Amber Archive Jul 2007: by subject

A little question
- Ross Walker (Thu Jul 26 2007 - 07:51:55 PDT)
amber-developers: -y option in sander
- Geoff Wood (Thu Jul 19 2007 - 06:54:47 PDT)
AMBER: $AMBERHOME on PATH
- Francesco Pietra (Sun Jul 01 2007 - 13:50:39 PDT)
- M. L. Dodson (Sun Jul 01 2007 - 08:57:05 PDT)
- Francesco Pietra (Sun Jul 01 2007 - 07:38:03 PDT)
AMBER: (no subject)
- n.buis.soton.ac.uk (Thu Jul 19 2007 - 01:58:06 PDT)
AMBER: ????pig5678??????
- pig5678 (Thu Jul 12 2007 - 18:36:10 PDT)
- pig5678 (Tue Jul 10 2007 - 20:27:55 PDT)
- David A. Case (Tue Jul 10 2007 - 08:14:45 PDT)
AMBER: About amber7
- Carlos Simmerling (Tue Jul 03 2007 - 06:57:14 PDT)
- Saiful Islam (Tue Jul 03 2007 - 06:49:28 PDT)
AMBER: about wrap the trajectory
- Carlos Simmerling (Fri Jul 27 2007 - 09:10:49 PDT)
- Rachel (Fri Jul 27 2007 - 07:52:50 PDT)
- Carlos Simmerling (Fri Jul 27 2007 - 07:44:53 PDT)
- Rachel (Fri Jul 27 2007 - 07:38:12 PDT)
- Carlos Simmerling (Fri Jul 27 2007 - 07:23:30 PDT)
- Rachel (Fri Jul 27 2007 - 07:08:23 PDT)
- Carlos Simmerling (Fri Jul 27 2007 - 04:29:48 PDT)
- Rachel (Thu Jul 26 2007 - 09:43:48 PDT)
- Carlos Simmerling (Thu Jul 26 2007 - 09:28:33 PDT)
- Rachel (Thu Jul 26 2007 - 09:18:32 PDT)
AMBER: adding organic molecule to polypeptide residue
- FyD (Sat Jul 28 2007 - 02:05:18 PDT)
- Lili Peng (Thu Jul 26 2007 - 15:36:29 PDT)
AMBER: adding water molecules in lipid bilayer model
- Vijay Manickam Achari (Tue Jul 10 2007 - 19:00:30 PDT)
- Fenghui Fan (Mon Jul 09 2007 - 16:11:45 PDT)
- M. L. Dodson (Mon Jul 09 2007 - 05:59:01 PDT)
- Vijay Manickam Achari (Sun Jul 08 2007 - 20:22:46 PDT)
AMBER: amber7 and xleap
- Ross Walker (Sun Jul 01 2007 - 10:32:45 PDT)
- Saiful Islam (Sun Jul 01 2007 - 06:43:45 PDT)
- Saiful Islam (Sat Jun 30 2007 - 20:37:00 PDT)
AMBER: Amber9 analyze timecorr manual ambigous
- David A. Case (Thu Jul 12 2007 - 15:58:30 PDT)
- Nicolas Lux Fawzi (Thu Jul 12 2007 - 15:11:30 PDT)
- David A. Case (Thu Jul 12 2007 - 12:55:15 PDT)
- Nicolas Lux Fawzi (Thu Jul 12 2007 - 12:26:19 PDT)
AMBER: Amber9 parallel compilation openmpi issues
- David A. Case (Wed Jul 25 2007 - 09:09:18 PDT)
- Mark Williamson (Wed Jul 25 2007 - 08:28:06 PDT)
- Francesco Pietra (Wed Jul 25 2007 - 07:44:46 PDT)
- Benjamin Juhl (Wed Jul 25 2007 - 07:18:28 PDT)
- Francesco Pietra (Wed Jul 25 2007 - 07:00:58 PDT)
- Mark Williamson (Wed Jul 25 2007 - 06:33:35 PDT)
- Francesco Pietra (Tue Jul 24 2007 - 23:24:22 PDT)
AMBER: antechamber
- Francesco Pietra (Tue Jul 10 2007 - 00:04:39 PDT)
- M. L. Dodson (Mon Jul 09 2007 - 17:08:27 PDT)
- Francesco Pietra (Mon Jul 09 2007 - 14:57:45 PDT)
- Barbault Florent (Mon Jul 09 2007 - 07:59:03 PDT)
- David A. Case (Mon Jul 09 2007 - 07:41:23 PDT)
- Marie Brut (Mon Jul 09 2007 - 04:56:19 PDT)
AMBER: antechamber save prmtop inpcrd
- Francesco Pietra (Tue Jul 03 2007 - 10:55:11 PDT)
AMBER: antechamber: mopac charges
- David A. Case (Thu Jul 05 2007 - 13:24:09 PDT)
- Neelanjana Sengupta (Thu Jul 05 2007 - 12:26:30 PDT)
- David A. Case (Wed Jul 04 2007 - 16:27:02 PDT)
- Neelanjana Sengupta (Wed Jul 04 2007 - 16:21:02 PDT)
AMBER: Atoms in conatct to a specific atoms during MD
- Rafi Ahmad (Mon Jul 16 2007 - 06:23:38 PDT)
AMBER: Atoms in contact to a specific atoms during MD
- Mark Williamson (Mon Jul 16 2007 - 07:52:39 PDT)
AMBER: Average potential energies and conformer ratios
- Francesco Pietra (Mon Jul 30 2007 - 22:09:02 PDT)
AMBER: Bad residue/molecule data in prmtop
- Ross Walker (Wed Jul 25 2007 - 07:17:00 PDT)
- neva.mmb.pcb.ub.es (Wed Jul 25 2007 - 06:03:19 PDT)
