AMBER Archive (2006) - Nov 2006 By Author

Starting: Wed Nov 01 2006 - 02:38:55 CST
Ending: Thu Nov 30 2006 - 19:28:10 CST

• a a
  • Re: AMBER: How to apply a force to some atom in a residues? (Thu Nov 30 2006 - 00:45:04 CST)
  • AMBER: DNA helix end stable? (Tue Nov 28 2006 - 21:35:11 CST)
  • AMBER: How to apply a force to some atom in a residues? (Tue Nov 28 2006 - 21:36:15 CST)
  • Re: AMBER: nmode output with ptraj (Tue Nov 28 2006 - 21:18:32 CST)
  • Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences? (Mon Nov 27 2006 - 04:29:42 CST)
  • AMBER: Did Antechamber support tertiary amines? How can I get the prepin file for it? (Mon Nov 27 2006 - 02:50:12 CST)
  • Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences? (Fri Nov 24 2006 - 20:27:26 CST)
  • Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnected sequences? (Fri Nov 24 2006 - 03:29:26 CST)
  • AMBER: NTR for implicit solvent? How to defin restrain for two disconnected sequences? (Fri Nov 24 2006 - 00:13:38 CST)
  • AMBER: saltconc for explicit solvent calculation. (Thu Nov 09 2006 - 11:51:36 CST)
• Adrian Roitberg
  • Re: AMBER: Unit of force (Wed Nov 08 2006 - 06:57:00 CST)
  • Re: AMBER: PTRAJ RMS: dumping RMSd vs time data (Sat Nov 04 2006 - 07:00:40 CST)
  • Re: AMBER: ab initio terminology query (Wed Nov 01 2006 - 13:01:38 CST)
  • Re: AMBER: GBSA implicit chloroform (Wed Nov 01 2006 - 11:22:14 CST)
• Andreas Svrcek-Seiler
  • Re: AMBER: Langevin temperature control vs berendson heat bath (Thu Nov 30 2006 - 06:06:22 CST)
  • Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? (Mon Nov 06 2006 - 11:13:37 CST)
  • Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? (Mon Nov 06 2006 - 03:17:11 CST)
• Andres Palencia
  • Re: AMBER: Ptraj: radial distribution and correlation coefficient (Tue Nov 14 2006 - 14:13:39 CST)
  • AMBER: Amber H-bond print? (Thu Nov 09 2006 - 03:07:46 CST)
• Andy Purkiss-Trew
  • Re: RE: AMBER: Radius of gyration (Fri Nov 24 2006 - 13:38:28 CST)
  • RE: AMBER: Radius of gyration (Fri Nov 24 2006 - 13:34:52 CST)
  • RE: AMBER: Radius of gyration (Fri Nov 24 2006 - 06:58:53 CST)
• Angelo
  • AMBER: Biomolecular Simulation 2007 (Thu Nov 09 2006 - 10:03:43 CST)
  • Re: AMBER: PCA results with explicit Vs Implicit solvation (Mon Nov 06 2006 - 11:14:47 CST)
  • Re: AMBER: leap usage (Thu Nov 02 2006 - 10:39:57 CST)
• anna.schrey_at_gmx.de
  • AMBER: Confusion about PBC (Wed Nov 29 2006 - 10:26:04 CST)
• Austin B. Yongye
  • AMBER: Ptraj: diffusion rate (Tue Nov 21 2006 - 15:03:52 CST)
  • AMBER: Ptraj: correlation time (Tue Nov 21 2006 - 15:05:52 CST)
  • Re: AMBER: GLYCAM and ff98 atom-types] (Thu Nov 16 2006 - 13:53:03 CST)
  • Re: AMBER: Ptraj: radial distribution and correlation coefficient (Tue Nov 14 2006 - 13:02:27 CST)
  • Re: AMBER: Ptraj: radial distribution and correlation coefficient (Tue Nov 14 2006 - 12:50:01 CST)
  • AMBER: Ptraj: radial distribution and correlation coefficient (Tue Nov 14 2006 - 12:10:39 CST)
• AYTUG TUNCEL
  • AMBER: error about the number of snapshots (Tue Nov 07 2006 - 15:11:24 CST)
• Bill Ross
  • RE: AMBER: Combining Residues in LEaP for Lipid Bilayers (Mon Nov 20 2006 - 12:58:11 CST)
  • Re: AMBER: problems with saving self-built molecules parameters (Mon Nov 20 2006 - 12:55:00 CST)
  • Re: AMBER: erroneous placement of TER card (Thu Nov 16 2006 - 13:06:25 CST)
  • Re: AMBER: erroneous placement of TER card (Thu Nov 16 2006 - 12:54:50 CST)
  • Re: AMBER: Restraints of the strand-endings? (Tue Nov 14 2006 - 16:19:06 CST)
  • Re: AMBER: PTRAJ: radius of gyration (Fri Nov 10 2006 - 13:04:06 CST)
• Biswa Ranjan Meher
  • AMBER: klambda for TI method. (Tue Nov 07 2006 - 06:59:15 CST)
• Carles Jaime Cardiel
  • Re: RE: AMBER: Radius of gyration (Fri Nov 24 2006 - 12:25:02 CST)
• Carlos Simmerling
  • Re: AMBER: Langevin temperature control vs berendson heat bath (Thu Nov 30 2006 - 06:23:24 CST)
  • Re: AMBER: How to apply a force to some atom in a residues? (Thu Nov 30 2006 - 06:13:42 CST)
  • Re: AMBER: Langevin temperature control vs berendson heat bath (Wed Nov 29 2006 - 13:02:20 CST)
  • Re: AMBER: How to apply a force to some atom in a residues? (Wed Nov 29 2006 - 06:26:19 CST)
  • Re: AMBER: DNA helix end stable? (Wed Nov 29 2006 - 06:24:14 CST)
  • Re: AMBER: ambpdb -pqr (Tue Nov 28 2006 - 15:03:18 CST)
  • Re: AMBER: How to specify user defined force fields or its parameters in amber?? (Tue Nov 28 2006 - 08:07:18 CST)
  • Re: AMBER: How to specify user defined force fields or its parameters in amber?? (Tue Nov 28 2006 - 06:11:51 CST)
  • Re: AMBER: helices in GB simulations (Mon Nov 27 2006 - 12:12:02 CST)
  • Re: AMBER: problem of the REMD with nmr constraints (Fri Nov 24 2006 - 08:35:25 CST)
  • Re: AMBER: Snapshots (pdbs) from a trajectory. (Thu Nov 23 2006 - 11:25:31 CST)
  • Re: Fwd: AMBER: sander error: rst file crash (Sat Nov 11 2006 - 06:38:52 CST)
  • Re: AMBER: vlimit exceeded for step 0, vmax = infinity (Fri Nov 10 2006 - 08:58:26 CST)
  • Re: AMBER: sander error: rst file crash (Fri Nov 10 2006 - 07:26:16 CST)
  • Re: AMBER: saltconc for explicit solvent calculation. (Thu Nov 09 2006 - 12:14:21 CST)
  • Re: AMBER: vlimit exceeded for step 0, vmax = infinity (Wed Nov 08 2006 - 12:35:21 CST)
  • Re: AMBER: simulating a small chain protein in water box (Wed Nov 08 2006 - 11:50:59 CST)
