AMBER Archive (2008) - Dec 2008 By Thread

Starting: Mon Dec 01 2008 - 01:30:02 CST
Ending: Wed Dec 31 2008 - 22:44:33 CST

• Re: AMBER: Running Amber8 - Sander David A. Case (Mon Dec 01 2008 - 09:37:32 CST)
• Re: AMBER: using packmol file in Amber oguz gurbulak (Tue Dec 02 2008 - 05:06:10 CST)
  • Re: AMBER: using packmol file in Amber David A. Case (Tue Dec 02 2008 - 06:14:47 CST)
    • Re: AMBER: using packmol file in Amber oguz gurbulak (Tue Dec 02 2008 - 08:02:59 CST)
    • Re: AMBER: using packmol file in Amber David A. Case (Tue Dec 02 2008 - 08:19:20 CST)
    • Re: AMBER: using packmol file in Amber oguz gurbulak (Thu Dec 04 2008 - 09:36:03 CST)
    • Re: AMBER: using packmol file in Amber David A. Case (Thu Dec 04 2008 - 10:32:49 CST)
    • Re: AMBER: using packmol file in Amber oguz gurbulak (Fri Dec 05 2008 - 09:49:39 CST)
    • Re: AMBER: using packmol file in Amber David A. Case (Fri Dec 05 2008 - 09:58:51 CST)
    • Re: AMBER: using packmol file in Amber oguz gurbulak (Mon Dec 15 2008 - 09:57:08 CST)
    • Re: AMBER: using packmol file in Amber Gustavo Seabra (Mon Dec 15 2008 - 10:39:53 CST)
• Re: AMBER: subroutine Work : Jarynski work theorem Gustavo Seabra (Wed Dec 03 2008 - 07:59:06 CST)
• Re: AMBER: Problem running NEB in AMBER10 Chris C. (Wed Dec 03 2008 - 12:29:48 CST)
• Re: AMBER: seeking help regrading Zinc protein GBSA minimization Sergey Samsonov (Mon Dec 01 2008 - 02:14:36 CST)
  • Re: AMBER: seeking help regrading Zinc protein GBSA minimization Carlos Simmerling (Mon Dec 01 2008 - 05:16:02 CST)
• Re: AMBER: Is there an easy way to calculate the electric field at the center of a group of atoms David A. Case (Mon Dec 01 2008 - 09:34:47 CST)
• Re: AMBER: N(CN2)- ion David A. Case (Mon Dec 01 2008 - 08:47:14 CST)
  • Re: AMBER: N(CN2)- ion babak minoofar (Thu Dec 04 2008 - 10:00:58 CST)
    • Re: AMBER: N(CN2)- ion David A. Case (Fri Dec 05 2008 - 06:23:05 CST)
    • Re: AMBER: N(CN2)- ion babak minoofar (Fri Dec 12 2008 - 03:29:54 CST)
• AMBER: QM/MM and unpaired spin Markus Kaukonen (Mon Dec 01 2008 - 01:30:02 CST)
  • RE: AMBER: QM/MM and unpaired spin Ross Walker (Mon Dec 01 2008 - 10:40:20 CST)
  • Re: AMBER: QM/MM and unpaired spin Gustavo Seabra (Tue Dec 02 2008 - 21:11:25 CST)
    • RE: AMBER: QM/MM and unpaired spin Ross Walker (Tue Dec 02 2008 - 21:42:37 CST)
      • AMBER: DNA-Gold parameters Xioling Chuang (Wed Dec 03 2008 - 05:37:55 CST)
      • Re: AMBER: QM/MM and unpaired spin Gustavo Seabra (Wed Dec 03 2008 - 07:53:00 CST)
• AMBER: reg.dnasaveparm&tcrd balaji nagarajan (Mon Dec 01 2008 - 08:05:52 CST)
  • Re: AMBER: reg.dnasaveparm&tcrd David A. Case (Mon Dec 01 2008 - 08:29:41 CST)
    • RE: AMBER: reg.dnasaveparm&tcrd balaji nagarajan (Mon Dec 01 2008 - 10:51:00 CST)
  • RE: AMBER: reg.dnasaveparm&tcrd Ross Walker (Mon Dec 01 2008 - 10:44:57 CST)
    • RE: AMBER: reg.dnasaveparm&tcrd balaji nagarajan (Mon Dec 01 2008 - 10:56:44 CST)
• AMBER: How do you evaluate forces on a fixed atom? Bill K (Mon Dec 01 2008 - 12:45:42 CST)
  • Re: AMBER: How do you evaluate forces on a fixed atom? David A. Case (Tue Dec 02 2008 - 08:39:37 CST)
    • Re: AMBER: How do you evaluate forces on a fixed atom? Bill K (Tue Dec 02 2008 - 19:54:35 CST)
• AMBER: makeDIST_RST error -- no map function for HH TYR Ryan Pavlovicz (Mon Dec 01 2008 - 13:30:01 CST)
  • Re: AMBER: makeDIST_RST error -- no map function for HH TYR David A. Case (Mon Dec 01 2008 - 15:22:46 CST)
• AMBER: Variable PBCAL values in MM-PBSA calculations Daniel Oehme (Mon Dec 01 2008 - 17:45:23 CST)
  • RE: AMBER: Variable PBCAL values in MM-PBSA calculations Ray Luo (Mon Dec 01 2008 - 19:55:37 CST)
    • Re: AMBER: Variable PBCAL values in MM-PBSA calculations Daniel Oehme (Thu Dec 04 2008 - 00:34:42 CST)
      • RE: AMBER: Variable PBCAL values in MM-PBSA calculations Ray Luo (Thu Dec 04 2008 - 13:06:45 CST)
      • Re: AMBER: Variable PBCAL values in MM-PBSA calculations Daniel Oehme (Sun Dec 07 2008 - 23:56:58 CST)
• AMBER: Simulating peptide linkers with AMBER Sasha Buzko (Tue Dec 02 2008 - 14:03:42 CST)
• AMBER: MM/GBSA Error during deccomposition N.R. Jena (Wed Dec 03 2008 - 06:01:04 CST)