AMBER: Basic AMBER question
- Ross Walker (Wed Jul 11 2007 - 13:07:42 PDT)
- Melinda Layten (Wed Jul 11 2007 - 13:05:11 PDT)
- Lili Peng (Wed Jul 11 2007 - 12:15:48 PDT)
AMBER: Belly Restraints and Distance Restraints
- Seth Lilavivat (Wed Jul 11 2007 - 12:13:04 PDT)
AMBER: bound magnesium ions in proteins with GBSA
- Wei Chen (Wed Jul 18 2007 - 09:01:26 PDT)
AMBER: bug in nonbond_list.f (nee ew_setup.f)
- Dan Kidger (Mon Jul 02 2007 - 02:42:58 PDT)
AMBER: Bug report: a bug of xleap associated with NumLock
- David A. Case (Tue Jul 24 2007 - 08:16:07 PDT)
- Ye Mei (Mon Jul 23 2007 - 23:15:27 PDT)
AMBER: can open PDB file in xleap
- Vijay Manickam Achari (Sun Jul 15 2007 - 18:44:17 PDT)
AMBER: Can t open PDB file in xleap
- Benjamin Juhl (Mon Jul 16 2007 - 03:53:16 PDT)
AMBER: Can't open PDB file in xleap
- Vijay Manickam Achari (Mon Jul 16 2007 - 02:43:16 PDT)
AMBER: computational Ala scan
- Sergio Wong (Wed Jul 11 2007 - 16:36:58 PDT)
AMBER: Convergence criteria in replica exchange simulations
- Carlos Simmerling (Thu Jul 05 2007 - 05:26:26 PDT)
- Seongeun Yang (Thu Jul 05 2007 - 04:18:17 PDT)
AMBER: convergence criterion not reached
- David A. Case (Mon Jul 02 2007 - 18:14:53 PDT)
- Jena M (Mon Jul 02 2007 - 16:53:22 PDT)
AMBER: convergence in classical MD
- Carlos Simmerling (Mon Jul 16 2007 - 04:37:09 PDT)
- Seongeun Yang (Mon Jul 16 2007 - 04:23:01 PDT)
AMBER: corrected reaction field energy and PBCAL
- AYTUG TUNCEL (Sun Jul 08 2007 - 17:40:53 PDT)
AMBER: Could not find cntrl namelist
- Francesco Pietra (Wed Jul 11 2007 - 14:52:25 PDT)
- Francesco Pietra (Wed Jul 11 2007 - 14:50:37 PDT)
- Robert Duke (Wed Jul 11 2007 - 10:47:57 PDT)
- Francesco Pietra (Wed Jul 11 2007 - 08:10:42 PDT)
- Francesco Pietra (Tue Jul 10 2007 - 23:48:59 PDT)
- Robert Duke (Wed Jul 11 2007 - 06:07:36 PDT)
- Francesco Pietra (Wed Jul 11 2007 - 03:14:51 PDT)
- Francesco Pietra (Tue Jul 10 2007 - 23:48:41 PDT)
- Robert Duke (Tue Jul 10 2007 - 19:21:07 PDT)
- Ross Walker (Tue Jul 10 2007 - 14:57:39 PDT)
- Ross Walker (Tue Jul 10 2007 - 16:00:38 PDT)
- David A. Case (Tue Jul 10 2007 - 16:04:15 PDT)
- M. L. Dodson (Tue Jul 10 2007 - 15:25:17 PDT)
- Robert Duke (Tue Jul 10 2007 - 14:57:54 PDT)
- Francesco Pietra (Tue Jul 10 2007 - 14:11:48 PDT)
- Ross Walker (Tue Jul 10 2007 - 11:21:12 PDT)
- David A. Case (Tue Jul 10 2007 - 10:52:10 PDT)
- Francesco Pietra (Mon Jul 09 2007 - 23:26:54 PDT)
- Ross Walker (Mon Jul 09 2007 - 14:38:01 PDT)
- Francesco Pietra (Mon Jul 09 2007 - 14:31:18 PDT)
- Francesco Pietra (Mon Jul 09 2007 - 14:22:30 PDT)
- Thomas Cheatham III (Mon Jul 09 2007 - 14:17:23 PDT)
- M. L. Dodson (Mon Jul 09 2007 - 14:09:06 PDT)
- Francesco Pietra (Mon Jul 09 2007 - 13:53:43 PDT)
- Ross Walker (Mon Jul 09 2007 - 10:26:29 PDT)
- M. L. Dodson (Mon Jul 09 2007 - 10:10:58 PDT)
- Francesco Pietra (Mon Jul 09 2007 - 09:56:58 PDT)
AMBER: crg file
- Ross Walker (Wed Jul 25 2007 - 08:26:28 PDT)
- umbrita itl (Wed Jul 25 2007 - 07:43:17 PDT)
AMBER: Cutoff list exceeds largest sphere in unit cell
- neville forlemu (Sat Jul 14 2007 - 19:09:36 PDT)
- Barbault Florent (Fri Jul 13 2007 - 11:54:36 PDT)
- Robert Duke (Fri Jul 13 2007 - 09:30:40 PDT)
- Andrew Borgert (Fri Jul 13 2007 - 09:27:44 PDT)
- Andrew Borgert (Fri Jul 13 2007 - 09:18:05 PDT)
AMBER: DNA denatures during MD simulation
- Prashanth Athri (Mon Jul 23 2007 - 15:51:32 PDT)
- Thomas Cheatham (Mon Jul 23 2007 - 12:49:49 PDT)
- Carlos Simmerling (Mon Jul 23 2007 - 12:44:35 PDT)
- Prashanth Athri (Mon Jul 23 2007 - 12:38:12 PDT)
AMBER: DNA RNA recognition problem
