Amber Archive Feb 2009: by subject

[AMBER] (no subject)
- Carlos Simmerling (Thu Feb 26 2009 - 08:24:40 PST)
- Lake, Thomas (Thu Feb 26 2009 - 08:19:53 PST)
- Thomas Cheatham III (Wed Feb 25 2009 - 16:48:56 PST)
- waleed zalloum (Wed Feb 25 2009 - 08:41:14 PST)
- Beale, John (Tue Feb 24 2009 - 03:59:51 PST)
- Andrew Olson (Thu Feb 19 2009 - 11:46:24 PST)
- Carlos Simmerling (Tue Feb 17 2009 - 05:10:49 PST)
- Beale, John (Tue Feb 17 2009 - 05:02:25 PST)
[AMBER] (NTB /= 0 && NTP /= 0) but IFBOX == 0 error
- David A. Case (Wed Feb 18 2009 - 12:35:12 PST)
- Majeed Shaik (Wed Feb 18 2009 - 12:09:17 PST)
[AMBER] -MMTSB instalation flag ?
- Scott Brozell (Tue Feb 03 2009 - 09:38:11 PST)
- Marek Malý (Tue Feb 03 2009 - 09:15:04 PST)
- Scott Brozell (Tue Feb 03 2009 - 09:06:47 PST)
- Marek Malý (Tue Feb 03 2009 - 07:31:38 PST)
[AMBER] ./configure_amber: line 1211: cd: netcdf/src: No such file or directory
- David A. Case (Wed Feb 18 2009 - 10:11:56 PST)
- Andrew Olson (Wed Feb 18 2009 - 09:08:57 PST)
[AMBER] A beginner's question for using AMBER to do cell membrane simulation and molecular transportation
- Xu Dong (Sat Feb 21 2009 - 13:40:03 PST)
- Carlos Simmerling (Sat Feb 21 2009 - 13:33:31 PST)
- Xu Dong (Sat Feb 21 2009 - 12:27:29 PST)
[AMBER] A problem with xleap and pdb file
- Ross Walker (Fri Feb 27 2009 - 07:55:23 PST)
- Peter Gannett (Fri Feb 27 2009 - 06:32:20 PST)
- nancy4619 (Fri Feb 27 2009 - 06:20:17 PST)
- David A. Case (Fri Feb 27 2009 - 05:56:26 PST)
- nancy4619 (Fri Feb 27 2009 - 04:28:01 PST)
[AMBER] a query
- Molecular Dynamics (Sat Feb 28 2009 - 11:45:46 PST)
[AMBER] a question about umbrella sampling (US)
- xiaoqin huang (Wed Feb 04 2009 - 14:23:12 PST)
- Carlos Simmerling (Wed Feb 04 2009 - 09:20:46 PST)
- xiaoqin huang (Wed Feb 04 2009 - 09:12:02 PST)
[AMBER] About the croase grainded FF
- Vlad Cojocaru (Tue Feb 24 2009 - 00:40:53 PST)
- James W (Mon Feb 23 2009 - 23:58:12 PST)
[AMBER] ACS computational chemistry awards - March 9th deadline
- Carlos Simmerling (Fri Feb 20 2009 - 08:27:18 PST)
[AMBER] adding MG2 problem
- Rausch, Felix (Wed Feb 04 2009 - 05:04:51 PST)
- Scott Brozell (Tue Feb 03 2009 - 11:09:32 PST)
[AMBER] Amber 9 Install - AMBERBUILDFLAGS error
- David A. Case (Mon Feb 16 2009 - 20:29:41 PST)
- ben rodriguez (Mon Feb 16 2009 - 19:39:14 PST)
[AMBER] amber tools reading netcdf files
- Cojocaru,Vlad (Tue Feb 24 2009 - 10:46:27 PST)
- Chris Moth (Tue Feb 24 2009 - 09:35:22 PST)
- Jeremy Harris (Tue Feb 24 2009 - 07:54:09 PST)
[AMBER] amber9 installation problem in SMP IA64
- Ross Walker (Thu Feb 12 2009 - 06:54:49 PST)
- Vijay Manickam Achari (Thu Feb 12 2009 - 01:21:01 PST)
- Vijay Manickam Achari (Thu Feb 12 2009 - 01:13:55 PST)
- David A. Case (Wed Feb 11 2009 - 05:07:48 PST)
- Vijay Manickam Achari (Wed Feb 11 2009 - 01:36:31 PST)
- Ross Walker (Tue Feb 10 2009 - 09:56:22 PST)
- David A. Case (Tue Feb 10 2009 - 04:41:29 PST)
- Vijay Manickam Achari (Tue Feb 10 2009 - 00:30:55 PST)
- David A. Case (Fri Feb 06 2009 - 05:25:55 PST)
- Vijay Manickam Achari (Thu Feb 05 2009 - 23:00:16 PST)
[AMBER] AMBER: chiral restraint on protein
- David A. Case (Wed Feb 11 2009 - 04:56:05 PST)
- amit jain (Tue Feb 10 2009 - 16:48:12 PST)
[AMBER] Antechamber
- kureeckal ramesh (Thu Feb 19 2009 - 17:36:03 PST)
[AMBER] Any link to a major QM code?
