (or water/hydrophobic-solvent) box ranga nath (Wed Mar 18 2009 - 23:27:54 CDT)
  • Re: [AMBER] simulation in water-oil (or water/hydrophobic-solvent) box David A. Case (Thu Mar 19 2009 - 12:38:52 CDT)
    • [AMBER] protein PDB Chih-Ying Lin (Thu Mar 19 2009 - 15:43:15 CDT)
    • Re: [AMBER] simulation in water-oil (or water/hydrophobic-solvent) box ranga nath (Sat Mar 21 2009 - 21:04:13 CDT)
• [AMBER] Metal in MD simulation priya priya (Thu Mar 19 2009 - 01:25:09 CDT)
  • Re: [AMBER] Metal in MD simulation Jagadeesh, M.N., Ph.D. (Thu Mar 19 2009 - 09:48:28 CDT)
  • RE: [AMBER] Metal in MD simulation Ross Walker (Thu Mar 19 2009 - 10:12:24 CDT)
  • Re: [AMBER] Metal in MD simulation Bill Ross (Thu Mar 19 2009 - 16:22:12 CDT)
  • Re: [AMBER] Metal in MD simulation priya priya (Fri Mar 20 2009 - 01:15:06 CDT)
• [AMBER] About mm-pbsa å»–é�’å�Ž (Thu Mar 19 2009 - 01:48:21 CDT)
• [AMBER] [about advanced tutorial 1] How could I get conformations for gaussian that have minimum energy? Youn Kyeung Lee (Thu Mar 19 2009 - 02:31:16 CDT)
  • Re: [AMBER] [about advanced tutorial 1] How could I get conformations for gaussian that have minimum energy? FyD (Sun Mar 22 2009 - 15:12:17 CDT)
• [AMBER] error for nmode Dechang Li (Thu Mar 19 2009 - 06:00:09 CDT)
  • Re: [AMBER] error for nmode David A. Case (Thu Mar 19 2009 - 06:31:24 CDT)
• [AMBER] pmemd compile error.... Giorgos Lamprinidis (Thu Mar 19 2009 - 10:06:04 CDT)
  • Re: [AMBER] pmemd compile error.... Robert Duke (Thu Mar 19 2009 - 10:24:29 CDT)
    • Re: [AMBER] pmemd compile error.... Yiannis Georgiadis (Tue Mar 24 2009 - 15:10:27 CDT)
      • Re: [AMBER] pmemd compile error.... case (Tue Mar 24 2009 - 07:12:46 CDT)
      • Re: [AMBER] pmemd compile error.... Robert Duke (Tue Mar 24 2009 - 07:19:45 CDT)
  • Re: [AMBER] pmemd compile error.... Robert Duke (Thu Mar 19 2009 - 10:25:04 CDT)
• [AMBER] Parametrisation of Silicon based molecules for Amber simulations ? Marek Malý (Thu Mar 19 2009 - 18:49:21 CDT)
• [AMBER] analysing DNA trajectory balaji nagarajan (Fri Mar 20 2009 - 00:09:10 CDT)
  • Re: [AMBER] analysing DNA trajectory Bala subramanian (Fri Mar 20 2009 - 03:06:08 CDT)
• [AMBER] Help needed in amber parallel installation sushobhan_at_iiar.res.in (Fri Mar 20 2009 - 01:39:36 CDT)
  • Re: [AMBER] Help needed in amber parallel installation Carlos Simmerling (Fri Mar 20 2009 - 06:34:31 CDT)
  • RE: [AMBER] Help needed in amber parallel installation Ross Walker (Fri Mar 20 2009 - 10:40:30 CDT)
• [AMBER] QM/MM charges Jacopo Sgrignani (Fri Mar 20 2009 - 04:38:30 CDT)
  • RE: [AMBER] QM/MM charges Ross Walker (Fri Mar 20 2009 - 10:37:34 CDT)
• [AMBER] Announcement of Model(l)ing'09 - The annual 2009 MGMS Meeting in Erlangen, Germany Harald Lanig (Fri Mar 20 2009 - 06:25:09 CDT)
• [AMBER] MMGBSA IG Value Rajesh Raju (Fri Mar 20 2009 - 12:20:52 CDT)
  • Re: [AMBER] MMGBSA IG Value Carlos Simmerling (Fri Mar 20 2009 - 12:25:38 CDT)
    • Re: [AMBER] MMGBSA IG Value Rajesh Raju (Fri Mar 20 2009 - 12:36:37 CDT)
      • Re: [AMBER] MMGBSA IG Value Carlos Simmerling (Fri Mar 20 2009 - 12:42:14 CDT)