- David A. Case (Thu Jul 19 2007 - 08:01:17 PDT)
- Steve Seibold (Thu Jul 19 2007 - 06:51:43 PDT)
AMBER: Error during compilation on a SGI Irix machine
- David A. Case (Wed Jul 18 2007 - 21:34:18 PDT)
- Ruchi Sachdeva (Wed Jul 18 2007 - 21:18:30 PDT)
- Carlos Simmerling (Wed Jul 18 2007 - 09:57:27 PDT)
- Ruchi Sachdeva (Wed Jul 18 2007 - 09:47:30 PDT)
AMBER: errors in SHIFTS execution
- Thomas Pochapsky (Mon Jul 30 2007 - 10:06:04 PDT)
- David A. Case (Mon Jul 30 2007 - 08:37:26 PDT)
- Thomas Pochapsky (Mon Jul 30 2007 - 07:06:19 PDT)
- Thomas Pochapsky (Mon Jul 30 2007 - 06:49:47 PDT)
- David A. Case (Sun Jul 29 2007 - 08:44:05 PDT)
- Tom Pochapsky (Sat Jul 28 2007 - 04:58:57 PDT)
AMBER: extract protein energy from MD trajectory
- Carlos Simmerling (Wed Jul 11 2007 - 01:34:31 PDT)
- Mikyung (Tue Jul 10 2007 - 23:58:31 PDT)
- Carlos Simmerling (Tue Jul 10 2007 - 15:08:32 PDT)
- Mikyung (Tue Jul 10 2007 - 14:47:53 PDT)
AMBER: FLAG LENNARD_JONES_ACOEF NAN
- Greg Gannon (Fri Jul 27 2007 - 08:55:52 PDT)
- David A. Case (Fri Jul 27 2007 - 08:19:49 PDT)
- Greg Gannon (Fri Jul 27 2007 - 07:41:46 PDT)
AMBER: Fwd: Amber9 parallel compilation openmpi issues
- David A. Case (Wed Jul 25 2007 - 15:48:55 PDT)
- Mark Williamson (Wed Jul 25 2007 - 15:20:37 PDT)
- Francesco Pietra (Wed Jul 25 2007 - 15:01:40 PDT)
- David A. Case (Wed Jul 25 2007 - 14:32:32 PDT)
- Francesco Pietra (Wed Jul 25 2007 - 13:43:08 PDT)
- David A. Case (Wed Jul 25 2007 - 12:56:24 PDT)
- Mark Williamson (Wed Jul 25 2007 - 12:19:29 PDT)
- David A. Case (Wed Jul 25 2007 - 10:36:43 PDT)
- Francesco Pietra (Wed Jul 25 2007 - 10:07:15 PDT)
- Ross Walker (Wed Jul 25 2007 - 08:25:58 PDT)
- Francesco Pietra (Wed Jul 25 2007 - 06:24:10 PDT)
AMBER: Fwd: antechamber save prmtop inpcrd
- Francesco Pietra (Wed Jul 04 2007 - 14:08:02 PDT)
- David A. Case (Wed Jul 04 2007 - 13:15:21 PDT)
- Francesco Pietra (Wed Jul 04 2007 - 09:54:08 PDT)
- David A. Case (Wed Jul 04 2007 - 08:53:04 PDT)
- Francesco Pietra (Tue Jul 03 2007 - 23:14:23 PDT)
AMBER: Gaff Charge
- David A. Case (Mon Jul 16 2007 - 22:18:17 PDT)
- Colby C (Mon Jul 16 2007 - 20:39:15 PDT)
AMBER: GDP UNKNOWN ATOM TYPE: O3 warning
- j j (Sat Jul 21 2007 - 10:21:32 PDT)
AMBER: General AMBER questions
- David A. Case (Wed Jul 18 2007 - 16:12:34 PDT)
- Lili Peng (Tue Jul 17 2007 - 15:51:32 PDT)
AMBER: Generation of ESP(ind) within atomic charges derivation for polarizable force field
- Anela Ivanova (Wed Jul 04 2007 - 05:26:02 PDT)
AMBER: help with phosphotyrosine
- Samantha Kaye (Tue Jul 17 2007 - 06:00:23 PDT)
- David A. Case (Mon Jul 16 2007 - 11:11:51 PDT)
- Samantha Kaye (Mon Jul 16 2007 - 08:45:36 PDT)
AMBER: heme force field
- Marcelo Puiatti (Mon Jul 30 2007 - 06:08:52 PDT)
- hadi behzadi (Mon Jul 30 2007 - 04:55:07 PDT)
AMBER: how to create an O linked N-acetylglucosamine in a protein
- ming hui (Mon Jul 16 2007 - 20:41:40 PDT)
AMBER: How to extract energy of molecule from the system with explicit water molecules
- priya priya (Fri Jul 06 2007 - 05:25:02 PDT)
- priya priya (Fri Jul 06 2007 - 03:39:58 PDT)
- priya priya (Thu Jul 05 2007 - 23:58:28 PDT)
- Carlos Simmerling (Thu Jul 05 2007 - 09:45:14 PDT)
- priya priya (Thu Jul 05 2007 - 09:40:41 PDT)
- Carlos Simmerling (Thu Jul 05 2007 - 09:04:12 PDT)
- priya priya (Thu Jul 05 2007 - 08:57:59 PDT)
- Carlos Simmerling (Thu Jul 05 2007 - 08:25:42 PDT)
- priya priya (Thu Jul 05 2007 - 08:10:23 PDT)
- Carlos Simmerling (Thu Jul 05 2007 - 07:36:05 PDT)
- priya priya (Thu Jul 05 2007 - 07:31:03 PDT)
AMBER: How to use antechamber properly?