  • Re: AMBER: vlimit exceeded for step 0, vmax = infinity (Wed Nov 08 2006 - 11:46:27 CST)
  • Re: AMBER: question about the topology file (Wed Nov 08 2006 - 06:18:58 CST)
  • Re: AMBER: Potential Energy Calculation (Mon Nov 06 2006 - 06:32:35 CST)
  • Re: AMBER: Zn metal library (Mon Nov 06 2006 - 06:26:52 CST)
  • Re: AMBER: Simulation a small chain of amino acids - error in MD simulation (Fri Nov 03 2006 - 12:05:22 CST)
  • Re: AMBER: ntt=1 in simulated annealing (Fri Nov 03 2006 - 05:48:06 CST)
  • Re: AMBER: Can we use the distance restraint in Replica-exchange simulation with AMBER8 (Thu Nov 02 2006 - 14:28:33 CST)
• Cenk Andac
  • Re: AMBER: NAD ?? (Mon Nov 13 2006 - 08:46:47 CST)
  • Re: AMBER: NAD ?? (Fri Nov 10 2006 - 17:20:53 CST)
  • Re: AMBER: NAD ?? (Fri Nov 10 2006 - 17:27:35 CST)
  • Re: AMBER: NAD ?? (Wed Nov 08 2006 - 09:55:38 CST)
  • Re: AMBER: problem with NAD+ parameters (Mon Nov 06 2006 - 16:05:52 CST)
• Changge Ji
  • AMBER: Charge fitting in Amber (Tue Nov 28 2006 - 10:50:20 CST)
  • AMBER: how can i treat with long "mask" in ptraj analysis. (Sun Nov 26 2006 - 10:22:00 CST)
• Chengwen Chen
  • AMBER: How to run QM/MM simulation of DNA duplex bound with platinum moietes (Thu Nov 30 2006 - 02:07:28 CST)
  • AMBER: How to run MD simulation of a silicon containing complex with AMBER9? (Thu Nov 30 2006 - 01:06:54 CST)
  • AMBER: parameters for silicon atom (Mon Nov 20 2006 - 01:45:07 CST)
  • AMBER: what to do with the counter ions when minimizing average structure of DNA? (Tue Nov 14 2006 - 05:09:25 CST)
• Chris Moth
  • top2mol2.c scanf format string bug (Mon Nov 06 2006 - 18:19:36 CST)
• Christian Roth
  • RE: AMBER: error in tleap test (Wed Nov 15 2006 - 12:18:07 CST)
  • AMBER: error in tleap test (Tue Nov 14 2006 - 18:40:24 CST)
• Christopher Gaughan
  • Re: AMBER: Problem with mask when using distance in ptraj (Sun Nov 26 2006 - 08:28:29 CST)
  • AMBER: Problem with mask when using distance in ptraj (Wed Nov 22 2006 - 13:36:23 CST)
• cristian obiol
  • Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences? (Fri Nov 24 2006 - 04:24:28 CST)
• darden
  • Re: AMBER: too big EEL values in the minimisation output (Thu Nov 02 2006 - 13:13:29 CST)
  • Re: AMBER: too big EEL values in the minimisation output (Wed Nov 01 2006 - 12:08:27 CST)
• Dave S Walker
  • Re: AMBER: NONB values adjusted? (Tue Nov 28 2006 - 13:48:36 CST)
  • AMBER: NONB values adjusted? (Tue Nov 28 2006 - 01:37:28 CST)
• Dave, Sonya
  • AMBER: simulating a small chain protein in water box (Wed Nov 08 2006 - 10:03:46 CST)
  • RE: AMBER: Simulation a small chain of amino acids - error in MD simulation (Fri Nov 03 2006 - 13:20:55 CST)
  • AMBER: Simulation a small chain of amino acids - error in MD simulation (Fri Nov 03 2006 - 11:54:06 CST)
• David A. Case
  • Re: AMBER: amber9 parralel compiling (Thu Nov 30 2006 - 17:54:08 CST)
  • Re: AMBER: How to recompile sander for single-processor use in AMBER 8? (Thu Nov 30 2006 - 17:19:10 CST)
  • Re: AMBER: amber9 parralel compiling (Thu Nov 30 2006 - 10:50:47 CST)
  • Re: AMBER: nmode output with ptraj (Tue Nov 28 2006 - 20:36:33 CST)
  • Re: AMBER: Periodic simulations with net charge (Tue Nov 28 2006 - 20:03:22 CST)
  • Re: AMBER: xleap (Tue Nov 28 2006 - 10:02:13 CST)
  • Re: AMBER: (Tue Nov 28 2006 - 09:53:48 CST)
  • Re: AMBER: minimization of Hydrogens with xLeaP (Mon Nov 27 2006 - 20:19:48 CST)
  • Re: AMBER: Problem Installing Amber in SGI Irix 6.5 (Mon Nov 27 2006 - 19:56:14 CST)
  • Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences? (Sat Nov 25 2006 - 02:51:06 CST)
  • Re: AMBER: amber9 serial compile with pathscale on SuSe10.1/AMD64 (Fri Nov 24 2006 - 18:43:20 CST)
  • Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnected sequences? (Fri Nov 24 2006 - 01:02:21 CST)
  • Re: AMBER: Snapshots (pdbs) from a trajectory. (Thu Nov 23 2006 - 21:58:34 CST)
  • Re: AMBER: SHAKE problem after minimization (Wed Nov 22 2006 - 16:24:44 CST)
  • Re: AMBER: Ptraj syntax change Amber8->Amber9 ? (Wed Nov 22 2006 - 15:22:37 CST)
  • Re: AMBER: Problem with mask when using distance in ptraj (Wed Nov 22 2006 - 15:07:29 CST)
  • AMBER: Re: installation instructions (Wed Nov 22 2006 - 10:48:17 CST)
  • Re: AMBER: Combining Residues in LEaP for Lipid Bilayers (Tue Nov 21 2006 - 10:16:06 CST)
  • Re: AMBER: the energy and temperature both increasing during the simulation with NTT=0 (Tue Nov 21 2006 - 00:09:28 CST)
  • Re: AMBER: problems with saving self-built molecules parameters (Mon Nov 20 2006 - 11:33:25 CST)
  • Re: AMBER: Combining Residues in LEaP for Lipid Bilayers (Mon Nov 20 2006 - 11:35:04 CST)
  • Re: AMBER: erroneous placement of TER card (Thu Nov 16 2006 - 12:59:28 CST)
  • Re: AMBER: Xleap woes (Thu Nov 16 2006 - 12:39:39 CST)
  • Re: AMBER: pqr file (Thu Nov 16 2006 - 10:53:46 CST)
  • Re: AMBER: erroneous placement of TER card (Thu Nov 16 2006 - 10:20:32 CST)
  • Re: AMBER: Error in compliling LEAP on Fedora 5 (Wed Nov 15 2006 - 19:24:34 CST)
  • Re: AMBER: ntt=1 in simulated annealing (Wed Nov 15 2006 - 10:46:58 CST)
  • Re: AMBER: how to remove the rotation of system in periodic condition? (Wed Nov 15 2006 - 10:34:01 CST)
  • Re: Fwd: AMBER: sander error: rst file crash (Sun Nov 12 2006 - 20:44:48 CST)
  • Re: AMBER: sander error: rst file crash (Fri Nov 10 2006 - 15:11:15 CST)