- Gustavo Seabra (Mon Feb 16 2009 - 08:51:03 PST)
- Francesco Pietra (Mon Feb 16 2009 - 06:47:04 PST)
- Adrian Roitberg (Sun Feb 15 2009 - 18:59:01 PST)
- Gustavo Seabra (Sun Feb 15 2009 - 16:17:32 PST)
- Francesco Pietra (Sun Feb 15 2009 - 09:58:30 PST)
[AMBER] APS & ff03
- Mahmoud A. A. Ibrahim (Mon Feb 09 2009 - 06:49:56 PST)
[AMBER] array out of bound in Amber10 tests
- Shan-ho Tsai (Mon Feb 16 2009 - 08:53:05 PST)
- Carlos Simmerling (Fri Feb 13 2009 - 08:38:04 PST)
- Shan-ho Tsai (Wed Feb 11 2009 - 14:24:10 PST)
- Carlos Simmerling (Wed Feb 11 2009 - 08:14:49 PST)
- Shan-ho Tsai (Wed Feb 11 2009 - 07:38:23 PST)
- David A. Case (Tue Feb 10 2009 - 13:30:36 PST)
- Shan-ho Tsai (Tue Feb 10 2009 - 13:04:43 PST)
- David A. Case (Tue Feb 10 2009 - 08:39:43 PST)
- Shan-ho Tsai (Tue Feb 10 2009 - 08:19:42 PST)
[AMBER] atoms fly out of the box in NVT calculations
- iccy liu (Sun Feb 15 2009 - 15:34:37 PST)
- Ross Walker (Thu Feb 12 2009 - 18:22:57 PST)
- Carlos Simmerling (Thu Feb 12 2009 - 14:05:10 PST)
- iccy liu (Thu Feb 12 2009 - 13:48:24 PST)
[AMBER] Beginner question
- Heath Watts (Fri Feb 13 2009 - 17:20:46 PST)
- Heath Watts (Fri Feb 13 2009 - 17:19:44 PST)
- Barbault Florent (Fri Feb 13 2009 - 13:25:13 PST)
- Carlos Simmerling (Fri Feb 13 2009 - 13:24:37 PST)
- Heath Watts (Fri Feb 13 2009 - 13:18:42 PST)
[AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint?
- liu junjun (Mon Feb 02 2009 - 08:25:41 PST)
- David A. Case (Sun Feb 01 2009 - 10:35:03 PST)
- Carlos Simmerling (Sun Feb 01 2009 - 09:55:54 PST)
- liu junjun (Sat Jan 31 2009 - 23:51:39 PST)
[AMBER] can ptraj output the trajectory of the residue CM?
- Jose Borreguero (Mon Feb 16 2009 - 11:47:34 PST)
[AMBER] Chlorine containing molecule
- Carlos Simmerling (Wed Feb 11 2009 - 05:48:27 PST)
- CHAMI F. (Wed Feb 11 2009 - 05:39:19 PST)
[AMBER] Citing AMBER Tools...
- David A. Case (Thu Feb 05 2009 - 07:44:37 PST)
- Aydin, Cihan (Sat Jan 31 2009 - 21:08:36 PST)
[AMBER] Compiling Carnal Amber7 in Amber9
- Bill Ross (Thu Feb 12 2009 - 12:32:29 PST)
- Ross Walker (Thu Feb 12 2009 - 06:55:54 PST)
- David A. Case (Thu Feb 12 2009 - 04:58:03 PST)
- Vijay Manickam Achari (Thu Feb 12 2009 - 01:12:29 PST)
- Bill Ross (Wed Feb 11 2009 - 11:04:53 PST)
- Ross Walker (Wed Feb 11 2009 - 08:53:10 PST)
- Vijay Manickam Achari (Tue Feb 10 2009 - 23:58:08 PST)
- Bill Ross (Thu Feb 05 2009 - 09:36:00 PST)
- Vijay Manickam Achari (Wed Feb 04 2009 - 19:21:14 PST)
[AMBER] compiling errors
- Ross Walker (Wed Feb 04 2009 - 16:48:14 PST)
- Carlos Simmerling (Wed Feb 04 2009 - 16:35:28 PST)
- Gard Nelson (Wed Feb 04 2009 - 16:30:22 PST)
[AMBER] Confusion regarding box size
- parul sharma (Tue Feb 10 2009 - 05:29:38 PST)
- Wei Zhang (Tue Feb 10 2009 - 05:07:38 PST)
- vallespardojl.chem.leidenuniv.nl (Tue Feb 10 2009 - 00:35:24 PST)
- parul sharma (Mon Feb 09 2009 - 23:20:01 PST)
[AMBER] constph tutorial help
- Prem Prakash Pathak (Tue Feb 17 2009 - 04:53:37 PST)
[AMBER] contant force pulling simulation with amber 10
- Gustavo Seabra (Mon Feb 16 2009 - 10:11:40 PST)
- li hui (Mon Feb 16 2009 - 09:01:36 PST)
[AMBER] creating a restart file from md.out
- Carlos Simmerling (Tue Feb 03 2009 - 07:34:44 PST)
- oguz gurbulak (Tue Feb 03 2009 - 07:29:47 PST)
- Carlos Simmerling (Tue Feb 03 2009 - 05:36:44 PST)
- oguz gurbulak (Tue Feb 03 2009 - 05:22:45 PST)
- Carlos Simmerling (Tue Feb 03 2009 - 03:30:44 PST)
- oguz gurbulak (Tue Feb 03 2009 - 02:44:10 PST)
[AMBER] Current Amber10 bugfix.all doesn't apply cleanly
- Mark Dixon (Fri Feb 27 2009 - 08:44:28 PST)
- Mark Dixon (Thu Feb 26 2009 - 03:54:03 PST)
[AMBER] density and volume in NVT ensamble
- Andrew Purkiss-Trew (Mon Feb 16 2009 - 06:45:25 PST)
- oguz gurbulak (Mon Feb 16 2009 - 06:32:07 PST)
- Adrian Roitberg (Fri Feb 06 2009 - 06:31:24 PST)
- Carlos Simmerling (Mon Feb 16 2009 - 06:30:02 PST)
- oguz gurbulak (Mon Feb 16 2009 - 06:27:01 PST)
- oguz gurbulak (Mon Feb 16 2009 - 06:25:52 PST)
- Andrew Purkiss-Trew (Mon Feb 16 2009 - 06:14:40 PST)
- Carlos Simmerling (Mon Feb 16 2009 - 06:04:22 PST)
- oguz gurbulak (Mon Feb 16 2009 - 05:58:13 PST)