- 한재범 (Mon Jul 02 2007 - 22:57:33 PDT)
AMBER: incoherent intermediate scattering function
- Jason Whitte (Tue Jul 17 2007 - 15:59:21 PDT)
AMBER: Input required for RESP
- FyD (Tue Jul 10 2007 - 23:21:42 PDT)
- Neelanjana Sengupta (Tue Jul 10 2007 - 11:03:54 PDT)
AMBER: Known residue, unknown error in teLeap
- Neelanjana Sengupta (Tue Jul 17 2007 - 11:58:12 PDT)
- Neelanjana Sengupta (Tue Jul 17 2007 - 11:53:16 PDT)
- David A. Case (Tue Jul 17 2007 - 09:49:41 PDT)
- Neelanjana Sengupta (Tue Jul 17 2007 - 09:33:39 PDT)
- David A. Case (Mon Jul 16 2007 - 18:32:16 PDT)
- Neelanjana Sengupta (Mon Jul 16 2007 - 12:19:07 PDT)
AMBER: large RMS fluctuations in turning off VDW interactions by TI
- Thomas Steinbrecher (Fri Jul 06 2007 - 10:55:32 PDT)
- David Mobley (Thu Jul 05 2007 - 08:56:43 PDT)
- Holly Freedman (Wed Jul 04 2007 - 12:53:01 PDT)
- steinbrt.scripps.edu (Wed Jul 04 2007 - 05:51:08 PDT)
- David Mobley (Tue Jul 03 2007 - 12:55:54 PDT)
- Holly Freedman (Tue Jul 03 2007 - 10:14:29 PDT)
- David A. Case (Mon Jul 02 2007 - 23:34:13 PDT)
- Holly Freedman (Mon Jul 02 2007 - 13:51:12 PDT)
- David A. Case (Mon Jul 02 2007 - 13:20:27 PDT)
- David Mobley (Mon Jul 02 2007 - 13:03:17 PDT)
- Julien Michel (Sun Jul 01 2007 - 15:42:53 PDT)
- Holly Freedman (Sun Jul 01 2007 - 12:54:11 PDT)
- Holly Freedman (Sun Jul 01 2007 - 12:13:17 PDT)
AMBER: Linux install
- David A. Case (Tue Jul 31 2007 - 08:35:37 PDT)
- Beale, John (Tue Jul 31 2007 - 04:55:34 PDT)
AMBER: manganese ion
- Davide Moiani (Wed Jul 11 2007 - 14:47:18 PDT)
- neetu.imtech.res.in (Tue Jul 10 2007 - 21:03:54 PDT)
- Davide Moiani (Tue Jul 10 2007 - 09:47:38 PDT)
- Guillermo Mulliert Carlín (Tue Jul 10 2007 - 01:39:40 PDT)
- Davide Moiani (Mon Jul 09 2007 - 14:02:31 PDT)
AMBER: md potential energy
- Francesco Pietra (Mon Jul 23 2007 - 09:14:48 PDT)
AMBER: MD simulation error
- Lili Peng (Wed Jul 25 2007 - 11:21:24 PDT)
- Ross Walker (Wed Jul 25 2007 - 10:54:30 PDT)
- Carlos Simmerling (Wed Jul 25 2007 - 10:41:42 PDT)
- Lili Peng (Wed Jul 25 2007 - 10:38:10 PDT)
- Ross Walker (Tue Jul 24 2007 - 18:01:13 PDT)
- David A. Case (Tue Jul 24 2007 - 17:55:09 PDT)
- Lili Peng (Tue Jul 24 2007 - 16:53:59 PDT)
AMBER: methods to approach two atoms
- Jena M (Thu Jul 26 2007 - 06:53:09 PDT)
AMBER: mm_pbsa and energy decomposition (missing BELE for MM in 1)
- Alessandro Nascimento (Tue Jul 31 2007 - 14:34:12 PDT)
AMBER: modelling substrate binding
- Mattias Blomberg (Mon Jul 16 2007 - 06:53:15 PDT)
AMBER: Molecular Dynamic Simulations using TIP4P water - Please Help
- David A. Case (Thu Jul 12 2007 - 16:03:45 PDT)
- Ross Walker (Thu Jul 12 2007 - 15:06:56 PDT)
- Hashem Taha (Thu Jul 12 2007 - 14:45:50 PDT)
- Robert Duke (Thu Jul 12 2007 - 13:55:15 PDT)
- Hashem Taha (Thu Jul 12 2007 - 13:31:59 PDT)
AMBER: MPI error message
- Ross Walker (Mon Jul 23 2007 - 10:56:35 PDT)
- Taryn Hartley (Mon Jul 23 2007 - 10:39:27 PDT)
AMBER: MPI Quiescence problem in REMD
- Carlos Simmerling (Wed Jul 11 2007 - 10:08:23 PDT)
- In Hee Park (Wed Jul 11 2007 - 09:41:47 PDT)
- Carlos Simmerling (Wed Jul 11 2007 - 02:28:56 PDT)
- In Hee Park (Tue Jul 10 2007 - 21:03:08 PDT)
AMBER: MPI script
- Hashem Taha (Tue Jul 17 2007 - 13:10:46 PDT)
- Thomas Cheatham III (Fri Jul 13 2007 - 15:19:37 PDT)
- Carlos Simmerling (Fri Jul 13 2007 - 15:15:36 PDT)
- Taryn Hartley (Fri Jul 13 2007 - 15:06:45 PDT)
AMBER: Multiple residues position
- Carlos Simmerling (Fri Jul 13 2007 - 09:20:19 PDT)
- snoze pa (Fri Jul 13 2007 - 09:04:59 PDT)
AMBER: Ne van del waals potential
- Lishan Yao (Fri Jul 13 2007 - 09:09:37 PDT)
AMBER: netcdf support needed (Amber 9, sander imin = 5, -y flag)