  • Re: AMBER: vlimit exceeded for step 0, vmax = infinity (Fri Nov 10 2006 - 10:34:45 CST)
  • Re: AMBER: saltconc for explicit solvent calculation. (Thu Nov 09 2006 - 12:13:05 CST)
  • Re: AMBER: (Thu Nov 09 2006 - 12:11:55 CST)
  • Re: AMBER: problem in calculating EGB using sander for ligand containing F atom (Thu Nov 09 2006 - 10:14:06 CST)
  • Re: AMBER: vlimit exceeded for step 0, vmax = infinity (Wed Nov 08 2006 - 15:35:10 CST)
  • Re: AMBER: vlimit exceeded for step 0, vmax = infinity (Wed Nov 08 2006 - 10:48:01 CST)
  • Re: AMBER: Flag for removal of translational and rotational center-of-mass (COM) motion (Wed Nov 08 2006 - 10:35:24 CST)
  • Re: AMBER: NAD ?? (Wed Nov 08 2006 - 08:49:31 CST)
  • Re: AMBER: leap - compilation error (Tue Nov 07 2006 - 20:25:37 CST)
  • Re: AMBER: Format of the prmtop file (NUMBER_EXCLUDED_ATOMS) & (EXCLUDED_ATOMS_LIST) (Tue Nov 07 2006 - 19:51:48 CST)
  • Re: AMBER: top2mol2.c scanf format string bug (Tue Nov 07 2006 - 10:18:43 CST)
  • Re: AMBER: klambda for TI method. (Tue Nov 07 2006 - 10:06:21 CST)
  • Re: AMBER: PTRAJ RMS: dumping RMSd vs time data (Tue Nov 07 2006 - 01:26:13 CST)
  • Re: AMBER: How the ensemble average calculated in Gibbs, AMBER7? (Sun Nov 05 2006 - 21:26:02 CST)
  • Re: AMBER: ab initio terminology query (Wed Nov 01 2006 - 14:42:23 CST)
  • Re: AMBER: ab initio terminology query (Wed Nov 01 2006 - 11:30:50 CST)
  • Re: AMBER: GBSA implicit chloroform (Wed Nov 01 2006 - 10:56:07 CST)
  • Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft (Wed Nov 01 2006 - 10:54:06 CST)
• Ed Pate
  • AMBER: pmemd installation problem (Fri Nov 03 2006 - 12:51:36 CST)
• Einar Uggerud
  • AMBER: protonated phosphate (Tue Nov 28 2006 - 01:11:46 CST)
• Elijah Gregory
  • Re: RE: AMBER: Radius of gyration (Fri Nov 24 2006 - 14:33:50 CST)
• emilia wu
  • AMBER: optimatized structure is so much different from the original pdb structure (Thu Nov 16 2006 - 23:38:18 CST)
• Esther Brugger
  • AMBER: H-bond analysis (Ptraj) (Thu Nov 30 2006 - 19:28:10 CST)
  • Re: AMBER: watershell and image commands (Thu Nov 30 2006 - 18:04:04 CST)
  • AMBER: watershell command (Thu Nov 30 2006 - 17:16:52 CST)
  • AMBER: watershell and image commands (Thu Nov 30 2006 - 16:37:58 CST)
  • AMBER: ptraj----radial output files (Wed Nov 29 2006 - 14:03:20 CST)
  • RE: AMBER: NEWPDB.PDB from antechamber (Wed Nov 01 2006 - 13:10:20 CST)
  • AMBER: NEWPDB.PDB from antechamber (Wed Nov 01 2006 - 10:59:29 CST)
• Fenghui Fan
  • Re: AMBER: RE: Amber: ZN-complex file (Tue Nov 28 2006 - 17:47:19 CST)
  • Re: AMBER: prepin file nan (Tue Nov 28 2006 - 08:48:33 CST)
  • AMBER: prepin file nan (Mon Nov 27 2006 - 21:28:16 CST)
  • AMBER: bond information (Sun Nov 26 2006 - 22:10:42 CST)
  • Re: AMBER: respin file (Sun Nov 26 2006 - 18:42:09 CST)
  • AMBER: ZN prepin (Sun Nov 26 2006 - 16:29:31 CST)
  • Re: AMBER: respin file (Sun Nov 26 2006 - 11:12:01 CST)
  • AMBER: how to get complete prepin file (Sat Nov 25 2006 - 23:02:20 CST)
  • Re: AMBER: respin file (Sat Nov 25 2006 - 21:15:53 CST)
  • Re: AMBER: respin file (Sat Nov 25 2006 - 19:49:58 CST)
  • AMBER: respin file (Sat Nov 25 2006 - 16:23:46 CST)
  • AMBER: resp (Sat Nov 25 2006 - 15:03:00 CST)
  • AMBER: respin file (Sat Nov 25 2006 - 01:06:49 CST)
  • AMBER: bondtype problem (Fri Nov 24 2006 - 18:22:23 CST)
  • AMBER: Antechamber and gaussian questions (Fri Nov 24 2006 - 16:04:40 CST)
  • Re: AMBER: ammonia parameters (Thu Nov 23 2006 - 09:40:05 CST)
  • Re: AMBER: problems with saving self-built molecules parameters (Mon Nov 20 2006 - 12:10:21 CST)
  • Re: AMBER: problems with saving self-built molecules parameters (Mon Nov 20 2006 - 09:06:53 CST)
  • Re: AMBER: problems with saving self-built molecules parameters (Mon Nov 20 2006 - 07:57:10 CST)
  • Re: AMBER: GLYCAM and ff98 atom-types (Thu Nov 16 2006 - 13:16:34 CST)
  • Re: AMBER: Xleap woes (Thu Nov 16 2006 - 13:22:59 CST)
  • Re: AMBER: gfortran/gcc versus ifort/icc (Tue Nov 14 2006 - 11:40:13 CST)
  • AMBER: The plc.frcmod file in the old version tutorial (Sun Nov 12 2006 - 20:50:29 CST)
  • AMBER: ZN-CYS prepin and frcmd file (Sun Nov 12 2006 - 20:16:37 CST)
  • AMBER: bond command between Zn and a CYM residue in one chain of a protein complex (Fri Nov 10 2006 - 23:25:01 CST)
  • Re: AMBER: antechamber:tutorial (Thu Nov 09 2006 - 13:10:17 CST)
  • Re: AMBER: Building Library (Thu Nov 09 2006 - 12:21:57 CST)
  • Re: AMBER: building a box (Tue Nov 07 2006 - 11:49:54 CST)
  • AMBER: Zn metal library (Sun Nov 05 2006 - 21:51:19 CST)
  • Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? (Sun Nov 05 2006 - 18:22:26 CST)
  • Re: AMBER: Combine amber-force field and gaff94 for one molecule? (Sun Nov 05 2006 - 14:13:57 CST)
  • Re: AMBER: Combine amber-force field and gaff94 for one molecule? (Sun Nov 05 2006 - 12:30:27 CST)
  • AMBER: trajout script (Sun Nov 05 2006 - 10:23:57 CST)
  • RE: AMBER: Amber: disufide bond (Sun Nov 05 2006 - 08:02:48 CST)
  • Re: AMBER: PTRAJ RMS: dumping RMSd vs time data (Sun Nov 05 2006 - 00:31:25 CST)
  • AMBER: Amber: disufide bond (Sat Nov 04 2006 - 22:29:57 CST)
• FyD
  • Re: AMBER: Charge fitting in Amber (Wed Nov 29 2006 - 01:16:38 CST)
  • Re: AMBER: RE: Amber: ZN-complex file (Wed Nov 29 2006 - 01:21:19 CST)
  • Re: AMBER: Ethanol (Wed Nov 22 2006 - 06:22:28 CST)