[AMBER] DFT SK parameter for P atom
- Qizhi Cui (Mon Feb 02 2009 - 13:37:41 PST)
- Adrian Roitberg (Mon Feb 02 2009 - 12:24:00 PST)
- Qizhi Cui (Mon Feb 02 2009 - 11:59:19 PST)
[AMBER] dipole correlation function
- Jeffrey (Thu Feb 19 2009 - 17:31:08 PST)
- Carlos Simmerling (Thu Feb 19 2009 - 09:23:03 PST)
- Jeffrey (Thu Feb 19 2009 - 08:39:15 PST)
- Carlos Simmerling (Thu Feb 19 2009 - 06:39:16 PST)
- Jeffrey (Thu Feb 19 2009 - 06:18:20 PST)
[AMBER] distance calculation by reading in the restraint file
- xiaoqin huang (Fri Feb 06 2009 - 15:28:59 PST)
- David A. Case (Fri Feb 06 2009 - 14:35:55 PST)
- David A. Case (Fri Feb 06 2009 - 14:03:08 PST)
- xiaoqin huang (Fri Feb 06 2009 - 10:34:34 PST)
- xiaoqin huang (Fri Feb 06 2009 - 09:52:56 PST)
[AMBER] distance matrix plot and secondary structure analysis
- Carlos Simmerling (Thu Feb 19 2009 - 04:48:57 PST)
- Siddharth Rastogi (Wed Feb 18 2009 - 22:17:47 PST)
[AMBER] DM complexation
- Carlos Simmerling (Tue Feb 17 2009 - 07:59:15 PST)
- . .. (Tue Feb 17 2009 - 07:36:01 PST)
- Carlos Simmerling (Tue Feb 17 2009 - 07:28:34 PST)
- . .. (Tue Feb 17 2009 - 07:10:49 PST)
[AMBER] Dr. Ramesh here
- kureeckal ramesh (Mon Feb 02 2009 - 06:22:51 PST)
[AMBER] Equilibration Scaling to System Size
- Carlos Simmerling (Tue Feb 24 2009 - 14:49:10 PST)
- Hopkins, Robert (Tue Feb 24 2009 - 14:31:37 PST)
[AMBER] error in executing sander.MPI in amber9
- Atro Tossavainen (Thu Feb 05 2009 - 03:08:59 PST)
- Vijay Manickam Achari (Thu Feb 05 2009 - 00:37:09 PST)
[AMBER] Error in using Amber
- sri noraima othman (Wed Feb 25 2009 - 22:27:14 PST)
- Ross Walker (Wed Feb 25 2009 - 22:03:12 PST)
- sri noraima othman (Wed Feb 25 2009 - 19:27:29 PST)
[AMBER] error in xleap: ligand binding using MMand QMMM tech
- Gustavo Seabra (Thu Feb 12 2009 - 06:32:17 PST)
- kureeckal ramesh (Thu Feb 12 2009 - 02:27:41 PST)
[AMBER] Error installing Amber
- David Patiño (Tue Feb 17 2009 - 06:58:05 PST)
- David A. Case (Mon Feb 16 2009 - 06:21:41 PST)
- David Patiño (Mon Feb 16 2009 - 04:02:31 PST)
[AMBER] Error running sander.MPI
- Anselm Horn (Tue Feb 17 2009 - 02:28:47 PST)
- Rausch, Felix (Tue Feb 17 2009 - 00:15:19 PST)
- Carlos Simmerling (Mon Feb 16 2009 - 03:51:08 PST)
- Vijay Manickam Achari (Mon Feb 16 2009 - 00:23:05 PST)
[AMBER] extra torsion terms in tleap.top-file
- Astrid Maaß (Thu Feb 26 2009 - 06:32:30 PST)
[AMBER] extract frames from a .mdcrd
- Carlos Simmerling (Tue Feb 10 2009 - 02:58:12 PST)
- vallespardojl.chem.leidenuniv.nl (Tue Feb 10 2009 - 00:52:19 PST)
- Bill Ross (Fri Feb 06 2009 - 11:13:27 PST)
- Carlos Simmerling (Fri Feb 06 2009 - 03:12:00 PST)
- vallespardojl.chem.leidenuniv.nl (Fri Feb 06 2009 - 02:48:23 PST)
[AMBER] follow-up to previous discussion: nmr refinement of dimer
- David A. Case (Tue Feb 24 2009 - 05:15:27 PST)
- Sally Pias (Mon Feb 23 2009 - 23:50:41 PST)
[AMBER] formate parameters
- Dmitri Nilov (Tue Feb 10 2009 - 06:47:31 PST)
[AMBER] g(r) extrapolation
- Lorenzo Gontrani (Thu Feb 19 2009 - 01:23:19 PST)
- Thomas Cheatham III (Wed Feb 18 2009 - 09:15:36 PST)
- Lorenzo Gontrani (Wed Feb 18 2009 - 07:16:26 PST)
[AMBER] glycam and solvateoct command
- Lachele Foley (Lists) (Wed Feb 18 2009 - 07:00:34 PST)
- Heath Watts (Tue Feb 17 2009 - 14:31:35 PST)
- Barbault Florent (Tue Feb 17 2009 - 12:13:58 PST)
- Heath Watts (Tue Feb 17 2009 - 11:51:13 PST)
[AMBER] H-bond information
- Beale, John (Thu Feb 12 2009 - 07:32:30 PST)
[AMBER] H-Bonds
- Beale, John (Thu Feb 26 2009 - 06:38:04 PST)
[AMBER] hbond analysis
- Carlos Simmerling (Mon Feb 09 2009 - 10:52:14 PST)
- Bala subramanian (Mon Feb 09 2009 - 10:33:39 PST)
- aneesh cna (Mon Feb 09 2009 - 09:55:25 PST)
[AMBER] how can i deal with large number atoms
- Wang,Ying (Wed Feb 04 2009 - 21:04:23 PST)
[AMBER] How to build reference coordinate file for targeted MD
- Ross Walker (Fri Feb 06 2009 - 00:14:14 PST)
- gmail (Thu Feb 05 2009 - 21:20:59 PST)
- xiaonan zhang (Thu Feb 05 2009 - 04:00:38 PST)
- Carlos Simmerling (Thu Feb 05 2009 - 03:19:12 PST)
- gmail (Wed Feb 04 2009 - 22:44:22 PST)
[AMBER] How to constrain the hydrogen bonding distances...