- Geoff Wood (Mon Jul 23 2007 - 10:23:46 PDT)
AMBER: Non bond list overflow
- David A. Case (Sun Jul 15 2007 - 16:50:11 PDT)
AMBER: Non-standard amino acid residue
- FyD (Thu Jul 19 2007 - 04:26:39 PDT)
- Sergey Samsonov (Thu Jul 19 2007 - 02:45:52 PDT)
- FyD (Wed Jul 18 2007 - 07:50:55 PDT)
- Sergey Samsonov (Wed Jul 18 2007 - 07:19:42 PDT)
- Sergey Samsonov (Tue Jul 17 2007 - 08:37:03 PDT)
- David A. Case (Tue Jul 17 2007 - 07:53:46 PDT)
- FyD (Tue Jul 17 2007 - 06:41:57 PDT)
- Sergey Samsonov (Tue Jul 17 2007 - 05:30:14 PDT)
- FyD (Mon Jul 16 2007 - 09:45:07 PDT)
- Sergey Samsonov (Mon Jul 16 2007 - 07:44:32 PDT)
AMBER: not getting topology and restraint file
- Prem Prakash Pathak (Wed Jul 25 2007 - 06:45:57 PDT)
- Carlos Simmerling (Wed Jul 25 2007 - 03:16:02 PDT)
- Prem Prakash Pathak (Tue Jul 24 2007 - 21:11:00 PDT)
- Carlos Simmerling (Tue Jul 24 2007 - 07:46:49 PDT)
- Prem Prakash Pathak (Tue Jul 24 2007 - 07:09:40 PDT)
AMBER: Nucleic acid : nonplanarity
- Mathy Froeyen (Wed Jul 04 2007 - 06:57:08 PDT)
- Sophie Barbe (Wed Jul 04 2007 - 05:37:26 PDT)
- Sophie Barbe (Tue Jul 03 2007 - 08:48:07 PDT)
AMBER: Nudget Elastic Band query
- Francesco Pietra (Thu Jul 05 2007 - 13:28:31 PDT)
- Carlos Simmerling (Thu Jul 05 2007 - 12:08:31 PDT)
- Francesco Pietra (Thu Jul 05 2007 - 12:02:19 PDT)
- Carlos Simmerling (Thu Jul 05 2007 - 10:53:53 PDT)
- Francesco Pietra (Thu Jul 05 2007 - 10:43:43 PDT)
AMBER: O-acetylated sugar
- Toshifumi Yui (Tue Jul 03 2007 - 05:26:12 PDT)
AMBER: offending restraint
- Carlos Simmerling (Sun Jul 22 2007 - 04:32:51 PDT)
- David A. Case (Sat Jul 21 2007 - 18:35:51 PDT)
- Jena M (Sat Jul 21 2007 - 17:15:42 PDT)
AMBER: parallel compilation
- Francesco Pietra (Tue Jul 24 2007 - 23:10:17 PDT)
- Ye Mei (Tue Jul 24 2007 - 19:27:04 PDT)
- Francesco Pietra (Tue Jul 24 2007 - 08:02:01 PDT)
- Ye Mei (Tue Jul 24 2007 - 07:26:26 PDT)
- Francesco Pietra (Tue Jul 24 2007 - 07:07:10 PDT)
- Ye Mei (Tue Jul 24 2007 - 03:15:28 PDT)
- Ye Mei (Tue Jul 24 2007 - 03:07:31 PDT)
- Francesco Pietra (Tue Jul 24 2007 - 00:19:58 PDT)
- Francesco Pietra (Tue Jul 24 2007 - 00:17:03 PDT)
- Ye Mei (Mon Jul 23 2007 - 23:44:43 PDT)
- Francesco Pietra (Mon Jul 23 2007 - 23:19:56 PDT)
- David A. Case (Mon Jul 23 2007 - 07:55:02 PDT)
- Francesco Pietra (Mon Jul 23 2007 - 03:16:35 PDT)
AMBER: PCA with ptraj
- Chris Moth (Sun Jul 29 2007 - 05:27:32 PDT)
- ravishk kumar (Sat Jul 28 2007 - 05:02:13 PDT)
AMBER: potential energy calculation
- Lili Peng (Wed Jul 18 2007 - 13:47:57 PDT)
- Rajendra P. OJHA (Tue Jul 17 2007 - 23:03:55 PDT)
- David A. Case (Tue Jul 17 2007 - 16:08:54 PDT)
- Lili Peng (Tue Jul 17 2007 - 15:46:55 PDT)
- Carlos Simmerling (Mon Jul 16 2007 - 18:34:01 PDT)
- Lili Peng (Mon Jul 16 2007 - 17:03:55 PDT)
AMBER: problem in compiling amber with suse 9.1 i686, finally in leap
- Prem Prakash Pathak (Tue Jul 24 2007 - 21:12:48 PDT)
- David A. Case (Tue Jul 24 2007 - 08:20:30 PDT)
- Prem Prakash Pathak (Tue Jul 24 2007 - 05:30:31 PDT)
- Ross Walker (Mon Jul 23 2007 - 08:52:00 PDT)
- Steven Winfield (Mon Jul 23 2007 - 08:43:17 PDT)
- Prem Prakash Pathak (Mon Jul 23 2007 - 08:39:21 PDT)
AMBER: problem in compiling amber9 and running amber9
- Mark Williamson (Sat Jul 21 2007 - 07:21:18 PDT)
- Prem Prakash Pathak (Sat Jul 21 2007 - 05:27:18 PDT)
AMBER: problem in installing amber9
- Syed Tarique Moin (Fri Jul 20 2007 - 22:18:05 PDT)
AMBER: Problem while creating input files in antechamber
- Benjamin Juhl (Tue Jul 31 2007 - 00:08:35 PDT)
- Anju Sharma (Mon Jul 30 2007 - 22:33:12 PDT)
AMBER: Problem while saving .top and .crd files.