  • Re: AMBER: MM/GBSA Error during deccomposition Barbault Florent (Wed Dec 03 2008 - 14:32:14 CST)
    • Re: AMBER: MM/GBSA Error during deccomposition N.R. Jena (Thu Dec 04 2008 - 05:01:36 CST)
      • Re: AMBER: MM/GBSA Error during deccomposition Cristina Sisu (Thu Dec 04 2008 - 05:27:48 CST)
      • Re: AMBER: MM/GBSA Error during deccomposition N.R. Jena (Thu Dec 04 2008 - 07:08:45 CST)
      • Re: AMBER: MM/GBSA Error during deccomposition N.R. Jena (Thu Dec 04 2008 - 22:13:44 CST)
• AMBER: ptraj: how to select all non-hydrogen atoms Mingfeng Yang (Wed Dec 03 2008 - 13:37:00 CST)
  • Re: AMBER: ptraj: how to select all non-hydrogen atoms Hannes Kopitz (Wed Dec 03 2008 - 14:27:33 CST)
    • AMBER: unable to open pdb file Taufik Al-Sarraj (Wed Dec 03 2008 - 20:44:09 CST)
      • Re: AMBER: unable to open pdb file David A. Case (Thu Dec 04 2008 - 05:41:32 CST)
• AMBER: makeDIST_RST computation of r3 value with IAT < 0 Ryan Pavlovicz (Wed Dec 03 2008 - 17:13:32 CST)
  • Re: AMBER: makeDIST_RST computation of r3 value with IAT < 0 David A. Case (Fri Dec 05 2008 - 10:45:20 CST)
• AMBER: reg unstability of structure in md balaji nagarajan (Wed Dec 03 2008 - 22:17:51 CST)
  • Re: AMBER: reg unstability of structure in md Carlos Simmerling (Thu Dec 04 2008 - 05:28:12 CST)
    • RE: AMBER: reg unstability of structure in md balaji nagarajan (Thu Dec 04 2008 - 22:32:21 CST)
      • Re: AMBER: reg unstability of structure in md N.R. Jena (Fri Dec 05 2008 - 00:48:50 CST)
      • Re: AMBER: reg unstability of structure in md Carlos Simmerling (Fri Dec 05 2008 - 05:41:40 CST)
• AMBER: side chain expression Yunierkis Perez Castillo (Thu Dec 04 2008 - 10:43:14 CST)
• AMBER: LINMIN error in geometrically constrained minimization @ MM-PB/SA conditions Alexander Metz (Thu Dec 04 2008 - 11:04:03 CST)
• AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 Hazard, E. Starr (Fri Dec 05 2008 - 14:12:54 CST)
  • RE: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 Ross Walker (Fri Dec 05 2008 - 14:26:30 CST)
    • Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 Starr Hazard (Fri Dec 05 2008 - 14:53:14 CST)
  • Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 David Watson (Fri Dec 05 2008 - 14:32:45 CST)
    • Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 Starr Hazard (Fri Dec 05 2008 - 15:10:11 CST)
      • Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 Robert Duke (Fri Dec 05 2008 - 15:15:55 CST)
      • Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 David Watson (Fri Dec 05 2008 - 15:53:15 CST)
      • Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 Starr Hazard (Fri Dec 05 2008 - 16:11:58 CST)
      • Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 David Watson (Fri Dec 05 2008 - 16:30:32 CST)
      • Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 Robert Duke (Fri Dec 05 2008 - 16:46:57 CST)
  • Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 Robert Duke (Fri Dec 05 2008 - 14:32:04 CST)
  • Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 sychen (Fri Dec 05 2008 - 21:46:20 CST)
• AMBER: regad-tutorial-dna-polyAT balaji nagarajan (Sun Dec 07 2008 - 22:45:10 CST)
  • Re: AMBER: regad-tutorial-dna-polyAT jani sahil (Sun Dec 07 2008 - 23:13:30 CST)
    • RE: AMBER: regad-tutorial-dna-polyAT balaji nagarajan (Mon Dec 08 2008 - 00:40:39 CST)
• AMBER: GB offset for proteins Sally Pias (Sun Dec 07 2008 - 23:14:58 CST)
  • Re: AMBER: GB offset for proteins David A. Case (Wed Dec 24 2008 - 13:11:21 CST)
• AMBER: reg-adding ions balaji nagarajan (Mon Dec 08 2008 - 02:20:05 CST)
  • RE: AMBER: reg-adding ions Ross Walker (Mon Dec 08 2008 - 10:33:18 CST)
    • RE: AMBER: reg-adding ions balaji nagarajan (Mon Dec 08 2008 - 22:32:14 CST)
      • RE: AMBER: reg-adding ions Ross Walker (Tue Dec 09 2008 - 09:05:04 CST)
• AMBER: interaction energies Marina Grabar (Mon Dec 08 2008 - 05:29:36 CST)
  • Re: AMBER: interaction energies David A. Case (Mon Dec 08 2008 - 10:59:28 CST)
    • AMBER: prep files ATP-MG++ and for phosphorylated threonine mirzo_at_jinr.ru (Tue Dec 09 2008 - 02:01:42 CST)