- David A. Case (Wed Feb 18 2009 - 06:28:56 PST)
- Carlos Simmerling (Wed Feb 18 2009 - 06:25:47 PST)
- Majeed Shaik (Wed Feb 18 2009 - 06:11:37 PST)
[AMBER] how to get amber 10
- Ross Walker (Tue Feb 10 2009 - 19:20:33 PST)
- Prem Prakash Pathak (Tue Feb 10 2009 - 18:42:37 PST)
[AMBER] How to get the energy of a molecule in a whole system
- Wang,Ying (Tue Feb 17 2009 - 08:28:39 PST)
[AMBER] How to jude whether the trajectory is stable or not
- Jeffrey (Thu Feb 12 2009 - 18:33:53 PST)
[AMBER] I need a professional help about xleap and pdb file
- Peter Gannett (Fri Feb 27 2009 - 06:17:31 PST)
- nancy4619 (Fri Feb 27 2009 - 05:56:14 PST)
[AMBER] IG not change at each restart of NPT simulation
- Adrian Roitberg (Wed Feb 18 2009 - 06:46:36 PST)
- Robert Duke (Wed Feb 18 2009 - 06:15:00 PST)
- Carlos Simmerling (Wed Feb 18 2009 - 06:04:47 PST)
- Robert Duke (Wed Feb 18 2009 - 05:57:35 PST)
- Jeffrey (Wed Feb 18 2009 - 04:49:47 PST)
[AMBER] IMPORTANT INFO: Regarding Anonymous postings to the AMBER mailing list.
- Ross Walker (Sat Feb 28 2009 - 14:19:16 PST)
[AMBER] install Amber 10 to Macbook
- David Watson (Sun Feb 15 2009 - 11:52:36 PST)
- Tyler Luchko (Sun Feb 15 2009 - 11:27:53 PST)
- David A. Case (Sat Feb 14 2009 - 15:17:53 PST)
- Adrien Delmont (Sat Feb 14 2009 - 03:06:50 PST)
[AMBER] Iron 2+ parameters
- FyD (Mon Feb 16 2009 - 10:25:45 PST)
- Syed Tarique Moin (Mon Feb 16 2009 - 08:25:34 PST)
- Hrvoje Brkić (Mon Feb 16 2009 - 05:53:57 PST)
[AMBER] Irregularity in box during md
- Bill Ross (Tue Feb 10 2009 - 09:24:12 PST)
- Carlos Simmerling (Tue Feb 10 2009 - 02:57:02 PST)
- parul sharma (Tue Feb 10 2009 - 02:35:18 PST)
[AMBER] Langevin dynamics
- David A. Case (Mon Feb 02 2009 - 11:24:59 PST)
- Antonios Samiotakis (Mon Feb 02 2009 - 09:54:31 PST)
[AMBER] linux install problem
- Gustavo Seabra (Thu Feb 19 2009 - 12:47:18 PST)
- Andrew Olson (Thu Feb 19 2009 - 10:44:14 PST)
[AMBER] MD analysis
- oguz gurbulak (Sat Feb 07 2009 - 06:56:10 PST)
[AMBER] MD simulation at constant pH
- Francesco Pietra (Thu Feb 26 2009 - 02:52:47 PST)
[AMBER] md simulation on parallel PMEMD
- Robert Duke (Mon Feb 02 2009 - 06:03:59 PST)
- Carlos Simmerling (Mon Feb 02 2009 - 05:55:44 PST)
- David A. Case (Mon Feb 02 2009 - 05:54:58 PST)
- oguz gurbulak (Mon Feb 02 2009 - 05:32:31 PST)
[AMBER] MD simulation with a partially flexible system
- Carlos Simmerling (Wed Feb 18 2009 - 04:35:40 PST)
- Jeffrey (Tue Feb 17 2009 - 18:19:47 PST)
- Carlos Simmerling (Tue Feb 17 2009 - 06:45:33 PST)
- Jeffrey (Tue Feb 17 2009 - 06:38:10 PST)
[AMBER] MD simulations on a protein with FAD and NADH
- FyD (Fri Feb 27 2009 - 00:24:37 PST)
- Ross Walker (Thu Feb 26 2009 - 20:32:05 PST)
- Mannan (Thu Feb 26 2009 - 17:11:54 PST)
[AMBER] Micelles set-up??
- Alexander Schierholt (Tue Feb 03 2009 - 02:09:52 PST)
[AMBER] MKL error ?