- Ross Walker (Mon Jul 30 2007 - 21:28:42 PDT)
- Anju Sharma (Mon Jul 30 2007 - 20:47:39 PDT)
AMBER: Problem with leaprc
- David A. Case (Wed Jul 04 2007 - 13:31:29 PDT)
- yen li (Wed Jul 04 2007 - 11:21:22 PDT)
- David A. Case (Wed Jul 04 2007 - 09:15:39 PDT)
- yen li (Wed Jul 04 2007 - 05:23:49 PDT)
- David A. Case (Mon Jul 02 2007 - 07:44:59 PDT)
- yen li (Sun Jul 01 2007 - 10:36:14 PDT)
- yen li (Sun Jul 01 2007 - 06:10:09 PDT)
AMBER: Problem with running Sander
- Ross Walker (Tue Jul 10 2007 - 16:09:29 PDT)
- David A. Case (Tue Jul 10 2007 - 16:17:56 PDT)
- Lili Peng (Tue Jul 10 2007 - 16:01:11 PDT)
- Lili Peng (Tue Jul 10 2007 - 15:58:22 PDT)
- David A. Case (Tue Jul 10 2007 - 15:39:31 PDT)
- Lili Peng (Tue Jul 10 2007 - 14:50:45 PDT)
- Carlos Simmerling (Sun Jul 08 2007 - 04:28:58 PDT)
- David A. Case (Sat Jul 07 2007 - 21:59:05 PDT)
- Lili Peng (Sat Jul 07 2007 - 16:10:06 PDT)
AMBER: Problems during compilation
- Sébastien Kozlowskyj (Wed Jul 18 2007 - 02:26:06 PDT)
AMBER: Problems simulating a big system
- Jordi Camps (Tue Jul 17 2007 - 02:57:13 PDT)
- David A. Case (Mon Jul 16 2007 - 18:44:09 PDT)
- Jordi Camps (Mon Jul 16 2007 - 04:55:55 PDT)
AMBER: program bug?
- Carlos Simmerling (Thu Jul 12 2007 - 08:32:54 PDT)
- David A. Case (Thu Jul 12 2007 - 08:22:35 PDT)
- M. Maeda (Thu Jul 12 2007 - 04:29:03 PDT)
- Benjamin Juhl (Thu Jul 12 2007 - 00:17:31 PDT)
- M. Maeda (Wed Jul 11 2007 - 21:41:34 PDT)
- M. Maeda (Wed Jul 11 2007 - 21:47:19 PDT)
- David A. Case (Mon Jul 09 2007 - 07:48:35 PDT)
- M. Maeda (Sun Jul 08 2007 - 19:24:58 PDT)
AMBER: ptraj error
- FyD (Fri Jul 20 2007 - 14:21:17 PDT)
AMBER: ptraj: RMS per residues and per time
- Jianyin Shao (Fri Jul 06 2007 - 00:54:06 PDT)
- Sascha Rehm (Tue Jul 03 2007 - 07:03:04 PDT)
AMBER: QM-MM output interpretation
- Ross Walker (Mon Jul 30 2007 - 21:11:50 PDT)
- Francesco Pietra (Mon Jul 30 2007 - 10:59:13 PDT)
- Ross Walker (Mon Jul 30 2007 - 08:51:36 PDT)
- Francesco Pietra (Mon Jul 30 2007 - 07:08:36 PDT)
AMBER: QM/MM LJ parameters
- Ross Walker (Thu Jul 05 2007 - 17:58:49 PDT)
- Evan Kelly (Thu Jul 05 2007 - 16:31:35 PDT)
AMBER: QMMM to follow reaction involving water
- M. L. Dodson (Tue Jul 31 2007 - 08:14:57 PDT)
- Ross Walker (Mon Jul 30 2007 - 21:49:23 PDT)
- Gustavo Seabra (Mon Jul 30 2007 - 12:41:17 PDT)
- M. L. Dodson (Mon Jul 30 2007 - 11:23:14 PDT)
AMBER: question about formatted mdrcrd files...
- Cenk Andac (Sun Jul 22 2007 - 18:37:43 PDT)
- Cenk Andac (Sun Jul 22 2007 - 17:51:02 PDT)
- David A. Case (Sun Jul 22 2007 - 16:30:06 PDT)
- Cenk Andac (Sun Jul 22 2007 - 09:47:45 PDT)
AMBER: question about iwrap
- Kailee (Thu Jul 12 2007 - 06:55:06 PDT)
- Carlos Simmerling (Thu Jul 12 2007 - 06:28:29 PDT)
- Kailee (Thu Jul 12 2007 - 06:17:32 PDT)
- Carlos Simmerling (Thu Jul 12 2007 - 04:34:08 PDT)
- Kailee (Thu Jul 12 2007 - 03:55:28 PDT)
- David A. Case (Wed Jul 11 2007 - 16:24:11 PDT)
- Kailee (Wed Jul 11 2007 - 06:17:29 PDT)
AMBER: Question about NAB (Nucleic Acid Builder)
- David A. Case (Wed Jul 11 2007 - 16:23:05 PDT)
- Cenk Andac (Wed Jul 11 2007 - 01:30:18 PDT)
AMBER: Question on TIP4P model
- Du, Shiyu (Mon Jul 09 2007 - 17:01:58 PDT)
AMBER: RE Amber: Simulated Annealing
- Francesco Pietra (Sat Jul 21 2007 - 08:13:11 PDT)
AMBER: refc error
- Lili Peng (Tue Jul 17 2007 - 15:40:26 PDT)
- Davide Moiani (Tue Jul 17 2007 - 14:00:20 PDT)
- Lili Peng (Tue Jul 17 2007 - 11:35:06 PDT)
- David A. Case (Mon Jul 16 2007 - 17:25:20 PDT)
- Davide Moiani (Mon Jul 16 2007 - 17:17:18 PDT)
- Lili Peng (Mon Jul 16 2007 - 17:08:18 PDT)
- Davide Moiani (Mon Jul 16 2007 - 17:03:42 PDT)
- Lili Peng (Mon Jul 16 2007 - 16:56:11 PDT)
AMBER: regarding distance restraints
- David A. Case (Mon Jul 23 2007 - 07:56:03 PDT)