      • Re: AMBER: prep files ATP-MG++ and for phosphorylated threonine Anselm Horn (Tue Dec 09 2008 - 04:06:17 CST)
      • Re: AMBER: prep files ATP-MG++ and for phosphorylated threonine mirzo_at_jinr.ru (Tue Dec 09 2008 - 04:23:08 CST)
• AMBER: Problem with MMPBSA Daniel Emery (Mon Dec 08 2008 - 10:28:22 CST)
  • RE: AMBER: Problem with MMPBSA Ray Luo (Mon Dec 08 2008 - 13:47:15 CST)
• AMBER: MM-PBSA : bad atom type: ZN jitrayut jitonnom (Mon Dec 08 2008 - 10:51:12 CST)
• AMBER: RESP GAUSSIAN AMBER SilasConnor_at_gmx.at (Mon Dec 08 2008 - 12:31:24 CST)
  • Re: AMBER: RESP GAUSSIAN AMBER FyD (Thu Dec 11 2008 - 05:42:20 CST)
    • RE: AMBER: RESP GAUSSIAN AMBER Ross Walker (Thu Dec 11 2008 - 22:00:27 CST)
      • AMBER: DNA: GB solvent with salt Catein Catherine (Fri Dec 12 2008 - 03:31:13 CST)
      • Re: AMBER: DNA: GB solvent with salt Carlos Simmerling (Fri Dec 12 2008 - 05:33:14 CST)
      • Re: AMBER: RESP GAUSSIAN AMBER Francesco Pietra (Fri Dec 12 2008 - 05:13:13 CST)
      • Re: AMBER: RESP GAUSSIAN AMBER FyD (Fri Dec 12 2008 - 09:16:01 CST)
      • RE: AMBER: RESP GAUSSIAN AMBER FyD (Fri Dec 12 2008 - 08:25:06 CST)
      • RE: AMBER: RESP GAUSSIAN AMBER Ross Walker (Fri Dec 12 2008 - 13:04:49 CST)
      • RE: AMBER: RESP GAUSSIAN AMBER Piotr Cieplak (Fri Dec 12 2008 - 14:12:20 CST)
      • RE: AMBER: RESP GAUSSIAN AMBER FyD (Sat Dec 13 2008 - 01:23:10 CST)
      • Re: AMBER: RESP GAUSSIAN AMBER Brent Krueger (Sun Dec 14 2008 - 20:52:14 CST)
      • RE: AMBER: RESP GAUSSIAN AMBER Ross Walker (Mon Dec 15 2008 - 11:36:27 CST)
      • Re: AMBER: RESP GAUSSIAN AMBER M. L. Dodson (Mon Dec 15 2008 - 11:52:48 CST)
      • Re: AMBER: RESP GAUSSIAN AMBER FyD (Mon Dec 15 2008 - 14:41:24 CST)
      • Re: AMBER: RESP GAUSSIAN AMBER M. L. Dodson (Mon Dec 15 2008 - 15:36:08 CST)
      • Re: AMBER: RESP GAUSSIAN AMBER FyD (Mon Dec 15 2008 - 16:05:46 CST)
      • RE: AMBER: RESP GAUSSIAN AMBER FyD (Wed Dec 17 2008 - 03:12:38 CST)
      • RE: AMBER: RESP GAUSSIAN AMBER FyD (Sat Dec 13 2008 - 02:02:23 CST)
• AMBER: RE: bugfix 11 & 12 Ross Walker (Mon Dec 08 2008 - 15:12:42 CST)
• AMBER: how to add new solvent type in Amber iccy liu (Mon Dec 08 2008 - 18:23:11 CST)
  • Re: AMBER: how to add new solvent type in Amber David A. Case (Wed Dec 10 2008 - 17:18:56 CST)
    • AMBER: solvent box again iccy liu (Tue Dec 16 2008 - 12:32:32 CST)
      • RE: AMBER: solvent box again Ross Walker (Tue Dec 16 2008 - 12:57:01 CST)
      • RE: AMBER: solvent box again iccy liu (Thu Dec 18 2008 - 13:41:41 CST)
      • Re: AMBER: solvent box again David A. Case (Tue Dec 16 2008 - 14:02:05 CST)
• AMBER: Radial Distribution Function prabhakar g (Mon Dec 08 2008 - 20:37:52 CST)
  • Re: AMBER: Radial Distribution Function Gustavo Seabra (Tue Dec 09 2008 - 09:38:54 CST)
    • Re: AMBER: Radial Distribution Function prabhakar g (Tue Dec 09 2008 - 21:33:27 CST)
      • Re: AMBER: Radial Distribution Function Gustavo Seabra (Wed Dec 10 2008 - 07:49:42 CST)
      • Re: AMBER: Radial Distribution Function prabhakar g (Fri Dec 12 2008 - 20:31:48 CST)
      • Re: AMBER: Radial Distribution Function Gustavo Seabra (Mon Dec 15 2008 - 01:41:02 CST)
• AMBER: (no subject) waleed zalloum (Tue Dec 09 2008 - 06:22:39 CST)
  • RE: AMBER: (no subject) Ross Walker (Tue Dec 09 2008 - 09:07:18 CST)
    • RE: AMBER: (no subject) Scott Brozell (Tue Dec 09 2008 - 09:17:06 CST)
• AMBER: Constant pH dynamics Beale, John (Tue Dec 09 2008 - 06:51:39 CST)
  • Re: AMBER: Constant pH dynamics Adrian Roitberg (Tue Dec 09 2008 - 10:24:17 CST)
  • Re: AMBER: Constant pH dynamics David A. Case (Tue Dec 09 2008 - 09:27:51 CST)
• AMBER: parallel installation balaji nagarajan (Tue Dec 09 2008 - 21:56:20 CST)
  • Re: AMBER: parallel installation David A. Case (Wed Dec 10 2008 - 07:09:00 CST)
• AMBER: forrtl severe(174) error with minimization and md john smith (Wed Dec 10 2008 - 00:20:57 CST)
  • RE: AMBER: forrtl severe(174) error with minimization and md Ross Walker (Wed Dec 10 2008 - 09:57:42 CST)
    • Re: AMBER: forrtl severe(174) error with minimization and md john smith (Mon Dec 15 2008 - 02:46:56 CST)
• AMBER: reg-antichamber run balaji nagarajan (Wed Dec 10 2008 - 11:08:17 CST)