• [AMBER] xmgrace Nancy (Fri Mar 20 2009 - 23:41:33 CDT)
  • Re: [AMBER] xmgrace mathew k varghese (Sat Mar 21 2009 - 00:18:32 CDT)
    • Re:Re: [AMBER] xmgrace Nancy (Sat Mar 21 2009 - 00:42:48 CDT)
• [AMBER] adding chain id to ptraj pdb output Paul Brandt (Sat Mar 21 2009 - 21:09:59 CDT)
  • Re: [AMBER] adding chain id to ptraj pdb output Bala subramanian (Mon Mar 23 2009 - 06:37:43 CDT)
  • Re: [AMBER] adding chain id to ptraj pdb output Joe Krahn (Mon Mar 23 2009 - 18:20:30 CDT)
• [AMBER] about mm-pbsa å»–é�’å�Ž (Mon Mar 23 2009 - 04:10:29 CDT)
• [AMBER] leap and chirality Karl Kirschner (Mon Mar 23 2009 - 04:54:29 CDT)
  • Re: [AMBER] leap and chirality David A. Case (Mon Mar 23 2009 - 08:16:14 CDT)
    • Re: [AMBER] leap and chirality Karl Kirschner (Mon Mar 23 2009 - 09:05:56 CDT)
      • Re: [AMBER] leap and chirality Wei Zhang (Mon Mar 23 2009 - 13:36:54 CDT)
      • Re: [AMBER] leap and chirality Karl Kirschner (Tue Mar 24 2009 - 03:11:38 CDT)
      • Re: [AMBER] leap and chirality Wei Zhang (Tue Mar 24 2009 - 07:55:47 CDT)
• [AMBER] problem in installing AMBER10 Dr. Debaprasad Giri (Mon Mar 23 2009 - 05:31:26 CDT)
  • Re: [AMBER] problem in installing AMBER10 David A. Case (Mon Mar 23 2009 - 06:07:17 CDT)
    • Re: [AMBER] problem in installing AMBER10 Dr. Debaprasad Giri (Fri Mar 27 2009 - 05:16:47 CDT)
      • Re: [AMBER] problem in installing AMBER10 David A. Case (Fri Mar 27 2009 - 07:05:31 CDT)
• [AMBER] Regarding use of PME along with Implict solvation jani sahil (Mon Mar 23 2009 - 05:38:39 CDT)
  • Re: [AMBER] Regarding use of PME along with Implict solvation parul sharma (Mon Mar 23 2009 - 05:55:24 CDT)
    • Re: [AMBER] Regarding use of PME along with Implict solvation jani sahil (Mon Mar 23 2009 - 08:04:15 CDT)
• [AMBER] helical parameters balaji nagarajan (Mon Mar 23 2009 - 11:21:04 CDT)
  • Re: [AMBER] helical parameters Bala subramanian (Mon Mar 23 2009 - 13:14:29 CDT)
• [AMBER] pmemd compile error Giorgos Lamprinidis (Mon Mar 23 2009 - 15:54:37 CDT)
  • Re: [AMBER] pmemd compile error Robert Duke (Mon Mar 23 2009 - 16:03:45 CDT)
• [AMBER] errors on reading time series file in WHAM calculation gmail (Mon Mar 23 2009 - 19:35:02 CDT)
  • Re: [AMBER] errors on reading time series file in WHAM calculation Jenny Iskrenova (Tue Mar 24 2009 - 09:35:51 CDT)
• [AMBER] validation of parameters and request of suggestions Jeffrey (Mon Mar 23 2009 - 21:16:35 CDT)
• [AMBER] continuam water Mannan (Mon Mar 23 2009 - 23:11:50 CDT)
  • Re: [AMBER] continuam water Carlos Simmerling (Tue Mar 24 2009 - 08:36:15 CDT)
    • [AMBER] POLARIZABLE WATER MODEL CHAMI F. (Tue Mar 24 2009 - 13:03:25 CDT)
• [AMBER] change in protein ligand order Hannes Wallnoefer (Tue Mar 24 2009 - 06:05:36 CDT)
  • Re: [AMBER] change in protein ligand order Hannes Loeffler (Tue Mar 24 2009 - 06:27:24 CDT)
    • Re: [AMBER] change in protein ligand order Hannes Wallnoefer (Tue Mar 24 2009 - 07:38:18 CDT)
  • Re: [AMBER] change in protein ligand order Bill Ross (Tue Mar 24 2009 - 13:07:42 CDT)
    • Re: [AMBER] change in protein ligand order Hannes Wallnoefer (Tue Mar 24 2009 - 15:45:16 CDT)