- Carlos Simmerling (Mon Jul 23 2007 - 04:26:27 PDT)
- gurpreet singh (Mon Jul 23 2007 - 03:46:39 PDT)
AMBER: related to new amber force field
- Carlos Simmerling (Fri Jul 13 2007 - 09:33:12 PDT)
- snoze pa (Fri Jul 13 2007 - 08:57:38 PDT)
AMBER: resp
- hadi behzadi (Tue Jul 31 2007 - 10:15:37 PDT)
- hadi behzadi (Tue Jul 31 2007 - 07:15:15 PDT)
AMBER: RESP charge generation
- FyD (Sun Jul 08 2007 - 03:19:16 PDT)
- Neelanjana Sengupta (Sat Jul 07 2007 - 16:08:07 PDT)
AMBER: RESP_compilation
- FyD (Mon Jul 16 2007 - 15:59:06 PDT)
- FyD (Mon Jul 16 2007 - 15:55:20 PDT)
- Karol Kaszuba (Mon Jul 16 2007 - 12:14:32 PDT)
AMBER: RESP_compilation_IT_WORKS
- Karol Kaszuba (Tue Jul 17 2007 - 01:32:59 PDT)
AMBER: rmsd residue wise
- ravishk kumar (Thu Jul 26 2007 - 06:02:20 PDT)
AMBER: running_RED-III
- FyD (Wed Jul 18 2007 - 18:33:20 PDT)
- Karol Kaszuba (Wed Jul 18 2007 - 12:02:10 PDT)
AMBER: Sander Error
- Colby C (Mon Jul 09 2007 - 08:39:50 PDT)
- Colby C (Tue Jul 03 2007 - 11:21:18 PDT)
AMBER: Saving (.)prepin file
- David A. Case (Tue Jul 10 2007 - 10:45:58 PDT)
- Johnson Agbo (Mon Jul 09 2007 - 11:22:40 PDT)
- Bill Ross (Mon Jul 02 2007 - 14:05:53 PDT)
- David A. Case (Mon Jul 02 2007 - 13:56:57 PDT)
- Johnson Agbo (Mon Jul 02 2007 - 13:35:00 PDT)
AMBER: secstruct command
- Tim Meyer (Fri Jul 20 2007 - 06:55:47 PDT)
- Holger Gohlke (Thu Jul 19 2007 - 11:22:37 PDT)
- Carlos Simmerling (Thu Jul 19 2007 - 10:46:30 PDT)
- Anna Díaz Cirac (Thu Jul 19 2007 - 10:35:42 PDT)
AMBER: Setting nonbonded cutoff to 1
- Ross Walker (Mon Jul 16 2007 - 10:43:28 PDT)
- Hayden Eastwood (Mon Jul 16 2007 - 10:27:45 PDT)
AMBER: SHAKE failure in TI calculation of zero sum model system of "ethane-to-ethane" in water
- Ye Mei (Mon Jul 23 2007 - 06:00:34 PDT)
AMBER: Simulated Annealing - Best way to create randomness
- Seth Lilavivat (Mon Jul 09 2007 - 08:03:29 PDT)
- Francesco Pietra (Sat Jul 07 2007 - 07:56:41 PDT)
AMBER: Simulated annealing - Nudget Elastic Band
- Francesco Pietra (Wed Jul 04 2007 - 06:13:41 PDT)
- Carlos Simmerling (Wed Jul 04 2007 - 03:39:10 PDT)
- Francesco Pietra (Wed Jul 04 2007 - 00:01:58 PDT)
AMBER: Slight_error_on_Compiling_Replica_Exchange
- j j (Wed Jul 04 2007 - 03:13:22 PDT)
- Ye Mei (Wed Jul 04 2007 - 02:30:09 PDT)
- j j (Wed Jul 04 2007 - 01:57:28 PDT)
AMBER: Slow Processor Loads when Using PMEMD
- David A. Case (Mon Jul 02 2007 - 18:24:09 PDT)
- Ross Walker (Mon Jul 02 2007 - 18:42:01 PDT)
- Jonathan Suever (Mon Jul 02 2007 - 17:28:48 PDT)
AMBER: Specific/Non-specific dihedral issue in Amber
- David A. Case (Tue Jul 17 2007 - 16:15:59 PDT)
- Narayanan Veeraraghavan (Tue Jul 17 2007 - 15:01:10 PDT)
- David A. Case (Mon Jul 16 2007 - 17:13:45 PDT)
- Bill Ross (Mon Jul 16 2007 - 16:38:26 PDT)
- Narayanan Veeraraghavan (Mon Jul 16 2007 - 14:35:53 PDT)
- Bill Ross (Mon Jul 09 2007 - 11:48:28 PDT)
- Narayanan Veeraraghavan (Mon Jul 09 2007 - 11:02:38 PDT)
- David A. Case (Mon Jul 09 2007 - 07:58:51 PDT)
- Narayanan Veeraraghavan (Mon Jul 09 2007 - 07:30:44 PDT)
AMBER: Stirp command in ptraj
- Carlos Simmerling (Fri Jul 06 2007 - 09:45:43 PDT)
- priya priya (Fri Jul 06 2007 - 09:41:05 PDT)
- priya priya (Fri Jul 06 2007 - 06:43:13 PDT)
- Steven Winfield (Fri Jul 06 2007 - 06:32:07 PDT)
- priya priya (Fri Jul 06 2007 - 06:27:27 PDT)
- Carlos Simmerling (Fri Jul 06 2007 - 06:14:20 PDT)
- priya priya (Fri Jul 06 2007 - 05:41:22 PDT)
- Steven Winfield (Fri Jul 06 2007 - 05:36:06 PDT)
- Carlos Simmerling (Fri Jul 06 2007 - 05:35:33 PDT)
- priya priya (Fri Jul 06 2007 - 05:33:11 PDT)
AMBER: Substitute for GAFF
- Evan Kelly (Fri Jul 06 2007 - 10:32:50 PDT)
AMBER: surface area over the trajectory
- Carlos Simmerling (Tue Jul 10 2007 - 12:09:51 PDT)
- Mikyung (Tue Jul 10 2007 - 09:20:12 PDT)