  • Re: AMBER: Ethanol (Fri Nov 17 2006 - 08:19:15 CST)
• Gabbar S. Daaku
  • Re: AMBER: optimatized structure is so much different from the original pdb structure (Fri Nov 17 2006 - 11:13:04 CST)
  • AMBER: GLYCAM and ff98 atom-types (Thu Nov 16 2006 - 12:11:05 CST)
• Gobind Singh Bisht
  • AMBER: How to specify a box with few walls rigid and others with periodic boundary conditions and then apply a pressure gradient across it? (Thu Nov 30 2006 - 01:34:28 CST)
  • Re: AMBER: How to specify user defined force fields or its parameters in amber?? (Tue Nov 28 2006 - 10:40:53 CST)
  • Re: AMBER: How to specify user defined force fields or its parameters in amber?? (Tue Nov 28 2006 - 08:34:36 CST)
  • Re: AMBER: How to specify user defined force fields or its parameters in amber?? (Tue Nov 28 2006 - 07:56:10 CST)
  • AMBER: How to specify user defined force fields or its parameters in amber?? (Tue Nov 28 2006 - 05:51:30 CST)
• Gregory Sandala
  • AMBER: erroneous placement of TER card (Thu Nov 16 2006 - 03:12:43 CST)
• Gustavo Seabra
  • Re: AMBER: How to specify user defined force fields or its parameters in amber?? (Thu Nov 30 2006 - 09:46:42 CST)
  • Re: AMBER: How to run QM/MM simulation of DNA duplex bound with platinum moietes (Thu Nov 30 2006 - 09:20:00 CST)
  • Re: AMBER: How to specify user defined force fields or its parameters in amber?? (Tue Nov 28 2006 - 09:18:49 CST)
  • Re: AMBER: <kein Betreff> (Mon Nov 13 2006 - 11:52:55 CST)
  • Re: AMBER: ab initio terminology query (Wed Nov 01 2006 - 10:50:27 CST)
• Hannes Loeffler
  • AMBER: ptraj grid (Sun Nov 26 2006 - 22:05:05 CST)
• harianto
  • Re: AMBER: ambpdb -pqr (Tue Nov 28 2006 - 15:03:26 CST)
• hayden
  • RE: AMBER: Amber: disufide bond (Sun Nov 05 2006 - 07:03:23 CST)
• Hayden Eastwood
  • RE: AMBER: Langevin temperature control vs berendson heat bath (Thu Nov 30 2006 - 05:23:37 CST)
  • AMBER: Langevin temperature control vs berendson heat bath (Wed Nov 29 2006 - 12:12:16 CST)
  • RE: AMBER: SHAKE problem after minimization (Wed Nov 22 2006 - 14:47:09 CST)
  • RE: AMBER: SHAKE problem after minimization (Wed Nov 22 2006 - 14:33:17 CST)
  • RE: AMBER: SHAKE problem after minimization (Wed Nov 22 2006 - 13:13:24 CST)
  • RE: AMBER: Potential Energy Calculation (Mon Nov 06 2006 - 06:47:00 CST)
  • RE: AMBER: ab initio terminology query (Wed Nov 01 2006 - 14:12:49 CST)
• hbluo
  • AMBER: Performing Interactive Essential Dynamics in Ptraj (Thu Nov 30 2006 - 18:58:11 CST)
  • AMBER: how to choose the parameter for the production/sampling run after the equilibration run (Fri Nov 03 2006 - 19:57:01 CST)
• HL Eastwood
  • AMBER: ab initio terminology query (Wed Nov 01 2006 - 05:38:24 CST)
• Holly Freedman
  • Re: AMBER: mm_pbsa does not terminate (Wed Nov 01 2006 - 13:34:17 CST)
  • Re: AMBER: mm_pbsa does not terminate (Wed Nov 01 2006 - 11:56:28 CST)
• Igor Schapiro
  • Re: AMBER: dihedral angle equation (Fri Nov 17 2006 - 08:24:29 CST)
  • Re: AMBER: dihedral angle equation (Fri Nov 17 2006 - 08:15:47 CST)
• Ilyas Yildirim
  • Re: AMBER: ambpdb -pqr (Tue Nov 28 2006 - 15:02:39 CST)
  • Re: AMBER: helices in GB simulations (Mon Nov 27 2006 - 16:09:04 CST)
  • Re: AMBER: respin file (Sun Nov 26 2006 - 11:45:20 CST)
  • Re: AMBER: respin file (Sun Nov 26 2006 - 02:03:33 CST)
  • Re: AMBER: respin file (Sat Nov 25 2006 - 20:45:37 CST)
  • Re: AMBER: respin file (Sat Nov 25 2006 - 19:07:04 CST)
  • Re: AMBER: H-Bond Terms in amber force field (Wed Nov 15 2006 - 18:05:13 CST)
  • AMBER: H-Bond Terms in amber force field (Wed Nov 15 2006 - 13:28:06 CST)
  • RE: AMBER: ab initio terminology query (Wed Nov 01 2006 - 14:38:58 CST)
• In Hee Park
  • AMBER: amber9 serial compile with pathscale on SuSe10.1/AMD64 (Fri Nov 24 2006 - 16:50:54 CST)
• Ivelin Georgiev
  • AMBER: Solvation Energies (Wed Nov 29 2006 - 08:31:13 CST)
• J. Zhang
  • Re: Re: AMBER: question about the topology file (Sun Nov 12 2006 - 19:42:20 CST)
  • AMBER: question about the topology file (Wed Nov 08 2006 - 03:24:10 CST)
• Jardas sucuriba
  • AMBER: matrix correl (Tue Nov 21 2006 - 07:05:41 CST)
• Jennie Thomas
  • AMBER: Periodic simulations with net charge (Tue Nov 28 2006 - 18:47:32 CST)
• Jianhui
  • AMBER: ptraj and mdvel question (Wed Nov 15 2006 - 13:07:06 CST)
• Jiri Sponer
  • Re: AMBER: Quantifying pi-pi interactions (Tue Nov 21 2006 - 10:14:32 CST)
  • Re: AMBER: H-Bond Terms in amber force field (Wed Nov 15 2006 - 18:30:48 CST)
  • Re: AMBER: H-Bond Terms in amber force field (Wed Nov 15 2006 - 17:20:18 CST)
  • Re: AMBER: Combine amber-force field and gaff94 for one molecule? (Sun Nov 05 2006 - 16:01:27 CST)
  • Re: AMBER: ab initio terminology query (Wed Nov 01 2006 - 13:43:13 CST)
  • Re: AMBER: ab initio terminology query (Wed Nov 01 2006 - 12:34:57 CST)
  • Re: AMBER: ab initio terminology query (Wed Nov 01 2006 - 12:27:44 CST)
  • Re: AMBER: ab initio terminology query (Wed Nov 01 2006 - 05:59:04 CST)
• jitrayut jitonnom
  • AMBER: Some warning !!! during SANDER ? (Wed Nov 22 2006 - 02:20:36 CST)
  • Re: AMBER: sander error: rst file crash (Sat Nov 11 2006 - 11:22:20 CST)
  • Fwd: AMBER: sander error: rst file crash (Sat Nov 11 2006 - 05:16:37 CST)
  • Fwd: AMBER: sander error: rst file crash (Fri Nov 10 2006 - 09:52:00 CST)