• [AMBER] validation of parameters and request suggestions Jeffrey (Tue Mar 24 2009 - 06:52:19 CDT)
• [AMBER] create new crd files from transformed coordinates Donald Keidel (Tue Mar 24 2009 - 20:49:03 CDT)
  • Re: [AMBER] create new crd files from transformed coordinates case (Wed Mar 25 2009 - 07:26:29 CDT)
• [AMBER] question about pair wise per-residue energy decomposition; idecomp=3 wfli_at_biophy.nju.edu.cn (Wed Mar 25 2009 - 04:48:29 CDT)
  • Re: [AMBER] question about pair wise per-residue energy decomposition; idecomp=3 case (Wed Mar 25 2009 - 13:58:02 CDT)
• [AMBER] About Free energy decomposition Rajesh Raju (Wed Mar 25 2009 - 09:08:00 CDT)
• [AMBER] Rosetta Academic Training Webinar Nir London (Wed Mar 25 2009 - 11:14:21 CDT)
• [AMBER] How to reproduce a parallel PMEMD run? Siang Yip (Wed Mar 25 2009 - 17:33:56 CDT)
  • Re: [AMBER] How to reproduce a parallel PMEMD run? Robert Duke (Wed Mar 25 2009 - 18:45:49 CDT)
• [AMBER] Amber 10 and core i7 Supat Jiranusornkul (Thu Mar 26 2009 - 04:13:10 CDT)
• [AMBER] To find radial distribution curve nicholus bhattacharjee (Thu Mar 26 2009 - 12:16:07 CDT)
• [AMBER] installing resp on linux 64bit aditya chhikara (Thu Mar 26 2009 - 12:24:27 CDT)
  • Re: [AMBER] installing resp on linux 64bit FyD (Thu Mar 26 2009 - 14:37:22 CDT)
    • Re: [AMBER] installing resp on linux 64bit aditya chhikara (Thu Mar 26 2009 - 16:36:50 CDT)
• [AMBER] Problem with "Atom does not have a type" Richard Tseng (Thu Mar 26 2009 - 18:17:19 CDT)
  • Re: [AMBER] Problem with "Atom does not have a type" David A. Case (Fri Mar 27 2009 - 06:44:22 CDT)
    • Re: [AMBER] Problem with "Atom does not have a type" Richard Tseng (Fri Mar 27 2009 - 16:51:32 CDT)
      • Re: [AMBER] Problem with "Atom does not have a type" Richard Tseng (Fri Mar 27 2009 - 17:08:34 CDT)
      • Re: [AMBER] Problem with "Atom does not have a type" David A. Case (Sat Mar 28 2009 - 08:25:33 CDT)
      • Re: [AMBER] Problem with "Atom does not have a type" Richard Tseng (Sun Mar 29 2009 - 14:20:37 CDT)
      • Re: [AMBER] Problem with "Atom does not have a type" case (Mon Mar 30 2009 - 07:46:59 CDT)
• [AMBER] Fwd: AMBER: MM-PBSA in AMBER 10 Daniel Oehme (Thu Mar 26 2009 - 18:44:59 CDT)
  • Re: [AMBER] Fwd: AMBER: MM-PBSA in AMBER 10 Ray Luo (Thu Mar 26 2009 - 18:54:17 CDT)
• [AMBER] Problem reading PDB file into XLEAP Hopkins, Robert (Thu Mar 26 2009 - 19:01:26 CDT)
  • Re: [AMBER] Problem reading PDB file into XLEAP David A. Case (Fri Mar 27 2009 - 07:39:26 CDT)
    • RE: [AMBER] Problem reading PDB file into XLEAP Hopkins, Robert (Fri Mar 27 2009 - 17:09:11 CDT)
      • Re: [AMBER] Problem reading PDB file into XLEAP David A. Case (Sat Mar 28 2009 - 08:28:53 CDT)
      • RE: [AMBER] Problem reading PDB file into XLEAP - SLEAP Hopkins, Robert (Sat Mar 28 2009 - 18:12:06 CDT)
      • Re: [AMBER] Problem reading PDB file into XLEAP - SLEAP Wei Zhang (Sat Mar 28 2009 - 18:29:20 CDT)
      • RE: [AMBER] Problem reading PDB file into XLEAP - SLEAP Hopkins, Robert (Sun Mar 29 2009 - 13:27:09 CDT)
      • Re: [AMBER] Problem reading PDB file into XLEAP - SLEAP David A. Case (Sun Mar 29 2009 - 13:37:35 CDT)