- Marek Malý (Thu Feb 05 2009 - 12:00:10 PST)
- Ross Walker (Thu Feb 05 2009 - 10:29:45 PST)
- Marek Malý (Thu Feb 05 2009 - 04:26:05 PST)
- Ross Walker (Tue Feb 03 2009 - 21:22:48 PST)
- Marek Malý (Tue Feb 03 2009 - 15:00:03 PST)
[AMBER] mpirun problem in HPC
- Ross Walker (Fri Feb 06 2009 - 00:05:37 PST)
- Vijay Manickam Achari (Thu Feb 05 2009 - 23:01:29 PST)
[AMBER] MSD and stress tensors
- oguz gurbulak (Fri Feb 06 2009 - 03:09:12 PST)
[AMBER] nab compile error with -scalapack
- chaitanya koppisetty (Tue Feb 03 2009 - 10:52:54 PST)
- David A. Case (Tue Feb 03 2009 - 06:27:24 PST)
- chaitanya koppisetty (Tue Feb 03 2009 - 05:23:46 PST)
[AMBER] NAB md function prints strange output
- David A. Case (Tue Feb 10 2009 - 04:46:40 PST)
- Jochen Heil (Tue Feb 10 2009 - 04:19:56 PST)
- David A. Case (Mon Feb 09 2009 - 04:58:43 PST)
- Jochen Heil (Mon Feb 09 2009 - 03:30:21 PST)
[AMBER] Need suggestion on payment for Ph.D student majored in molecular simulation
- Adrian Roitberg (Tue Feb 17 2009 - 10:57:56 PST)
- Xu Dong (Tue Feb 17 2009 - 10:54:58 PST)
[AMBER] New atom type with 7 bonds
- David A. Case (Mon Feb 16 2009 - 06:28:25 PST)
- Akansha Saxena (Fri Feb 13 2009 - 15:56:47 PST)
[AMBER] nmr refinement of dimer
- David A. Case (Thu Feb 12 2009 - 05:08:08 PST)
- Sally Pias (Thu Feb 12 2009 - 01:17:44 PST)
- David A. Case (Wed Feb 11 2009 - 05:02:37 PST)
- Therese Malliavin (Wed Feb 11 2009 - 02:57:06 PST)
- Sally Pias (Wed Feb 11 2009 - 01:05:56 PST)
[AMBER] non bonded parameteters index
- Adrian Roitberg (Thu Feb 12 2009 - 16:15:33 PST)
- Alessandro Nascimento (Thu Feb 12 2009 - 16:14:44 PST)
- Swarup Gupta (Thu Feb 12 2009 - 16:07:46 PST)
[AMBER] Normal errors on job kill?
- David A. Case (Mon Feb 16 2009 - 20:25:54 PST)
- ben rodriguez (Mon Feb 16 2009 - 18:35:43 PST)
[AMBER] NVT vs NPT
- Carlos Simmerling (Wed Feb 18 2009 - 04:18:49 PST)
- Chih-Ying Lin (Tue Feb 17 2009 - 19:23:05 PST)
[AMBER] Optimization problem
- Gustavo Seabra (Thu Feb 12 2009 - 06:48:23 PST)
- David A. Case (Thu Feb 12 2009 - 06:35:52 PST)
- Carlos Simmerling (Thu Feb 12 2009 - 06:21:28 PST)
- Daniel Emery (Thu Feb 12 2009 - 06:11:14 PST)
- David A. Case (Thu Feb 12 2009 - 04:58:17 PST)
- Daniel Emery (Thu Feb 12 2009 - 02:01:49 PST)
[AMBER] order of "upper" and "lower" bounds in the makeDIS_RST inputs
- David A. Case (Sat Feb 21 2009 - 15:51:38 PST)
- Piotr Cieplak (Fri Feb 20 2009 - 13:40:14 PST)
[AMBER] out error
- Carlos Simmerling (Tue Feb 03 2009 - 11:18:39 PST)
- . .. (Tue Feb 03 2009 - 10:58:46 PST)
[AMBER] paper of interest for FF development/solvent models
- David Mobley (Thu Feb 19 2009 - 07:15:04 PST)
[AMBER] parallel run error
- Carlos Simmerling (Tue Feb 17 2009 - 04:40:03 PST)
- balaji nagarajan (Tue Feb 17 2009 - 00:19:23 PST)
[AMBER] parameter files for D-amino acid
- Carlos Simmerling (Thu Feb 05 2009 - 07:10:18 PST)
- Andrew Purkiss-Trew (Thu Feb 05 2009 - 07:02:25 PST)
- Carlos Simmerling (Thu Feb 05 2009 - 07:06:09 PST)
- FyD (Thu Feb 05 2009 - 07:00:55 PST)
- vijayaraj.clri.res.in (Thu Feb 05 2009 - 06:49:56 PST)
- Carlos Simmerling (Thu Feb 05 2009 - 05:37:32 PST)
- Vsatheesh Patil (Thu Feb 05 2009 - 05:04:12 PST)
[AMBER] parmchk
- Ross Walker (Mon Feb 09 2009 - 08:28:20 PST)
- s. Bill (Mon Feb 09 2009 - 07:55:20 PST)
[AMBER] Parmchk wrongly calculates missing parameters (fwd)
- Gijs Schaftenaar (Fri Feb 20 2009 - 05:16:17 PST)
[AMBER] Partial entropy calculations ?
- Piotr Cieplak (Fri Feb 27 2009 - 10:44:21 PST)
- Marek Malý (Fri Feb 27 2009 - 10:21:29 PST)
[AMBER] PCL
- Ross Walker (Sat Feb 28 2009 - 09:23:30 PST)
- waleed zalloum (Sat Feb 28 2009 - 09:17:51 PST)
[AMBER] PDB of a specific frame
- Carlos Simmerling (Wed Feb 04 2009 - 11:52:49 PST)
- Jason A. Ford-Green (Wed Feb 04 2009 - 11:46:52 PST)
[AMBER] perform an analysis using ptraj
- oguz gurbulak (Tue Feb 24 2009 - 08:19:11 PST)
[AMBER] PLUMED release 1.0.0 available
- Massimiliano Bonomi (Thu Feb 26 2009 - 05:11:54 PST)
[AMBER] PME doesn't work
- Robert Duke (Mon Feb 23 2009 - 05:48:04 PST)
- Carlos Simmerling (Mon Feb 23 2009 - 04:08:07 PST)
- parul sharma (Mon Feb 23 2009 - 04:03:54 PST)
- Carlos Simmerling (Mon Feb 23 2009 - 03:19:27 PST)
- parul sharma (Mon Feb 23 2009 - 01:43:40 PST)
[AMBER] pmemd installation in intelmpi
- Vijay Manickam Achari (Thu Feb 05 2009 - 00:38:38 PST)
- Robert Duke (Wed Feb 04 2009 - 20:34:37 PST)
- Vijay Manickam Achari (Wed Feb 04 2009 - 19:16:06 PST)
[AMBER] pmemd on BlueGene/P?