  • AMBER: sander error: rst file crash (Fri Nov 10 2006 - 06:52:19 CST)
• Joe Nolan
  • Re: AMBER: Problem Installing Amber in SGI Irix 6.5 (Wed Nov 29 2006 - 06:40:58 CST)
• jojartb_at_pharm.u-szeged.hu
  • Re: AMBER: reading psf file (Sat Nov 18 2006 - 03:40:37 CST)
  • Re: AMBER: reading psf file (Sat Nov 18 2006 - 02:38:26 CST)
  • AMBER: reading psf file (Fri Nov 17 2006 - 17:24:24 CST)
• Jordi Camps
  • RE: AMBER: gfortran/gcc versus ifort/icc (Thu Nov 16 2006 - 10:22:55 CST)
  • RE: AMBER: gfortran/gcc versus ifort/icc (Wed Nov 15 2006 - 11:50:54 CST)
• Jordi Rodrigo De Losada
  • AMBER: Snapshots (pdbs) from a trajectory. (Thu Nov 23 2006 - 11:11:18 CST)
• Joshua
  • AMBER: strange temperature behavior when changing to constant pressure (Thu Nov 09 2006 - 13:52:33 CST)
• Junmei Wang
  • RE: AMBER: RE: Amber: ZN-complex file (Tue Nov 28 2006 - 17:54:56 CST)
  • AMBER: RE: Amber: ZN-complex file (Tue Nov 28 2006 - 17:21:40 CST)
  • RE: AMBER: bond information (Tue Nov 28 2006 - 16:16:03 CST)
  • RE: AMBER: Problem about dummy atoms when running antechamber (Tue Nov 28 2006 - 15:54:42 CST)
  • RE: AMBER: prepin file nan (Tue Nov 28 2006 - 15:47:03 CST)
  • RE: AMBER: NEWPDB.PDB from antechamber (Wed Nov 01 2006 - 13:42:42 CST)
  • RE: AMBER: NEWPDB.PDB from antechamber (Wed Nov 01 2006 - 11:19:27 CST)
• Kakali Sen
  • Re: AMBER: Unit of force (Wed Nov 08 2006 - 07:12:41 CST)
  • AMBER: Unit of force (Wed Nov 08 2006 - 05:06:16 CST)
  • AMBER: Re: Unit of force (Wed Nov 08 2006 - 00:41:30 CST)
• Keerthi Gottipati
  • AMBER: Amber9 installation error (Fri Nov 17 2006 - 18:12:53 CST)
  • AMBER: PCA results with explicit Vs Implicit solvation (Mon Nov 06 2006 - 10:32:16 CST)
• kepa koldo burusco
  • RE: AMBER: Radius of gyration (Fri Nov 24 2006 - 11:45:55 CST)
  • RE: AMBER: Combining Residues in LEaP for Lipid Bilayers (Fri Nov 24 2006 - 05:38:06 CST)
  • RE: AMBER: Radius of gyration (Fri Nov 24 2006 - 04:27:01 CST)
  • Re: AMBER: ntt=1 in simulated annealing (Wed Nov 15 2006 - 05:53:27 CST)
  • AMBER: PTRAJ: radius of gyration (Fri Nov 10 2006 - 11:05:09 CST)
  • Re: AMBER: building a box (Wed Nov 08 2006 - 06:08:32 CST)
  • AMBER: building a box (Tue Nov 07 2006 - 10:52:28 CST)
• Lachele Foley (Lists)
  • AMBER: phantom sander8 in dmesg (Mon Nov 27 2006 - 15:25:57 CST)
  • Re: AMBER: gfortran/gcc versus ifort/icc (Thu Nov 16 2006 - 14:49:23 CST)
  • Re: AMBER: gfortran/gcc versus ifort/icc (Wed Nov 15 2006 - 09:37:27 CST)
  • AMBER: gfortran/gcc versus ifort/icc (Tue Nov 14 2006 - 08:35:21 CST)
• Lee Kyung-koo
  • [RE]AMBER: RE: I got the error meassage in testcase of QMMM (Tue Nov 07 2006 - 10:59:16 CST)
  • [RE]AMBER: RE: I got the error meassage in testcase of QMMM (Tue Nov 07 2006 - 10:46:25 CST)
  • AMBER: I got the error meassage in testcase of QMMM (Fri Nov 03 2006 - 23:33:44 CST)
  • [RE]RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version (Thu Nov 02 2006 - 02:53:53 CST)
  • [RE]RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version (Wed Nov 01 2006 - 17:25:25 CST)
  • AMBER: Problem of QM/MM calculation with amber 9 parallel version (Wed Nov 01 2006 - 13:50:28 CST)
• linfu
  • Re: AMBER: prepin file nan (Tue Nov 28 2006 - 03:00:30 CST)
• Luis Gracia
  • Re: AMBER: gfortran/gcc versus ifort/icc (Wed Nov 15 2006 - 12:34:36 CST)
• Lwin, ThuZar
  • RE: AMBER: antechamber:tutorial. . (Thu Nov 09 2006 - 14:02:28 CST)
  • AMBER: FW: antechamber:tutorial (Thu Nov 09 2006 - 13:03:46 CST)
  • AMBER: antechamber:tutorial (Thu Nov 09 2006 - 12:48:58 CST)
• M. L. Dodson
  • Re: AMBER: respin file (Sun Nov 26 2006 - 12:05:33 CST)
  • Re: AMBER: respin file (Sat Nov 25 2006 - 08:37:05 CST)
  • AMBER: gfortran and amber9 success on FreeBSD (Sat Nov 18 2006 - 16:02:16 CST)
  • Re: AMBER: Xleap woes (Thu Nov 16 2006 - 14:14:07 CST)
  • Re: AMBER: Combine amber-force field and gaff94 for one molecule? (Sun Nov 05 2006 - 14:47:22 CST)
  • Re: AMBER: Combine amber-force field and gaff94 for one molecule? (Sun Nov 05 2006 - 13:35:34 CST)
• mahdi fathi
  • RE: AMBER: ff03 GLY HAs atom type (Tue Nov 21 2006 - 23:46:22 CST)
• Margaret S. Cheung
  • Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? (Mon Nov 06 2006 - 09:23:29 CST)
  • AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? (Sun Nov 05 2006 - 17:16:34 CST)
• Marie-Pierre Durrieu
  • AMBER: helices in GB simulations (Mon Nov 27 2006 - 11:43:41 CST)
• Mark Williamson
  • Re: AMBER: Amber9 patch bugfix.all issue on SunOS 5.1 (Tue Nov 28 2006 - 15:04:06 CST)
  • Re: AMBER: Unable to find mopac charges in divcon.out (Fri Nov 24 2006 - 07:54:34 CST)
  • Re: AMBER: Unable to find mopac charges in divcon.out (Thu Nov 23 2006 - 16:06:35 CST)
  • Re: AMBER: antechamber:tutorial (Thu Nov 09 2006 - 13:06:24 CST)
  • Re: AMBER: leap usage (Thu Nov 02 2006 - 09:26:42 CST)
• Markus Kaukonen
  • AMBER: Ptraj syntax change Amber8->Amber9 ? (Wed Nov 22 2006 - 04:35:26 CST)
• Markus Weingarth
  • AMBER: Problems with equilibrating the starting density (Fri Nov 03 2006 - 11:32:20 CST)
• Martin Peters
  • Re: AMBER: compile amber8 on IBM-sp4 (Thu Nov 23 2006 - 11:22:06 CST)
• Matthew Tessier
  • RE: AMBER: Combining Residues in LEaP for Lipid Bilayers (Mon Nov 20 2006 - 11:48:32 CST)
  • AMBER: Combining Residues in LEaP for Lipid Bilayers (Mon Nov 20 2006 - 11:09:13 CST)
• Michael John Hanby