  • Re: AMBER: reg-antichamber run David A. Case (Wed Dec 10 2008 - 17:14:31 CST)
    • Re: AMBER: reg-antichamber run FyD (Thu Dec 11 2008 - 03:57:26 CST)
• AMBER: Building Amber 10 with Intel MKL and compiler mini howto Ben Eisenbraun (Wed Dec 10 2008 - 11:45:04 CST)
• AMBER: Running md using glycam in AMBER Neha Gandhi (Thu Dec 11 2008 - 01:15:54 CST)
  • RE: AMBER: Running md using glycam in AMBER Matthew Tessier (Thu Dec 11 2008 - 14:52:28 CST)
• AMBER: Distorted ring... Waqas Nasir (Thu Dec 11 2008 - 05:48:45 CST)
  • Re: AMBER: Distorted ring... Carlos Simmerling (Thu Dec 11 2008 - 06:15:57 CST)
• AMBER: tutorial A1, file missing readit.f ABEL Stephane 175950 (Thu Dec 11 2008 - 06:22:41 CST)
  • Re: AMBER: tutorial A1, file missing readit.f David A. Case (Thu Dec 11 2008 - 07:19:38 CST)
• AMBER: Pulling using restraintmask Dirar Homouz (Thu Dec 11 2008 - 14:30:00 CST)
  • Re: AMBER: Pulling using restraintmask Alessandro Nascimento (Thu Dec 11 2008 - 14:58:51 CST)
• AMBER: reg.building ions balaji nagarajan (Fri Dec 12 2008 - 04:40:07 CST)
  • Re: AMBER: reg.building ions David A. Case (Fri Dec 12 2008 - 06:04:58 CST)
    • RE: AMBER: reg.building ions balaji nagarajan (Fri Dec 12 2008 - 06:14:57 CST)
      • Re: AMBER: reg.building ions David A. Case (Fri Dec 12 2008 - 06:42:28 CST)
    • AMBER: building new ions CHAMI F. (Fri Dec 12 2008 - 06:23:20 CST)
      • AMBER: building new ions CHAMI F. (Mon Dec 15 2008 - 07:50:50 CST)
      • Re: AMBER: building new ions FyD (Mon Dec 15 2008 - 08:09:04 CST)
• AMBER: ff99 (PK/IDIVF) saurabh agrawal (Fri Dec 12 2008 - 07:26:58 CST)
  • Re: AMBER: ff99 (PK/IDIVF) Carlos Simmerling (Fri Dec 12 2008 - 08:05:11 CST)
    • RE: AMBER: ff99 (PK/IDIVF) Ross Walker (Fri Dec 12 2008 - 11:06:22 CST)
      • RE: AMBER: ff99 (PK/IDIVF) saurabh agrawal (Sun Dec 14 2008 - 12:29:39 CST)
      • Re: AMBER: ff99 (PK/IDIVF) Carlos Simmerling (Sun Dec 14 2008 - 12:38:23 CST)
      • Re: AMBER: ff99 (PK/IDIVF) saurabh agrawal (Tue Dec 16 2008 - 05:47:09 CST)
      • Re: AMBER: ff99 (PK/IDIVF) Carlos Simmerling (Tue Dec 16 2008 - 06:01:32 CST)
• AMBER: ld: cannot find -lgcc_s moitrayee_at_mbu.iisc.ernet.in (Fri Dec 12 2008 - 07:52:08 CST)
  • Re: AMBER: ld: cannot find -lgcc_s David A. Case (Fri Dec 12 2008 - 08:26:00 CST)
• AMBER: reg.concentration of ions balaji nagarajan (Fri Dec 12 2008 - 10:34:49 CST)
• AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems ABEL Stephane 175950 (Fri Dec 12 2008 - 10:41:19 CST)
  • Re: AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems Jifeng Wang (Fri Dec 12 2008 - 10:50:56 CST)
    • Re: AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems FyD (Fri Dec 12 2008 - 11:14:05 CST)
• AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems ABEL Stephane 175950 (Fri Dec 12 2008 - 11:33:44 CST)
  • Re: AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems FyD (Fri Dec 12 2008 - 12:24:25 CST)
• AMBER: sgi4700 the time of MD simulation is 30 minute for 1ps about 2500 atom using 1cpu llduan_at_itcc.nju.edu.cn (Sat Dec 13 2008 - 08:36:45 CST)
  • Re: AMBER: sgi4700 the time of MD simulation is 30 minute for 1ps about 2500 atom using 1cpu steinbrt_at_rci.rutgers.edu (Sat Dec 13 2008 - 12:58:18 CST)
• AMBER: problem with toturial A3 (MM-PBSA) Maryam Hamzehee (Sat Dec 13 2008 - 09:22:58 CST)
  • Re: AMBER: problem with toturial A3 (MM-PBSA) Carlos Simmerling (Sat Dec 13 2008 - 09:35:13 CST)
    • Re: AMBER: problem with toturial A3 (MM-PBSA) Maryam Hamzehee (Sun Dec 14 2008 - 05:25:00 CST)
      • Re: AMBER: problem with toturial A3 (MM-PBSA) Carlos Simmerling (Tue Dec 16 2008 - 07:57:42 CST)
• AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC Atro Tossavainen (Sat Dec 13 2008 - 15:18:45 CST)
  • Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC Atro Tossavainen (Sat Dec 13 2008 - 16:12:30 CST)
  • Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC David A. Case (Sun Dec 14 2008 - 08:20:36 CST)
    • Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC Atro Tossavainen (Sun Dec 14 2008 - 14:11:53 CST)
      • Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC Atro Tossavainen (Mon Dec 15 2008 - 03:36:09 CST)
      • Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC Atro Tossavainen (Mon Dec 15 2008 - 04:06:51 CST)
      • Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC Atro Tossavainen (Mon Dec 15 2008 - 05:12:53 CST)
      • Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC David A. Case (Mon Dec 15 2008 - 06:54:33 CST)
      • Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC Atro Tossavainen (Mon Dec 15 2008 - 08:27:05 CST)
• AMBER: Calculating the dielectrostatic constant from simulation? Jeffrey (Mon Dec 15 2008 - 01:07:25 CST)
  • Re: AMBER: Calculating the dielectrostatic constant from simulation? Adrian Roitberg (Mon Dec 15 2008 - 07:44:09 CST)
    • Re: Re: AMBER: Calculating the dielectrostatic constant from simulation? Jeffrey (Mon Dec 15 2008 - 19:34:54 CST)
• AMBER: pressure component chengtao_at_sjtu.edu.cn (Mon Dec 15 2008 - 02:17:21 CST)
  • Re: AMBER: pressure component David A. Case (Mon Dec 15 2008 - 06:43:44 CST)
    • Re: AMBER: pressure component chengtao_at_sjtu.edu.cn (Tue Dec 16 2008 - 02:42:00 CST)
• AMBER: AMBER 10 PMEMD / SGI_MIPS Atro Tossavainen (Mon Dec 15 2008 - 06:51:16 CST)
  • Re: AMBER: AMBER 10 PMEMD / SGI_MIPS Robert Duke (Mon Dec 15 2008 - 07:45:34 CST)
    • Re: AMBER: AMBER 10 PMEMD / SGI_MIPS Atro Tossavainen (Mon Dec 15 2008 - 08:40:41 CST)
      • Re: AMBER: AMBER 10 PMEMD / SGI_MIPS Robert Duke (Mon Dec 15 2008 - 09:26:12 CST)
      • Re: AMBER: AMBER 10 PMEMD / SGI_MIPS Atro Tossavainen (Tue Dec 16 2008 - 06:17:48 CST)
      • RE: AMBER: AMBER 10 PMEMD / SGI_MIPS Ross Walker (Tue Dec 16 2008 - 10:16:11 CST)
• AMBER: Initial velocities based on date and time are NOT changing ? Markus Kaukonen (Mon Dec 15 2008 - 07:14:38 CST)
  • Re: AMBER: Initial velocities based on date and time are NOT changing ? David A. Case (Mon Dec 15 2008 - 07:38:03 CST)
    • Re: AMBER: Initial velocities based on date and time are NOT changing ? Markus Kaukonen (Tue Dec 16 2008 - 03:41:40 CST)
• AMBER: launching a job works with sander.MPI and fail with pmemd.MPI Thérèse Malliavin (Mon Dec 15 2008 - 08:41:55 CST)
  • RE: AMBER: launching a job works with sander.MPI and fail with pmemd.MPI Ross Walker (Mon Dec 15 2008 - 09:18:04 CST)
    • RE: AMBER: launching a job works with sander.MPI and fail with pmemd.MPI Thérèse Malliavin (Tue Dec 16 2008 - 06:57:05 CST)
      • Re: AMBER: launching a job works with sander.MPI and fail with pmemd.MPI Robert Duke (Tue Dec 16 2008 - 07:55:47 CST)
      • AMBER: comparison of MD trajectories recorded with pmemd and sander Thérèse Malliavin (Wed Dec 17 2008 - 08:04:26 CST)
      • Re: AMBER: comparison of MD trajectories recorded with pmemd and sander Carlos Simmerling (Wed Dec 17 2008 - 09:12:32 CST)
      • Re: AMBER: comparison of MD trajectories recorded with pmemd and sander Robert Duke (Wed Dec 17 2008 - 10:42:07 CST)
      • Re: AMBER: comparison of MD trajectories recorded with pmemd and sander Adrian Roitberg (Wed Dec 17 2008 - 10:40:23 CST)
      • Re: AMBER: comparison of MD trajectories recorded with pmemd and sander Thomas Cheatham III (Wed Dec 17 2008 - 11:16:47 CST)
      • Re: AMBER: comparison of MD trajectories recorded with pmemd and sander Robert Duke (Wed Dec 17 2008 - 11:02:25 CST)
      • RE: AMBER: comparison of MD trajectories recorded with pmemd and sander Ross Walker (Wed Dec 17 2008 - 11:01:37 CST)
      • Re: AMBER: comparison of MD trajectories recorded with pmemd and sander Robert Duke (Wed Dec 17 2008 - 11:18:46 CST)
      • Fw: AMBER: comparison of MD trajectories recorded with pmemd and sander Robert Duke (Wed Dec 17 2008 - 11:20:40 CST)
      • Re: AMBER: comparison of MD trajectories recorded with pmemd and sander Gustavo Seabra (Thu Dec 18 2008 - 08:58:13 CST)
  • Fw: AMBER: launching a job works with sander.MPI and fail with pmemd.MPI Robert Duke (Tue Dec 16 2008 - 08:56:13 CST)
    • AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) wl2290_at_columbia.edu (Fri Dec 19 2008 - 12:16:39 CST)
      • Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) David A. Case (Sat Dec 20 2008 - 17:48:23 CST)
      • Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) wl2290_at_columbia.edu (Mon Dec 22 2008 - 17:26:10 CST)
      • Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) David A. Case (Tue Dec 23 2008 - 07:26:15 CST)
      • Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) wl2290_at_columbia.edu (Tue Dec 23 2008 - 09:52:39 CST)
      • Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) wl2290_at_columbia.edu (Tue Dec 30 2008 - 11:54:58 CST)
      • Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) David A. Case (Tue Dec 30 2008 - 15:31:56 CST)
      • Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) wl2290_at_columbia.edu (Tue Dec 30 2008 - 16:15:59 CST)
• AMBER: relative weight of RDC constraints David Witte (Mon Dec 15 2008 - 10:21:34 CST)
  • Re: AMBER: relative weight of RDC constraints David A. Case (Mon Dec 15 2008 - 10:44:19 CST)
    • AMBER: distance restraint in minimization Taufik Al-Sarraj (Tue Dec 16 2008 - 12:46:22 CST)
      • Re: AMBER: distance restraint in minimization David A. Case (Tue Dec 16 2008 - 13:57:44 CST)
      • Re: AMBER: distance restraint in minimization Taufik Al-Sarraj (Tue Dec 16 2008 - 15:16:43 CST)
      • AMBER: distance restraint in minimization Taufik Al-Sarraj (Tue Dec 16 2008 - 16:44:35 CST)
      • Re: AMBER: distance restraint in minimization luzhenw1_at_msu.edu (Wed Dec 17 2008 - 09:10:49 CST)
      • Re: AMBER: distance restraint in minimization Taufik Al-Sarraj (Wed Dec 17 2008 - 11:44:55 CST)
      • Re: AMBER: distance restraint in minimization Jifeng Wang (Wed Dec 17 2008 - 12:16:08 CST)
      • Re: AMBER: distance restraint in minimization luzhenw1_at_msu.edu (Wed Dec 17 2008 - 12:17:28 CST)
      • Re: AMBER: distance restraint in minimization David A. Case (Wed Dec 17 2008 - 12:49:56 CST)
      • Re: AMBER: distance restraint in minimization Taufik Al-Sarraj (Wed Dec 17 2008 - 13:34:22 CST)
      • Re: AMBER: distance restraint in minimization Taufik Al-Sarraj (Wed Dec 17 2008 - 14:16:18 CST)
      • AMBER: distance restraint between non-bonded molecules Taufik Al-Sarraj (Wed Dec 17 2008 - 18:13:36 CST)
      • Re: AMBER: distance restraint between non-bonded molecules Carlos Simmerling (Thu Dec 18 2008 - 05:45:13 CST)
      • Re: AMBER: distance restraint between non-bonded molecules Taufik Al-Sarraj (Thu Dec 18 2008 - 10:49:51 CST)
      • Re: AMBER: distance restraint between non-bonded molecules Ilyas Yildirim (Thu Dec 18 2008 - 13:29:30 CST)
      • Re: AMBER: distance restraint between non-bonded molecules Taufik Al-Sarraj (Thu Dec 18 2008 - 14:41:05 CST)
      • Re: AMBER: distance restraint between non-bonded molecules Ilyas Yildirim (Thu Dec 18 2008 - 15:29:26 CST)
      • Re: AMBER: distance restraint between non-bonded molecules Taufik Al-Sarraj (Fri Dec 19 2008 - 09:14:51 CST)
      • Re: AMBER: distance restraint between non-bonded molecules Ilyas Yildirim (Fri Dec 19 2008 - 09:22:32 CST)
      • Re: AMBER: distance restraint between non-bonded molecules Carlos Simmerling (Fri Dec 19 2008 - 09:24:09 CST)
      • Re: AMBER: distance restraint in minimization Taufik Al-Sarraj (Wed Dec 17 2008 - 12:52:01 CST)
      • Re: AMBER: distance restraint in minimization Taufik Al-Sarraj (Wed Dec 17 2008 - 12:15:24 CST)
• AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III ABEL Stephane 175950 (Tue Dec 16 2008 - 05:28:56 CST)
  • Re: AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III FyD (Tue Dec 16 2008 - 06:17:15 CST)
• AMBER: alascan MUTANT_KEEP error Larry Layne (Tue Dec 16 2008 - 13:07:51 CST)
• AMBER: restraintmask - reference file is not working Dirar Homouz (Tue Dec 16 2008 - 18:05:24 CST)
  • Re: AMBER: restraintmask - reference file is not working Carlos Simmerling (Tue Dec 16 2008 - 18:38:14 CST)
    • RE: AMBER: restraintmask - reference file is not working Dirar Homouz (Tue Dec 16 2008 - 18:45:44 CST)
    • RE: AMBER: restraintmask - reference file is not working Dirar Homouz (Tue Dec 16 2008 - 18:51:08 CST)
      • Re: AMBER: restraintmask - reference file is not working Carlos Simmerling (Tue Dec 16 2008 - 19:05:03 CST)
