AMBER Archive (2009) - Feb 2009 By Subject

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About this archive

Starting: Sun Feb 01 2009 - 01:10:30 CST
Ending: Sat Feb 28 2009 - 18:23:49 CST

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

Last message date: Mon Nov 23 2009 - 12:37:20 CST
Archived on: Mon Nov 23 2009 - 12:37:23 CST

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