  • RE: AMBER: Amber9 patch bugfix.all issue on SunOS 5.1 (Tue Nov 28 2006 - 15:43:06 CST)
  • RE: AMBER: Amber9 patch bugfix.all issue on SunOS 5.1 (Tue Nov 28 2006 - 14:59:48 CST)
  • AMBER: Amber9 patch bugfix.all issue on SunOS 5.1 (Tue Nov 28 2006 - 12:06:16 CST)
• Michel Becker
  • AMBER: Restraints of the strand-endings? (Tue Nov 14 2006 - 14:22:36 CST)
  • AMBER: <kein Betreff> (Mon Nov 13 2006 - 05:21:58 CST)
  • AMBER: Combine amber-force field and gaff94 for one molecule? (Sun Nov 05 2006 - 11:45:05 CST)
• Miguel Ferreira
  • AMBER: PCA and projections (Wed Nov 01 2006 - 08:11:57 CST)
• Mingfeng Yang
  • Re: AMBER: Potential Energy Calculation (Mon Nov 06 2006 - 15:06:18 CST)
• Minwoo Han
  • AMBER: Problem about dummy atoms when running antechamber (Mon Nov 27 2006 - 03:29:29 CST)
• nadiav_at_soton.ac.uk
  • AMBER: nmode output with ptraj (Tue Nov 28 2006 - 09:59:02 CST)
  • Re: AMBER: GBSA implicit chloroform (Wed Nov 01 2006 - 11:13:22 CST)
  • AMBER: GBSA implicit chloroform (Wed Nov 01 2006 - 10:41:18 CST)
• Nicolas Lux Fawzi
  • Re: AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines (Fri Nov 24 2006 - 13:16:01 CST)
• Nikola Trbovic
  • Re: AMBER: amber9 parralel compiling (Thu Nov 30 2006 - 11:06:12 CST)
  • AMBER: amber9 parralel compiling (Thu Nov 30 2006 - 10:31:22 CST)
• Nitin Bhardwaj
  • AMBER: Atom Exclusion (Tue Nov 07 2006 - 23:44:30 CST)
  • AMBER: Format of the prmtop file (NUMBER_EXCLUDED_ATOMS) & (EXCLUDED_ATOMS_LIST) (Tue Nov 07 2006 - 15:08:42 CST)
  • Re: AMBER: Mutual exclusion of atoms (Mon Nov 06 2006 - 16:27:49 CST)
  • AMBER: Mutual exclusion of atoms (Mon Nov 06 2006 - 15:40:50 CST)
  • AMBER: Mutual exclusion of atoms (Sun Nov 05 2006 - 23:59:38 CST)
• nur avneet
  • AMBER: How to start a Simulation of a peptide in bilayer (Wed Nov 01 2006 - 03:28:31 CST)
• Pankaj Daga
  • AMBER: Error in compliling LEAP on Fedora 5 (Wed Nov 15 2006 - 16:56:58 CST)
• Peter Anderson
  • AMBER: How to recompile sander for single-processor use in AMBER 8? (Thu Nov 30 2006 - 15:41:27 CST)
• Peter Gannett
  • Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? (Sun Nov 05 2006 - 17:40:18 CST)
• Peter Trodler
  • AMBER: ammonia parameters (Thu Nov 23 2006 - 02:51:39 CST)
• Philip Cheung
  • AMBER: Re: Fluorine and Bromine Parameters in Amber 9 (Fri Nov 03 2006 - 13:56:52 CST)
• r. a.
  • Re: RE: AMBER: Radius of gyration (Mon Nov 27 2006 - 22:20:32 CST)
  • AMBER: Radius of gyration (Wed Nov 22 2006 - 04:11:14 CST)
  • Re: AMBER: PTRAJ RMS: dumping RMSd vs time data (Tue Nov 07 2006 - 01:41:35 CST)
  • Re: AMBER: PTRAJ RMS: dumping RMSd vs time data (Tue Nov 07 2006 - 00:44:35 CST)
  • AMBER: PTRAJ RMS: dumping RMSd vs time data (Sat Nov 04 2006 - 02:58:25 CST)
  • AMBER: PTRAJ RMS: dumping RMSd vs time data (Sat Nov 04 2006 - 02:45:25 CST)
• Rachel
  • Re: AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines (Fri Nov 24 2006 - 13:53:29 CST)
  • AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines (Fri Nov 24 2006 - 11:58:53 CST)
  • Re: AMBER: Unable to find mopac charges in divcon.out (Thu Nov 23 2006 - 17:22:06 CST)
  • AMBER: Unable to find mopac charges in divcon.out (Thu Nov 23 2006 - 13:31:55 CST)
  • Re: AMBER: SHAKE problem after minimization (Thu Nov 23 2006 - 12:37:24 CST)
  • Re: AMBER: compile amber8 on IBM-sp4 (Thu Nov 23 2006 - 11:45:04 CST)
  • Re: AMBER: compile amber8 on IBM-sp4 (Thu Nov 23 2006 - 10:37:18 CST)
  • Re: AMBER: compile amber8 on IBM-sp4 (Thu Nov 23 2006 - 07:14:09 CST)
  • Re: AMBER: compile amber8 on IBM-sp4 (Thu Nov 23 2006 - 03:56:53 CST)
  • Re: AMBER: SHAKE problem after minimization (Wed Nov 22 2006 - 13:37:15 CST)
  • Re: AMBER: SHAKE problem after minimization (Wed Nov 22 2006 - 12:43:50 CST)
  • Re: AMBER: compile amber8 on IBM-sp4 (Wed Nov 22 2006 - 12:34:19 CST)
  • Re: AMBER: SHAKE problem after minimization (Wed Nov 22 2006 - 09:42:34 CST)
  • AMBER: SHAKE problem after minimization (Wed Nov 22 2006 - 05:39:18 CST)
  • Re: AMBER: compile amber8 on IBM-sp4 (Wed Nov 22 2006 - 04:08:42 CST)
  • AMBER: compile amber8 on IBM-sp4 (Tue Nov 21 2006 - 11:56:13 CST)
  • Re: AMBER: problems with saving self-built molecules parameters (Mon Nov 20 2006 - 12:42:10 CST)
  • Re: AMBER: problems with saving self-built molecules parameters (Mon Nov 20 2006 - 11:18:00 CST)
  • Re: AMBER: problems with saving self-built molecules parameters (Mon Nov 20 2006 - 08:23:30 CST)
  • AMBER: problems with saving self-built molecules parameters (Mon Nov 20 2006 - 06:59:07 CST)
  • Re: AMBER: vlimit exceeded for step 0, vmax = infinity (Tue Nov 14 2006 - 16:44:44 CST)
  • Re: AMBER: vlimit exceeded for step 0, vmax = infinity (Mon Nov 13 2006 - 11:09:22 CST)
  • Re: AMBER: vlimit exceeded for step 0, vmax = infinity (Fri Nov 10 2006 - 09:54:26 CST)
  • Re: AMBER: vlimit exceeded for step 0, vmax = infinity (Fri Nov 10 2006 - 08:42:31 CST)
  • Re: AMBER: vlimit exceeded for step 0, vmax = infinity (Wed Nov 08 2006 - 11:31:12 CST)
  • AMBER: big bond energy change from minimization and md (heating) (Wed Nov 08 2006 - 10:40:12 CST)
  • AMBER: vlimit exceeded for step 0, vmax = infinity (Wed Nov 08 2006 - 06:59:00 CST)
  • Re: AMBER: too big EEL values in the minimisation output (Fri Nov 03 2006 - 06:09:54 CST)
  • Re: AMBER: too big EEL values in the minimisation output (Thu Nov 02 2006 - 12:08:00 CST)