- Hannes Loeffler (Fri Feb 06 2009 - 01:01:37 PST)
- Carlos P Sosa (Thu Feb 05 2009 - 12:48:57 PST)
- Robert Duke (Thu Feb 05 2009 - 05:42:32 PST)
- Hannes Loeffler (Thu Feb 05 2009 - 05:09:45 PST)
[AMBER] PMEMD vs GROMACS?
- Sasha Buzko (Tue Feb 24 2009 - 09:15:59 PST)
- Vlad Cojocaru (Tue Feb 24 2009 - 00:46:36 PST)
- Hannes Loeffler (Tue Feb 24 2009 - 00:39:29 PST)
- Vlad Cojocaru (Tue Feb 24 2009 - 00:24:16 PST)
- Sasha Buzko (Mon Feb 23 2009 - 11:55:27 PST)
[AMBER] PMF calculation
- David A. Case (Tue Feb 17 2009 - 18:23:20 PST)
- Arnaud (Tue Feb 17 2009 - 10:10:18 PST)
[AMBER] precision in the trajectory files
- Jenny Iskrenova (Tue Feb 03 2009 - 09:07:58 PST)
- David A. Case (Mon Feb 02 2009 - 06:55:40 PST)
- Adrian Roitberg (Mon Feb 02 2009 - 06:46:49 PST)
- Jenny Iskrenova (Mon Feb 02 2009 - 06:43:38 PST)
[AMBER] problem about trajectory analysis
- Thomas Cheatham III (Wed Feb 25 2009 - 16:57:49 PST)
- Adrien Delmont (Wed Feb 25 2009 - 06:24:41 PST)
[AMBER] problem compiling nmode.c
- Shan-ho Tsai (Thu Feb 19 2009 - 06:49:39 PST)
- David A. Case (Tue Feb 17 2009 - 18:45:03 PST)
- Shan-ho Tsai (Tue Feb 17 2009 - 12:38:00 PST)
[AMBER] problem with amber installation
- Ross Walker (Wed Feb 25 2009 - 07:05:26 PST)
- David A. Case (Wed Feb 25 2009 - 04:45:01 PST)
- Carlos Simmerling (Wed Feb 25 2009 - 03:25:34 PST)
- nicholus bhattacharjee (Tue Feb 24 2009 - 20:29:11 PST)
- Carlos Simmerling (Tue Feb 24 2009 - 03:47:20 PST)
- nicholus bhattacharjee (Mon Feb 23 2009 - 22:50:12 PST)
[AMBER] Problem with NVT and NPT
- Carlos Simmerling (Fri Feb 20 2009 - 05:30:26 PST)
- parul sharma (Fri Feb 20 2009 - 05:27:51 PST)
- Adrian Roitberg (Fri Feb 20 2009 - 05:14:23 PST)
- parul sharma (Fri Feb 20 2009 - 05:07:36 PST)
[AMBER] production run terminates due to (*) symbols in xxx.rst
- Vijay Manickam Achari (Thu Feb 05 2009 - 18:50:20 PST)
- Ross Walker (Thu Feb 05 2009 - 10:58:41 PST)
- Bill Ross (Thu Feb 05 2009 - 09:42:55 PST)
- Vijay Manickam Achari (Thu Feb 05 2009 - 02:58:26 PST)
- vallespardojl.chem.leidenuniv.nl (Thu Feb 05 2009 - 02:28:33 PST)
- Vijay Manickam Achari (Wed Feb 04 2009 - 20:17:38 PST)
[AMBER] projections of trajectories onto the first 2 principal eigenvectors
- Hannes Loeffler (Fri Feb 13 2009 - 01:33:19 PST)
- Hannes Loeffler (Fri Feb 13 2009 - 00:32:20 PST)
- Carra, Claudio (JSC-SK)[USRA] (Thu Feb 12 2009 - 10:22:20 PST)
[AMBER] protein monomerizartion times and simulation with implicit solvent
- Carlos Simmerling (Wed Feb 18 2009 - 04:16:00 PST)
- drugdesign (Wed Feb 18 2009 - 02:27:17 PST)
[AMBER] Protein motions comparison
- Hannes Loeffler (Thu Feb 19 2009 - 04:07:47 PST)
- Dmitry Osolodkin (Thu Feb 19 2009 - 03:58:24 PST)
[AMBER] ptraj analyze
- Thomas Cheatham III (Wed Feb 25 2009 - 16:45:17 PST)
- Beale, John (Wed Feb 25 2009 - 08:56:59 PST)
[AMBER] ptraj fails to recognize binary REMD output
- Kevin Wiehe (Fri Feb 06 2009 - 09:44:21 PST)
[AMBER] Question about improper torsions...
- David A. Case (Sat Feb 14 2009 - 05:32:21 PST)
- Antonios Samiotakis (Fri Feb 13 2009 - 14:57:03 PST)
[AMBER] Question about NAB module
- Wei Huang (Sat Feb 28 2009 - 16:23:49 PST)
[AMBER] question about ptraj hydrogen bond analysis
- Thomas Cheatham III (Wed Feb 18 2009 - 12:21:27 PST)
- monica bhattacharee (Wed Feb 18 2009 - 11:45:17 PST)
[AMBER] Question on heating for homology based model.