      • RE: AMBER: restraintmask - reference file is not working Dirar Homouz (Wed Dec 17 2008 - 03:41:00 CST)
      • Re: AMBER: restraintmask - reference file is not working Carlos Simmerling (Wed Dec 17 2008 - 07:19:25 CST)
      • RE: AMBER: restraintmask - reference file is not working Dirar Homouz (Wed Dec 17 2008 - 13:40:48 CST)
      • Re: AMBER: restraintmask - reference file is not working Carlos Simmerling (Wed Dec 17 2008 - 13:51:35 CST)
      • Re: AMBER: restraintmask - reference file is not working Carlos Simmerling (Thu Dec 18 2008 - 06:14:27 CST)
      • RE: AMBER: restraintmask - reference file is not working Dirar Homouz (Thu Dec 18 2008 - 17:46:23 CST)
• AMBER: unsubscribe amber Prem Prakash Pathak (Tue Dec 16 2008 - 21:09:54 CST)
• AMBER: AMBER minimization problems Lili Peng (Wed Dec 17 2008 - 01:14:00 CST)
  • RE: AMBER: AMBER minimization problems Ross Walker (Wed Dec 17 2008 - 10:18:06 CST)
    • Re: AMBER: AMBER minimization problems Lili Peng (Wed Dec 17 2008 - 10:35:58 CST)
      • RE: AMBER: AMBER minimization problems Ross Walker (Thu Dec 18 2008 - 11:46:45 CST)
      • Re: AMBER: AMBER minimization problems Lili Peng (Sat Dec 20 2008 - 17:53:54 CST)
      • Re: AMBER: AMBER minimization problems Robert Duke (Sat Dec 20 2008 - 18:10:03 CST)
• AMBER: from dihe parameters to torsional energy Jeffrey (Wed Dec 17 2008 - 03:15:17 CST)
  • RE: AMBER: from dihe parameters to torsional energy Ross Walker (Wed Dec 17 2008 - 10:36:14 CST)
    • RE: AMBER: from dihe parameters to torsional energy Ilyas Yildirim (Wed Dec 17 2008 - 11:10:13 CST)
      • RE: AMBER: from dihe parameters to torsional energy Ross Walker (Wed Dec 17 2008 - 11:28:21 CST)
      • Re: RE: AMBER: from dihe parameters to torsional energy Jeffrey (Wed Dec 17 2008 - 20:18:29 CST)
• AMBER: alascan error Larry Layne (Wed Dec 17 2008 - 14:19:22 CST)
• AMBER: Hydroxide ion in POL3 water D.J. Cole (Thu Dec 18 2008 - 06:13:58 CST)
• AMBER: Solvatebox problem musa özboyacý (Fri Dec 19 2008 - 04:24:56 CST)
  • Re: AMBER: Solvatebox problem David A. Case (Fri Dec 19 2008 - 07:19:18 CST)
• Re: AMBER: distance restraint between non-bonded molecules] Ilyas Yildirim (Fri Dec 19 2008 - 17:06:35 CST)
  • Re: AMBER: distance restraint between non-bonded molecules] Taufik Al-Sarraj (Sat Dec 20 2008 - 12:44:43 CST)
    • AMBER: xleap (measureGeom) Taufik Al-Sarraj (Sat Dec 20 2008 - 15:02:56 CST)
      • Re: AMBER: xleap (measureGeom) Scott Brozell (Mon Dec 22 2008 - 16:10:46 CST)
    • Re: AMBER: distance restraint between non-bonded molecules] Ilyas Yildirim (Sun Dec 21 2008 - 21:08:38 CST)
      • AMBER: Re: Taufik Al-Sarraj (Mon Dec 22 2008 - 12:08:17 CST)
• AMBER: idecomp=2 & RRES/LRES group specification In Hee Park (Fri Dec 19 2008 - 19:19:43 CST)
• AMBER: amber 9 compilation error with mvapich and intel compilers Amit Bajaj (Sat Dec 20 2008 - 08:17:03 CST)
  • Re: AMBER: amber 9 compilation error with mvapich and intel compilers David A. Case (Sat Dec 20 2008 - 16:42:28 CST)
    • Re: AMBER: amber 9 compilation error with mvapich and intel compilers Amit Bajaj (Sun Dec 21 2008 - 23:41:35 CST)
      • Re: AMBER: amber 9 compilation error with mvapich and intel compilers David A. Case (Mon Dec 22 2008 - 07:35:28 CST)
      • Re: AMBER: amber 9 compilation error with mvapich and intelcompilers Robert Duke (Mon Dec 22 2008 - 08:36:33 CST)
      • Re: AMBER: amber 9 compilation error with mvapich and intel compilers amit (Mon Dec 22 2008 - 11:12:41 CST)
      • RE: AMBER: amber 9 compilation error with mvapich and intel compilers Ross Walker (Mon Dec 22 2008 - 11:46:58 CST)
      • AMBER: Materials and methods Taufik Al-Sarraj (Mon Dec 22 2008 - 12:05:22 CST)
      • RE: AMBER: amber 9 compilation error with mvapich and intel compilers amit (Mon Dec 22 2008 - 12:15:34 CST)
• AMBER: Error: tutorial one for md simulation of DNA Catein Catherine (Sun Dec 21 2008 - 21:33:41 CST)
  • RE: AMBER: Error: tutorial one for md simulation of DNA balaji nagarajan (Sun Dec 21 2008 - 22:06:55 CST)
    • RE: AMBER: Error: tutorial one for md simulation of DNA Catein Catherine (Sun Dec 21 2008 - 23:12:32 CST)
• AMBER: balaji nagarajan (Mon Dec 22 2008 - 07:36:38 CST)