  • AMBER: too big EEL values in the minimisation output (Wed Nov 01 2006 - 11:01:17 CST)
• Rafi Ahmad
  • AMBER: Probelm with running Amber 9 parallelly (Thu Nov 09 2006 - 06:59:56 CST)
  • RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version (Thu Nov 02 2006 - 03:51:18 CST)
• Rajesh Murarka
  • AMBER: Flag for removal of translational and rotational center-of-mass (COM) motion (Wed Nov 08 2006 - 09:59:36 CST)
• Rama krishnan
  • AMBER: Unable to find solution for an error - "cannot successfully assign bond type" (Sat Nov 04 2006 - 04:06:51 CST)
• rebeca_at_mmb.pcb.ub.es
  • AMBER: minimization of Hydrogens with xLeaP (Mon Nov 27 2006 - 12:38:04 CST)
• Rita Cassia
  • Re: AMBER: Ethanol (Wed Nov 22 2006 - 03:33:24 CST)
  • AMBER: Ethanol (Fri Nov 17 2006 - 06:13:14 CST)
• Robert Duke
  • Re: AMBER: erroneous placement of TER card (Thu Nov 16 2006 - 10:47:23 CST)
  • Re: AMBER: erroneous placement of TER card (Thu Nov 16 2006 - 07:56:11 CST)
  • Re: AMBER: pmemd installation problem (Fri Nov 03 2006 - 13:09:52 CST)
• Ross Walker
  • RE: AMBER: SHAKE problem after minimization (Wed Nov 22 2006 - 11:59:58 CST)
  • RE: AMBER: compile amber8 on IBM-sp4 (Wed Nov 22 2006 - 11:55:45 CST)
  • RE: AMBER: Some warning !!! during SANDER ? (Wed Nov 22 2006 - 10:48:55 CST)
  • RE: AMBER: Amber9 installation error (Sat Nov 18 2006 - 11:20:39 CST)
  • RE: AMBER: <kein Betreff> (Mon Nov 13 2006 - 10:44:03 CST)
  • RE: AMBER: The plc.frcmod file in the old version tutorial (Mon Nov 13 2006 - 10:29:26 CST)
  • RE: AMBER: Zn metal library (Mon Nov 06 2006 - 00:08:20 CST)
  • AMBER: RE: I got the error meassage in testcase of QMMM (Sat Nov 04 2006 - 12:09:13 CST)
  • AMBER: (Sat Nov 04 2006 - 11:35:43 CST)
  • RE: AMBER: ntt=1 in simulated annealing (Fri Nov 03 2006 - 20:04:08 CST)
  • RE: AMBER: Problems with equilibrating the starting density (Fri Nov 03 2006 - 13:41:55 CST)
  • RE: AMBER: Simulation a small chain of amino acids - error in MD simulation (Fri Nov 03 2006 - 12:32:27 CST)
  • Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft (Fri Nov 03 2006 - 10:39:22 CST)
  • RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version (Thu Nov 02 2006 - 11:17:42 CST)
  • RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version (Thu Nov 02 2006 - 11:05:38 CST)
  • RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version (Wed Nov 01 2006 - 18:04:28 CST)
  • RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version (Wed Nov 01 2006 - 15:36:17 CST)
  • RE: AMBER: ab initio terminology query (Wed Nov 01 2006 - 14:51:43 CST)
  • RE: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft (Wed Nov 01 2006 - 11:21:02 CST)
  • RE: AMBER: ab initio terminology query (Wed Nov 01 2006 - 10:44:22 CST)
• Sandro Fornili
  • AMBER: ff03 GLY HAs atom type (Tue Nov 21 2006 - 10:21:01 CST)
• sangeeta
  • AMBER: Potential Energy Calculation (Mon Nov 06 2006 - 06:11:30 CST)
• Sayandeep Purkayasth
  • Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c (Thu Nov 02 2006 - 00:48:03 CST)
• Scott Brozell
  • Re: AMBER: compile amber8 on IBM-sp4 (Tue Nov 21 2006 - 12:38:49 CST)
  • Re: AMBER: error in tleap test (Wed Nov 15 2006 - 11:55:07 CST)
• Scott Pendley
  • Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? (Mon Nov 06 2006 - 11:28:48 CST)
  • Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? (Mon Nov 06 2006 - 11:20:43 CST)
• Seongeun Yang
  • AMBER: energy minimizations in amber8 vs. amber9 (Tue Nov 28 2006 - 01:43:35 CST)
• Sergey Samsonov
  • AMBER: Restarting with new topology (Thu Nov 23 2006 - 10:39:53 CST)
  • Re: AMBER: ntt=1 in simulated annealing (Wed Nov 15 2006 - 01:09:15 CST)
  • Re: AMBER: Problems amber mask in distance? (Wed Nov 08 2006 - 10:57:20 CST)
  • AMBER: Problems amber mask in distance? (Wed Nov 08 2006 - 10:39:18 CST)
  • Re: AMBER: grid output (Tue Nov 07 2006 - 10:46:07 CST)
  • Re: AMBER: grid output (Tue Nov 07 2006 - 02:35:28 CST)
  • Re: AMBER: Mass weights (Tue Nov 07 2006 - 02:06:14 CST)
  • AMBER: grid output (Wed Nov 01 2006 - 10:31:34 CST)
  • Re: AMBER: Closest(closest water) (Wed Nov 01 2006 - 02:38:55 CST)
  • AMBER: Mass weights (Wed Nov 01 2006 - 02:41:33 CST)
• SERGIO MIGUEL FERNANDES DOS SANTOS
  • AMBER: Acetone box (Tue Nov 14 2006 - 12:34:24 CST)
• Seth Lilavivat
  • AMBER: ambpdb -pqr (Tue Nov 28 2006 - 14:52:10 CST)
  • AMBER: Modifying a Force Field (Tue Nov 28 2006 - 09:27:08 CST)
  • AMBER: pqr file (Thu Nov 16 2006 - 10:43:55 CST)
• Shozeb Haider
  • AMBER: Xleap woes (Thu Nov 16 2006 - 17:07:01 CST)
• Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini)
  • AMBER: leap usage (Thu Nov 02 2006 - 03:41:34 CST)
• Steve Seibold
  • AMBER: xleap (Tue Nov 28 2006 - 08:33:48 CST)
  • AMBER: Building Library (Thu Nov 09 2006 - 13:40:30 CST)
  • AMBER: (Thu Nov 09 2006 - 11:03:14 CST)
  • AMBER: Building Library (Thu Nov 09 2006 - 10:52:08 CST)
• Steven Winfield
  • Re: AMBER: SHAKE problem after minimization (Wed Nov 22 2006 - 15:53:07 CST)
  • Re: AMBER: Error in compliling LEAP on Fedora 5 (Wed Nov 15 2006 - 18:10:33 CST)
  • Re: AMBER: ntt=1 in simulated annealing (Tue Nov 07 2006 - 05:26:28 CST)
• Tanya Johannsen
  • Re: AMBER: ntt=1 in simulated annealing (Tue Nov 14 2006 - 17:59:04 CST)
  • Re: AMBER: ntt=1 in simulated annealing (Fri Nov 03 2006 - 18:38:38 CST)