- Carlos Simmerling (Sun Feb 01 2009 - 09:47:02 PST)
[AMBER] Radius of Gyration
- priya priya (Tue Feb 03 2009 - 21:30:07 PST)
- Beale, John (Mon Feb 02 2009 - 09:34:35 PST)
[AMBER] RED-vIII: Scratch directory for Gaussian [NOT FOUND]
- FyD (Tue Feb 10 2009 - 07:05:56 PST)
- Patrick Schopf (Tue Feb 10 2009 - 06:15:42 PST)
[AMBER] reg . run TMD
- Carlos Simmerling (Tue Feb 10 2009 - 09:48:22 PST)
- balaji nagarajan (Tue Feb 10 2009 - 09:36:28 PST)
[AMBER] reg.targeted molecular dynamics
- Ross Walker (Fri Feb 27 2009 - 07:11:44 PST)
- balaji nagarajan (Fri Feb 27 2009 - 02:28:02 PST)
- Ross Walker (Wed Feb 25 2009 - 07:12:29 PST)
- Carlos Simmerling (Wed Feb 25 2009 - 03:21:39 PST)
- balaji nagarajan (Wed Feb 25 2009 - 01:34:57 PST)
- balaji nagarajan (Wed Feb 25 2009 - 01:18:10 PST)
- Carlos Simmerling (Mon Feb 23 2009 - 03:16:00 PST)
- balaji nagarajan (Sun Feb 22 2009 - 22:45:18 PST)
- Carlos Simmerling (Sun Feb 22 2009 - 07:06:32 PST)
- balaji nagarajan (Sun Feb 22 2009 - 06:45:29 PST)
- Carlos Simmerling (Sat Feb 21 2009 - 04:35:05 PST)
- balaji nagarajan (Fri Feb 20 2009 - 21:10:50 PST)
- balaji nagarajan (Wed Feb 18 2009 - 06:07:09 PST)
- Simon Becker (Wed Feb 18 2009 - 03:38:54 PST)
- balaji nagarajan (Tue Feb 17 2009 - 21:26:49 PST)
[AMBER] REM_hybrid test fails on AIX
- Shan-ho Tsai (Thu Feb 05 2009 - 08:44:43 PST)
[AMBER] REMD fixed atoms
- Carlos Simmerling (Sun Feb 01 2009 - 10:00:33 PST)
[AMBER] Resp charge
- Jason A. Ford-Green (Fri Feb 06 2009 - 12:38:29 PST)
- . .. (Fri Feb 06 2009 - 09:34:12 PST)
[AMBER] Restarting an MD Simulation
- Ross Walker (Wed Feb 04 2009 - 19:24:56 PST)
- Ross Walker (Wed Feb 04 2009 - 19:03:36 PST)
- Hopkins, Robert (Wed Feb 04 2009 - 16:34:16 PST)
[AMBER] restraint angle
- David A. Case (Tue Feb 17 2009 - 09:52:49 PST)
- m m (Tue Feb 17 2009 - 09:17:00 PST)
[AMBER] Scaling of dipole interactions
- Diddo Diddens (Tue Feb 10 2009 - 06:33:18 PST)
[AMBER] Scientific Linux 5.2
- Catein Catherine (Tue Feb 17 2009 - 23:13:23 PST)
[AMBER] script to convert GLYCAM ff in CHARMM format
- Lachele Foley (Lists) (Fri Feb 06 2009 - 06:57:17 PST)
- ABEL Stephane 175950 (Fri Feb 06 2009 - 06:39:04 PST)
[AMBER] second derivative matrix
- David A. Case (Mon Feb 09 2009 - 07:05:18 PST)
- Adrian Roitberg (Mon Feb 09 2009 - 06:29:51 PST)
- Marie Brut (Mon Feb 09 2009 - 00:53:01 PST)
[AMBER] second derivative matrix calculation
- David A. Case (Fri Feb 06 2009 - 05:19:52 PST)
- Marie Brut (Fri Feb 06 2009 - 02:47:18 PST)
[AMBER] secstruct
- Carlos Simmerling (Thu Feb 19 2009 - 06:45:47 PST)
- Maxime Louet (Thu Feb 19 2009 - 06:17:17 PST)
- Beale, John (Thu Feb 19 2009 - 05:22:20 PST)
- Carlos Simmerling (Thu Feb 19 2009 - 05:30:16 PST)
[AMBER] Simulated annealing
- Ibrahim Moustafa (Thu Feb 26 2009 - 08:32:32 PST)
- Hu, Shaowen (JSC-SK)[Universities Space Research Association (USRA)] (Thu Feb 26 2009 - 08:30:47 PST)
- Carlos Simmerling (Thu Feb 26 2009 - 08:27:04 PST)
- Hu, Shaowen (JSC-SK)[Universities Space Research Association (USRA)] (Thu Feb 26 2009 - 08:22:59 PST)
- Carlos Simmerling (Thu Feb 26 2009 - 07:55:41 PST)
- David A. Case (Thu Feb 26 2009 - 07:52:18 PST)
- Ibrahim Moustafa (Thu Feb 26 2009 - 07:28:44 PST)
- Carlos Simmerling (Wed Feb 25 2009 - 17:31:30 PST)
- Ibrahim Moustafa (Wed Feb 25 2009 - 16:26:37 PST)
[AMBER] Solvating inside of a channel
- Daniel Smith (Mon Feb 09 2009 - 13:03:16 PST)
[AMBER] Solvating the interior of a channel
- Daniel Smith (Sun Feb 15 2009 - 14:40:23 PST)
- Daniel Smith (Fri Feb 13 2009 - 13:02:24 PST)
- Jason A. Ford-Green (Wed Feb 11 2009 - 08:04:24 PST)
- Shozeb Haider (Wed Feb 11 2009 - 05:15:07 PST)
- Daniel Smith (Tue Feb 10 2009 - 12:42:09 PST)
[AMBER] Solvation potential and free energies
- David A. Case (Fri Feb 06 2009 - 05:34:25 PST)
- Lorenzo Gontrani (Thu Feb 05 2009 - 04:34:47 PST)
- Carlos Simmerling (Thu Feb 05 2009 - 04:33:08 PST)
- guardiani.fi.infn.it (Thu Feb 05 2009 - 04:27:21 PST)
[AMBER] Stability of a long NPT md trajectory?