- Carlos Simmerling (Tue Jul 10 2007 - 03:33:44 PDT)
- mkseo (Mon Jul 09 2007 - 15:55:18 PDT)
- Carlos Simmerling (Mon Jul 09 2007 - 15:30:54 PDT)
- mkseo (Mon Jul 09 2007 - 14:52:32 PDT)
AMBER: temperature fluctuation in REMD
- David A. Case (Fri Jul 20 2007 - 09:16:46 PDT)
- priya priya (Fri Jul 20 2007 - 08:00:30 PDT)
- Carlos Simmerling (Fri Jul 20 2007 - 07:34:35 PDT)
- priya priya (Fri Jul 20 2007 - 07:23:08 PDT)
- Carlos Simmerling (Fri Jul 20 2007 - 06:57:13 PDT)
- priya priya (Fri Jul 20 2007 - 06:36:12 PDT)
- priya priya (Fri Jul 20 2007 - 06:13:32 PDT)
- Adrian Roitberg (Fri Jul 20 2007 - 05:44:01 PDT)
- Carlos Simmerling (Fri Jul 20 2007 - 05:34:03 PDT)
- priya priya (Fri Jul 20 2007 - 05:11:17 PDT)
- Carlos Simmerling (Fri Jul 20 2007 - 04:44:36 PDT)
- priya priya (Fri Jul 20 2007 - 03:58:48 PDT)
AMBER: testing amber9 for parallel use
- Carlos Simmerling (Thu Jul 05 2007 - 05:22:20 PDT)
- Sally Pias (Wed Jul 04 2007 - 23:47:22 PDT)
AMBER: tgtrmsmask and tgtfitmask
- David A. Case (Tue Jul 10 2007 - 09:01:27 PDT)
- Carlos Simmerling (Tue Jul 10 2007 - 04:26:08 PDT)
- Holly Freedman (Mon Jul 09 2007 - 19:03:39 PDT)
AMBER: thermodynamic data for conformers
- Francesco Pietra (Sun Jul 29 2007 - 10:11:11 PDT)
AMBER: TIP4P MD simulations
- Robert Duke (Mon Jul 09 2007 - 12:35:04 PDT)
- David A. Case (Mon Jul 09 2007 - 11:31:15 PDT)
- Melinda Layten (Mon Jul 09 2007 - 11:05:39 PDT)
- Hashem Taha (Mon Jul 09 2007 - 10:53:28 PDT)
AMBER: Truncated Octahedron box volume
- Ilyas Yildirim (Sun Jul 22 2007 - 19:52:16 PDT)
AMBER: using amber to minimize structure obatined from cyana
- David A. Case (Mon Jul 23 2007 - 07:52:00 PDT)
- Prem Prakash Pathak (Mon Jul 23 2007 - 00:27:26 PDT)
AMBER: Verifying Bond Angles
- Seth Lilavivat (Wed Jul 18 2007 - 14:32:30 PDT)
AMBER: what's the problem of "Missing BELE for MM in 1 (residue 246)" in MM-GBSA?
- tonglei (Sun Jul 29 2007 - 20:45:24 PDT)
AMBER: Who has the structure file of beta-chitin?
- WANG,YING (Tue Jul 03 2007 - 11:19:11 PDT)
AMBER: xleap and amber7
- Saiful Islam (Tue Jul 10 2007 - 05:47:00 PDT)
- Benjamin Juhl (Mon Jul 09 2007 - 00:08:57 PDT)
- Saiful Islam (Fri Jul 06 2007 - 19:23:35 PDT)
- Carlos Simmerling (Thu Jul 05 2007 - 05:23:44 PDT)
- Ilyas Yildirim (Wed Jul 04 2007 - 21:53:37 PDT)
- Saiful Islam (Wed Jul 04 2007 - 20:53:42 PDT)
- Adrian Roitberg (Mon Jul 02 2007 - 07:20:28 PDT)
- Saiful Islam (Mon Jul 02 2007 - 07:05:34 PDT)
- Ross Walker (Sun Jul 01 2007 - 10:33:15 PDT)
- Saiful Islam (Sat Jun 30 2007 - 21:22:43 PDT)
AMBER: 来自pig5678的邮件
- pig5678 (Mon Jul 09 2007 - 23:59:22 PDT)
AMBER:charge file
- umbrita itl (Wed Jul 25 2007 - 08:36:11 PDT)
Contact TSRI: Ross Walker
- Ross Walker (Wed Jul 25 2007 - 08:31:53 PDT)
help:- regarding "perl" in analyzing the simulation
- Ross Walker (Mon Jul 30 2007 - 09:38:33 PDT)
how to create an O linked N-acetylglucosamine in a
- Austin B. Yongye (Mon Jul 16 2007 - 23:22:12 PDT)
how to create an O linked N-acetylglucosamine in a protein
- Karl Kirschner (Tue Jul 17 2007 - 06:39:43 PDT)
- ming hui (Mon Jul 16 2007 - 20:44:08 PDT)
MPI error message
- Ross Walker (Tue Jul 24 2007 - 14:31:12 PDT)
- Gustavo Seabra (Tue Jul 24 2007 - 12:32:52 PDT)
- Taryn Hartley (Tue Jul 24 2007 - 12:00:25 PDT)
Problem with sander.MPI
- Ross Walker (Mon Jul 30 2007 - 07:12:58 PDT)
Query
- Ross Walker (Fri Jul 27 2007 - 08:24:56 PDT)
- Ross Walker (Mon Jul 23 2007 - 08:13:13 PDT)
RED problem
- FyD (Mon Jul 23 2007 - 05:08:14 PDT)
- Sergey Samsonov (Mon Jul 23 2007 - 04:35:32 PDT)
SV: AMBER: Atoms in contact to a specific atoms during MD
- Bill Ross (Mon Jul 16 2007 - 12:49:45 PDT)
- Mark Williamson (Mon Jul 16 2007 - 08:18:00 PDT)
- Rafi Ahmad (Mon Jul 16 2007 - 08:04:46 PDT)

Amber Archive Jul 2007 by subject