• [AMBER] Antechamber problem Å·ÑôµÂ·½ (Thu Mar 26 2009 - 23:44:24 CDT)
  • Re: [AMBER] Antechamber problem David A. Case (Fri Mar 27 2009 - 07:29:48 CDT)
  • Re: [AMBER] Antechamber problem Junmei Wang (Fri Mar 27 2009 - 16:21:33 CDT)
    • RE: [AMBER] Antechamber problem Å·ÑôµÂ·½ (Fri Mar 27 2009 - 19:55:03 CDT)
• [AMBER] problem using amoeba Hemant Gangwar (Fri Mar 27 2009 - 05:41:26 CDT)
  • Re: [AMBER] problem using amoeba Robert Duke (Fri Mar 27 2009 - 07:22:31 CDT)
• [AMBER] Question Kshatresh Dutta Dubey (Fri Mar 27 2009 - 08:06:09 CDT)
  • RE: [AMBER] Question Rausch, Felix (Fri Mar 27 2009 - 08:37:29 CDT)
    • Re: [AMBER] Question Kshatresh Dutta Dubey (Sat Mar 28 2009 - 04:16:03 CDT)
      • Re: [AMBER] Question David A. Case (Sat Mar 28 2009 - 08:38:49 CDT)
  • [AMBER] BINDER/xaLeap Taufik Al-Sarraj (Mon Mar 30 2009 - 20:00:10 CDT)
    • RE: [AMBER] BINDER/xaLeap Ross Walker (Mon Mar 30 2009 - 20:29:46 CDT)
      • RE: [AMBER] BINDER/xaLeap taufik.alsarraj_at_utoronto.ca (Mon Mar 30 2009 - 21:16:32 CDT)
      • [AMBER] ambmol2? Taufik Al-Sarraj (Tue Mar 31 2009 - 17:28:51 CDT)
      • Re: [AMBER] ambmol2? Junmei Wang (Tue Mar 31 2009 - 18:08:25 CDT)
      • Re: [AMBER] ambmol2? Taufik Al-Sarraj (Tue Mar 31 2009 - 21:15:00 CDT)
      • Re: [AMBER] ambmol2? Junmei Wang (Tue Mar 31 2009 - 21:41:35 CDT)
• [AMBER] PMEMD 9 on MVAPICH / Infiniband problem Nick Holway (Fri Mar 27 2009 - 10:55:38 CDT)
  • RE: [AMBER] PMEMD 9 on MVAPICH / Infiniband problem Ross Walker (Fri Mar 27 2009 - 20:04:04 CDT)
    • Re: [AMBER] PMEMD 9 on MVAPICH / Infiniband problem fohm fohm (Tue Mar 31 2009 - 06:04:10 CDT)
      • Re: [AMBER] PMEMD 9 on MVAPICH / Infiniband problem Robert Duke (Tue Mar 31 2009 - 07:21:22 CDT)
• [AMBER] Load protein complex to Xleap (Combine) Rilei Yu (Fri Mar 27 2009 - 21:30:04 CDT)
  • Re: [AMBER] Load protein complex to Xleap (Combine) David A. Case (Sat Mar 28 2009 - 16:39:35 CDT)
  • Re: [AMBER] Load protein complex to Xleap (Combine) Rilei Yu (Sat Mar 28 2009 - 20:17:21 CDT)
    • Re: [AMBER] Load protein complex to Xleap (Combine) David A. Case (Sat Mar 28 2009 - 21:26:58 CDT)
  • Re: [AMBER] Load protein complex to Xleap (Combine) Rilei Yu (Sat Mar 28 2009 - 22:07:47 CDT)
  • Re: [AMBER] Load protein complex to Xleap (Combine) Rilei Yu (Sat Mar 28 2009 - 23:00:00 CDT)
    • Re: [AMBER] Load protein complex to Xleap (Combine) David A. Case (Sun Mar 29 2009 - 13:41:13 CDT)
• [AMBER] .rst file generation problem. Aravind S (Mon Mar 30 2009 - 00:48:55 CDT)
  • Re: [AMBER] .rst file generation problem. Aravind S (Mon Mar 30 2009 - 01:32:12 CDT)
  • Re: [AMBER] .rst file generation problem. Carlos Simmerling (Mon Mar 30 2009 - 06:30:58 CDT)
  • Re: [AMBER] .rst file generation problem. Aravind S (Tue Mar 31 2009 - 03:49:17 CDT)
    • Re: [AMBER] .rst file generation problem. Carlos Simmerling (Tue Mar 31 2009 - 06:28:35 CDT)
• [AMBER] "rfree: End of file on unit 5" Remya S R (Mon Mar 30 2009 - 01:21:53 CDT)
  • Re: [AMBER] "rfree: End of file on unit 5" mathew k varghese (Mon Mar 30 2009 - 04:57:44 CDT)