- Robert Duke (Tue Feb 10 2009 - 12:29:15 PST)
- Bill K (Tue Feb 10 2009 - 11:39:22 PST)
- Robert Duke (Tue Feb 10 2009 - 05:40:55 PST)
- Bill K (Mon Feb 09 2009 - 23:37:31 PST)
- Robert Duke (Mon Feb 09 2009 - 20:20:57 PST)
- Carlos Simmerling (Mon Feb 09 2009 - 19:10:55 PST)
- Robert Duke (Mon Feb 09 2009 - 18:21:31 PST)
- Adrian Roitberg (Mon Feb 09 2009 - 17:03:45 PST)
- Carlos Simmerling (Mon Feb 09 2009 - 16:56:50 PST)
- Bill K (Mon Feb 09 2009 - 12:56:53 PST)
- Robert Duke (Mon Feb 09 2009 - 05:25:10 PST)
- Carlos Simmerling (Mon Feb 09 2009 - 04:08:29 PST)
- Bill K (Sun Feb 08 2009 - 23:07:24 PST)
[AMBER] strip frames from crd file
- Carlos Simmerling (Mon Feb 02 2009 - 04:12:27 PST)
- aneesh cna (Mon Feb 02 2009 - 01:35:11 PST)
- aneesh cna (Mon Feb 02 2009 - 01:33:16 PST)
[AMBER] test charge
- Jenny Iskrenova (Fri Feb 20 2009 - 12:32:14 PST)
- Dan Kaps (Fri Feb 20 2009 - 08:58:17 PST)
- David A. Case (Thu Feb 19 2009 - 20:48:29 PST)
- Dan Kaps (Thu Feb 19 2009 - 18:22:31 PST)
- David A. Case (Wed Feb 18 2009 - 20:24:04 PST)
- Dan Kaps (Wed Feb 18 2009 - 18:27:32 PST)
[AMBER] Test run on Solaris 10 X 86
- Manikandan Chandrasekaran (Fri Feb 06 2009 - 09:39:54 PST)
- Atro Tossavainen (Wed Feb 04 2009 - 23:50:12 PST)
- Manikandan Chandrasekaran (Wed Feb 04 2009 - 10:37:21 PST)
- Atro Tossavainen (Wed Feb 04 2009 - 04:33:25 PST)
- Manikandan Chandrasekaran (Tue Feb 03 2009 - 12:28:37 PST)
- Atro Tossavainen (Mon Feb 02 2009 - 15:06:49 PST)
- Manikandan Chandrasekaran (Mon Feb 02 2009 - 11:16:32 PST)
- Atro Tossavainen (Sat Jan 31 2009 - 23:10:30 PST)
[AMBER] the output files
- Ross Walker (Tue Feb 10 2009 - 09:45:37 PST)
- Carlos Simmerling (Tue Feb 10 2009 - 06:18:34 PST)
- oguz gurbulak (Tue Feb 10 2009 - 06:11:44 PST)
- Carlos Simmerling (Tue Feb 10 2009 - 03:22:04 PST)
- oguz gurbulak (Tue Feb 10 2009 - 03:14:58 PST)
- Carlos Simmerling (Mon Feb 09 2009 - 05:06:41 PST)
- oguz gurbulak (Mon Feb 09 2009 - 05:03:47 PST)
- Carlos Simmerling (Sun Feb 01 2009 - 10:11:51 PST)
- oguz gurbulak (Sun Feb 01 2009 - 03:13:02 PST)
[AMBER] tleap errors !!
- David A. Case (Thu Feb 26 2009 - 05:45:49 PST)
- Sampath Koppole (Thu Feb 26 2009 - 01:47:48 PST)
[AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun
- Carlos Simmerling (Wed Feb 04 2009 - 03:16:34 PST)
- drugdesign (Tue Feb 03 2009 - 21:46:19 PST)
- Carlos Simmerling (Tue Feb 03 2009 - 09:39:58 PST)
- Ross Walker (Tue Feb 03 2009 - 09:21:07 PST)
- Carlos Simmerling (Tue Feb 03 2009 - 09:17:53 PST)
- Ye MEI (Tue Feb 03 2009 - 09:12:54 PST)
- drugdesign (Tue Feb 03 2009 - 09:03:20 PST)
[AMBER] using Gromacs for analysis
- Bala subramanian (Fri Feb 27 2009 - 10:16:46 PST)
- oguz gurbulak (Fri Feb 27 2009 - 09:03:54 PST)
[AMBER] using ptraj
- Carlos Simmerling (Tue Feb 17 2009 - 06:29:07 PST)
- Molecular Dynamics (Tue Feb 17 2009 - 06:11:16 PST)
- Carlos Simmerling (Tue Feb 17 2009 - 05:34:33 PST)
- Molecular Dynamics (Tue Feb 17 2009 - 05:31:02 PST)
- Carlos Simmerling (Tue Feb 17 2009 - 04:37:15 PST)
- Molecular Dynamics (Tue Feb 17 2009 - 03:44:09 PST)
- Carlos Simmerling (Mon Feb 16 2009 - 12:41:54 PST)
- Molecular Dynamics (Mon Feb 16 2009 - 12:31:42 PST)
AMBER: GBSA EGB = NaN
- Markus Kaukonen (Thu Feb 19 2009 - 05:34:38 PST)
- Markus Kaukonen (Wed Feb 18 2009 - 04:26:28 PST)
AMBER: How do you evaluate forces on a fixed atom?
- Bill Kowallis (Wed Feb 18 2009 - 17:55:47 PST)
Antechamber
- FyD (Fri Feb 27 2009 - 05:12:16 PST)
- kureeckal ramesh (Fri Feb 27 2009 - 04:56:58 PST)
RE : [AMBER] RED-vIII: Scratch directory for Gaussian [NOT FOUND]
- ABEL Stephane 175950 (Tue Feb 10 2009 - 06:39:17 PST)
RE : [AMBER] script to convert GLYCAM ff in CHARMM format
- ABEL Stephane 175950 (Fri Feb 06 2009 - 07:03:19 PST)
Tutorial 5
- George Tzotzos (Sun Feb 01 2009 - 13:04:36 PST)

Amber Archive Feb 2009 by subject