  • RE: AMBER: Ross Walker (Mon Dec 22 2008 - 10:41:23 CST)
• AMBER: Playstation 3 Benchmarks Andrew Ring (Mon Dec 22 2008 - 18:40:44 CST)
  • Re: AMBER: Playstation 3 Benchmarks David Watson (Mon Dec 22 2008 - 19:17:57 CST)
  • RE: AMBER: Playstation 3 Benchmarks Ross Walker (Mon Dec 22 2008 - 19:20:38 CST)
• AMBER: installation amber9 in fedora9 Vijay Manickam Achari (Mon Dec 22 2008 - 22:44:12 CST)
  • Re: AMBER: installation amber9 in fedora9 Scott Brozell (Mon Dec 22 2008 - 23:41:22 CST)
  • Re: AMBER: installation amber9 in fedora9 sobereva (Tue Dec 23 2008 - 03:52:00 CST)
• AMBER: AMBER10 AMBERTools antechamber Starr Hazard (Tue Dec 23 2008 - 10:36:05 CST)
  • Re: AMBER: AMBER10 AMBERTools antechamber M. L. Dodson (Tue Dec 23 2008 - 10:45:46 CST)
  • RE: AMBER: AMBER10 AMBERTools antechamber Ross Walker (Tue Dec 23 2008 - 11:09:54 CST)
    • Re: AMBER: AMBER10 AMBERTools antechamber David A. Case (Tue Dec 23 2008 - 13:45:06 CST)
      • Re: AMBER: AMBER10 AMBERTools antechamber M. L. Dodson (Tue Dec 23 2008 - 14:00:13 CST)
• AMBER: Switching function in NAMD musa özboyacý (Tue Dec 23 2008 - 13:52:37 CST)
  • Re: AMBER: Switching function in NAMD Adrian Roitberg (Tue Dec 23 2008 - 13:56:58 CST)
• AMBER: about mmpbsa out data ecustipp (Tue Dec 23 2008 - 20:21:22 CST)
  • Re: AMBER: about mmpbsa out data steinbrt_at_rci.rutgers.edu (Tue Dec 23 2008 - 22:53:02 CST)
    • Re:Re: AMBER: about mmpbsa out data ecustipp (Wed Dec 24 2008 - 03:11:50 CST)
• AMBER: installation amber9 in fedora9 using bash shell Vijay Manickam Achari (Tue Dec 23 2008 - 22:05:28 CST)
  • Re: AMBER: installation amber9 in fedora9 using bash shell David A. Case (Wed Dec 24 2008 - 13:07:35 CST)
• AMBER: How to build a cubic box of a newly synthesized compound? Jeffrey (Wed Dec 24 2008 - 00:34:13 CST)
  • Re: AMBER: How to build a cubic box of a newly synthesized compound? M. L. Dodson (Wed Dec 24 2008 - 11:45:23 CST)
• AMBER: xleap error Vijay Manickam Achari (Wed Dec 24 2008 - 03:58:17 CST)
  • Re: AMBER: xleap error David A. Case (Wed Dec 24 2008 - 13:02:11 CST)
• AMBER: Beale, John (Wed Dec 24 2008 - 07:19:48 CST)
• AMBER: mpirun Permission denied. drugdesign (Thu Dec 25 2008 - 00:49:31 CST)
  • Re: AMBER: mpirun Permission denied. Jackie. J. Shen (Tue Dec 30 2008 - 20:32:17 CST)
    • Re: AMBER: mpirun Permission denied. David Watson (Tue Dec 30 2008 - 23:04:40 CST)
• AMBER: a question about ff03ua oguz gurbulak (Thu Dec 25 2008 - 08:06:33 CST)
  • Re: AMBER: a question about ff03ua David A. Case (Thu Dec 25 2008 - 15:01:56 CST)
• AMBER: definition of dihedral in amber Jeffrey (Thu Dec 25 2008 - 09:38:38 CST)
• AMBER: vertex atom mismatch ecustipp (Fri Dec 26 2008 - 04:09:45 CST)
• AMBER: (no subject) Rajendra P. OJHA (Fri Dec 26 2008 - 06:35:12 CST)
  • Re: AMBER: (no subject) ecustipp_at_163.com (Mon Dec 29 2008 - 01:58:20 CST)
• AMBER: SMD-related questions Alessandro Nascimento (Mon Dec 29 2008 - 07:07:05 CST)
  • Re: AMBER: SMD-related questions M. L. Dodson (Mon Dec 29 2008 - 12:25:19 CST)
  • Re: AMBER: SMD-related questions Jackie. J. Shen (Tue Dec 30 2008 - 20:27:16 CST)
• AMBER: mwcovar limit? Carra, Claudio (JSC-SK)[USRA] (Mon Dec 29 2008 - 16:31:27 CST)
  • RE: AMBER: mwcovar limit? Ross Walker (Wed Dec 31 2008 - 22:44:33 CST)
• AMBER: FAD RESP charges and parameters Cenk \(Jenk\) Andac (Mon Dec 29 2008 - 16:51:49 CST)
  • Re: AMBER: FAD RESP charges and parameters FyD (Tue Dec 30 2008 - 02:45:01 CST)
    • Re: AMBER: FAD RESP charges and parameters Cenk \(Jenk\) Andac (Tue Dec 30 2008 - 06:28:41 CST)
      • Re: AMBER: FAD RESP charges and parameters FyD (Tue Dec 30 2008 - 08:19:15 CST)
      • Re: AMBER: FAD RESP charges and parameters Cenk \(Jenk\) Andac (Tue Dec 30 2008 - 10:03:17 CST)
• AMBER: mdout file details aneesh cna (Tue Dec 30 2008 - 00:20:40 CST)
  • Re: AMBER: mdout file details David A. Case (Wed Dec 31 2008 - 10:50:05 CST)
• AMBER: periodic boundary Sally Pias (Wed Dec 31 2008 - 02:37:25 CST)
• AMBER: RMS plot Beale, John (Wed Dec 31 2008 - 13:11:39 CST)

Last message date: Wed Dec 31 2008 - 22:47:27 CST
Archived on: Thu Jan 08 2009 - 16:01:50 CST