• [AMBER] mm_pbsa problem Giorgos Lamprinidis (Mon Mar 30 2009 - 05:02:07 CDT)
  • Re: [AMBER] mm_pbsa problem case (Mon Mar 30 2009 - 07:48:05 CDT)
    • Re: [AMBER] mm_pbsa problem Giorgos Lamprinidis (Mon Mar 30 2009 - 08:59:55 CDT)
      • RE: [AMBER] mm_pbsa problem Ray Luo (Mon Mar 30 2009 - 12:27:59 CDT)
• [AMBER] Creating conditions for biased MD Francesco Pietra (Mon Mar 30 2009 - 05:16:54 CDT)
  • Re: [AMBER] Creating conditions for biased MD Carlos Simmerling (Mon Mar 30 2009 - 06:56:36 CDT)
• [AMBER] amber tools installation Jayalakshmi Sridhar (Mon Mar 30 2009 - 10:44:57 CDT)
  • Re: [AMBER] amber tools installation case (Mon Mar 30 2009 - 11:28:38 CDT)
• [AMBER] Announcing NMR validation web interface iCing Alan (Mon Mar 30 2009 - 11:55:00 CDT)
• [AMBER] problem with the results in the .out file! Aravind S (Tue Mar 31 2009 - 00:30:57 CDT)
  • Re: [AMBER] problem with the results in the .out file! Gustavo Seabra (Tue Mar 31 2009 - 08:01:41 CDT)
• [AMBER] how to convert secstruct output file into plot or pictorial representation Siddharth Rastogi (Tue Mar 31 2009 - 05:56:37 CDT)
• [AMBER] modifying LYN Marius Retegan (Tue Mar 31 2009 - 08:36:21 CDT)
  • Re: [AMBER] modifying LYN FyD (Tue Mar 31 2009 - 10:41:56 CDT)
    • Re: [AMBER] modifying LYN Marius Retegan (Tue Mar 31 2009 - 11:58:06 CDT)
• [AMBER] combine many coord files into trajectory file Peter Gannett (Tue Mar 31 2009 - 08:51:16 CDT)
  • Re: [AMBER] combine many coord files into trajectory file Carlos Simmerling (Tue Mar 31 2009 - 08:55:58 CDT)
    • Re: [AMBER] combine many coord files into trajectory file Peter Gannett (Tue Mar 31 2009 - 09:25:00 CDT)
• [AMBER] Maxwell-Boltzmann distribution and ig=-1 Naser Alijabbari (Tue Mar 31 2009 - 20:35:43 CDT)
  • Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1 Carlos Simmerling (Tue Mar 31 2009 - 20:41:49 CDT)
    • Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1 Naser Alijabbari (Tue Mar 31 2009 - 21:15:13 CDT)
      • Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1 Carlos Simmerling (Tue Mar 31 2009 - 21:24:34 CDT)
      • Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1 Naser Alijabbari (Tue Mar 31 2009 - 21:43:28 CDT)
      • RE: [AMBER] Maxwell-Boltzmann distribution and ig=-1 Ross Walker (Tue Mar 31 2009 - 22:52:42 CDT)
• [AMBER] a layer of water Nancy (Tue Mar 31 2009 - 20:37:51 CDT)
  • Re: [AMBER] please help me out FyD (Mon Mar 09 2009 - 05:05:06 CDT)
    • Re: [AMBER] please help me out bharat lakhani (Thu Mar 12 2009 - 01:04:00 CDT)
      • Re: [AMBER] please help me out rpaduri_at_chem.wayne.edu (Thu Mar 12 2009 - 11:37:09 CDT)
      • Re: [AMBER] please help me out bharat lakhani (Sat Mar 14 2009 - 06:04:37 CDT)
      • Re: [AMBER] please help me out David A. Case (Sat Mar 14 2009 - 08:06:34 CDT)
      • RE: [AMBER] please help me out Ross Walker (Sat Mar 14 2009 - 11:54:22 CDT)
      • Re: [AMBER] please help me out bharat lakhani (Mon Mar 23 2009 - 02:58:52 CDT)
      • Re: [AMBER] please help me out bharat lakhani (Tue Mar 24 2009 - 08:57:18 CDT)

Last message date: Mon Nov 23 2009 - 11:49:36 CST
Archived on: Mon Nov 23 2009 - 11:49:38 CST