  • AMBER: ntt=1 in simulated annealing (Thu Nov 02 2006 - 21:44:19 CST)
• Thomas Cheatham
  • Re: AMBER: watershell and image commands (Thu Nov 30 2006 - 17:22:59 CST)
  • Re: AMBER: Problem with mask when using distance in ptraj (Wed Nov 22 2006 - 15:17:12 CST)
  • Re: AMBER: reading psf file (Fri Nov 17 2006 - 18:28:45 CST)
  • Re: AMBER: H-Bond Terms in amber force field (Wed Nov 15 2006 - 17:51:36 CST)
  • Re: AMBER: ptraj and mdvel question (Wed Nov 15 2006 - 17:37:13 CST)
  • Re: AMBER: Ptraj: radial distribution and correlation coefficient (Tue Nov 14 2006 - 13:17:40 CST)
  • Re: AMBER: Ptraj: radial distribution and correlation coefficient (Tue Nov 14 2006 - 12:34:57 CST)
  • Re: AMBER: grid output (Tue Nov 07 2006 - 10:25:39 CST)
  • Re: AMBER: Mass weights (Mon Nov 06 2006 - 22:58:54 CST)
  • Re: AMBER: grid output (Mon Nov 06 2006 - 22:30:25 CST)
  • Re: AMBER: PTRAJ RMS: dumping RMSd vs time data (Mon Nov 06 2006 - 22:18:20 CST)
  • Re: AMBER: trajout script (Mon Nov 06 2006 - 14:39:04 CST)
  • AMBER: ACS Chicago potential symposia and OASYS abstracts (Sat Nov 04 2006 - 15:04:47 CST)
• Thomas Steinbrecher
  • Re: AMBER: Confusion about PBC (Wed Nov 29 2006 - 10:40:05 CST)
  • Re: AMBER: NONB values adjusted? (Tue Nov 28 2006 - 10:31:33 CST)
  • Re: AMBER: MM_PBSA (Thu Nov 16 2006 - 10:21:55 CST)
  • Re: AMBER: Mutual exclusion of atoms (Mon Nov 06 2006 - 16:02:47 CST)
• Tomas Kubar
  • AMBER: leap - compilation error (Tue Nov 07 2006 - 03:47:33 CST)
• trudy_at_uoguelph.ca
  • Re: AMBER: Problem Installing Amber in SGI Irix 6.5 (Thu Nov 30 2006 - 09:31:02 CST)
  • Re: AMBER: Problem Installing Amber in SGI Irix 6.5 (Wed Nov 29 2006 - 08:50:51 CST)
  • Re: AMBER: Problem Installing Amber in SGI Irix 6.5 (Tue Nov 28 2006 - 09:41:07 CST)
  • AMBER: Problem Installing Amber in SGI Irix 6.5 (Mon Nov 27 2006 - 14:29:53 CST)
• uccadco_at_ucl.ac.uk
  • AMBER: (Tue Nov 28 2006 - 08:48:08 CST)
• Urszula Uciechowska
  • Re: AMBER: NAD ?? (Mon Nov 13 2006 - 03:08:45 CST)
  • Re: AMBER: NAD ?? (Fri Nov 10 2006 - 03:36:15 CST)
  • AMBER: NAD ?? (Wed Nov 08 2006 - 07:40:15 CST)
  • AMBER: problem with NAD+ parameters (Mon Nov 06 2006 - 08:27:16 CST)
• VANDANA KUMARI
  • AMBER: problem in calculating EGB using sander for ligand containing F atom (Wed Nov 08 2006 - 21:36:52 CST)
• vanessa wai
  • AMBER: MM-PBSA problem (Thu Nov 30 2006 - 19:27:06 CST)
• Varsha Goyal
  • AMBER: MM_PBSA (Wed Nov 15 2006 - 20:27:15 CST)
  • Re: AMBER: Interaction Energy Calculation (Thu Nov 02 2006 - 17:04:12 CST)
  • AMBER: Interaction Energy Calculation (Thu Nov 02 2006 - 15:34:28 CST)
• Viktor Hornak
  • Re: AMBER: Problems amber mask in distance? (Wed Nov 08 2006 - 10:50:59 CST)
• Vitor Manuel Sousa F?x
  • AMBER: dihedral angle equation (Fri Nov 17 2006 - 06:41:25 CST)
  • AMBER: opls_aa in amber (Thu Nov 16 2006 - 08:29:45 CST)
  • Re: AMBER: Interaction Energy Calculation (Thu Nov 02 2006 - 16:08:01 CST)
• wenfei Li
  • Re: AMBER: problem of the REMD with nmr constraints (Sat Nov 25 2006 - 19:56:05 CST)
  • AMBER: problem of the REMD with nmr constraints (Wed Nov 22 2006 - 19:57:32 CST)
  • AMBER: Can we use the distance restraint in Replica-exchange simulation with AMBER8 (Thu Nov 02 2006 - 06:44:18 CST)
• Xiaowei (David) Li
  • AMBER: the energy and temperature both increasing during the simulation with NTT=0 (Mon Nov 20 2006 - 12:50:00 CST)
• Xuebin Qiao
  • Re: AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines (Fri Nov 24 2006 - 22:55:14 CST)
  • Re: AMBER: compile amber8 on IBM-sp4 (Thu Nov 23 2006 - 08:23:36 CST)
  • Re: AMBER: compile amber8 on IBM-sp4 (Thu Nov 23 2006 - 06:26:12 CST)
  • Re: AMBER: compile amber8 on IBM-sp4 (Thu Nov 23 2006 - 06:21:07 CST)
  • Re: AMBER: compile amber8 on IBM-sp4 (Wed Nov 22 2006 - 21:51:57 CST)
• yipinl_at_umich.edu
  • AMBER: parameters for beta peptides (Thu Nov 16 2006 - 13:29:08 CST)
• Yong Duan
  • RE: AMBER: ff03 GLY HAs atom type (Tue Nov 21 2006 - 11:41:17 CST)
  • RE: AMBER: vlimit exceeded for step 0, vmax = infinity (Tue Nov 14 2006 - 17:05:08 CST)
  • RE: AMBER: vlimit exceeded for step 0, vmax = infinity (Mon Nov 13 2006 - 19:56:29 CST)
  • RE: AMBER: vlimit exceeded for step 0, vmax = infinity (Fri Nov 10 2006 - 15:55:23 CST)
  • RE: AMBER: ab initio terminology query (Wed Nov 01 2006 - 17:17:43 CST)
  • RE: AMBER: ab initio terminology query (Wed Nov 01 2006 - 12:53:39 CST)
• Yongmei Pan
  • AMBER: How the ensemble average calculated in Gibbs, AMBER7? (Wed Nov 01 2006 - 16:06:09 CST)
• Yu Chen
  • Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft (Fri Nov 03 2006 - 13:05:55 CST)
  • Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft (Fri Nov 03 2006 - 09:18:35 CST)
  • Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft (Wed Nov 01 2006 - 11:02:26 CST)
  • AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft (Wed Nov 01 2006 - 10:22:54 CST)
• zachary hartman
  • AMBER: Quantifying pi-pi interactions (Tue Nov 21 2006 - 09:51:30 CST)
• ÇÑ ¹Î¿ì
  • AMBER: Problem about dummy atoms when running antechamber (Mon Nov 27 2006 - 21:30:27 CST)
• ÕÅÓÂ
  • AMBER: how to remove the rotation of system in periodic condition? (Tue Nov 14 2006 - 06:10:22 CST)

Last message date: Sat Dec 30 2006 - 07:20:23 CST
Archived on: Wed Feb 21 2007 - 22:44:16 CST