Amber Archive Sep 2008: by subject

Amber 9
- Gustavo Seabra (Tue Sep 30 2008 - 12:12:19 PDT)
- mhamed.birzeit.edu (Tue Sep 30 2008 - 10:22:07 PDT)
AMBER:
- Ross Walker (Wed Sep 03 2008 - 14:14:21 PDT)
- Marisa Frechero (Wed Sep 03 2008 - 11:38:06 PDT)
AMBER: 3fe-4s cluster parameter file generation
- Bill Ross (Wed Sep 17 2008 - 11:04:32 PDT)
- Bill Ross (Wed Sep 17 2008 - 10:41:28 PDT)
- David A. Case (Wed Sep 17 2008 - 04:26:07 PDT)
- moitrayee.mbu.iisc.ernet.in (Tue Sep 16 2008 - 23:43:49 PDT)
- Bill Ross (Tue Sep 16 2008 - 12:36:24 PDT)
- Bill Ross (Tue Sep 16 2008 - 12:15:52 PDT)
- moitrayee.mbu.iisc.ernet.in (Tue Sep 16 2008 - 11:12:24 PDT)
- moitrayee.mbu.iisc.ernet.in (Tue Sep 16 2008 - 11:01:59 PDT)
- Bill Ross (Tue Sep 16 2008 - 10:47:00 PDT)
- moitrayee.mbu.iisc.ernet.in (Tue Sep 16 2008 - 04:39:25 PDT)
- Bill Ross (Mon Sep 15 2008 - 11:51:29 PDT)
- S.Sundar Raman (Mon Sep 15 2008 - 10:21:44 PDT)
- moitrayee.mbu.iisc.ernet.in (Mon Sep 15 2008 - 08:36:31 PDT)
- David A. Case (Mon Sep 15 2008 - 07:15:12 PDT)
- S.Sundar Raman (Mon Sep 15 2008 - 05:56:36 PDT)
- Hakkim Boy (Mon Sep 15 2008 - 05:30:04 PDT)
- moitrayee.mbu.iisc.ernet.in (Mon Sep 15 2008 - 04:46:56 PDT)
- David A. Case (Mon Sep 15 2008 - 05:06:08 PDT)
- moitrayee.mbu.iisc.ernet.in (Mon Sep 15 2008 - 04:20:19 PDT)
- David A. Case (Mon Sep 15 2008 - 04:15:52 PDT)
- moitrayee.mbu.iisc.ernet.in (Sun Sep 14 2008 - 23:35:39 PDT)
AMBER: a question
- Ross Walker (Mon Sep 29 2008 - 07:41:54 PDT)
- Adrien Delmont (Mon Sep 29 2008 - 05:53:51 PDT)
- oguz gurbulak (Mon Sep 29 2008 - 03:23:09 PDT)
- oguz gurbulak (Mon Sep 29 2008 - 02:55:29 PDT)
- Ross Walker (Sun Sep 28 2008 - 21:56:00 PDT)
- Adrien Delmont (Sun Sep 28 2008 - 15:08:00 PDT)
AMBER: a question about matrix command?
- TaoPaul (Tue Sep 02 2008 - 18:01:04 PDT)
AMBER: about NMR refinement in explicit solvent
- David A. Case (Thu Sep 11 2008 - 10:24:37 PDT)
- Rogelio Hernández (Tue Sep 09 2008 - 12:15:19 PDT)
AMBER: Ac-Co Parameters for Amber
- suhaib sh (Tue Sep 30 2008 - 15:18:48 PDT)
- suhaib sh (Tue Sep 30 2008 - 04:49:41 PDT)
AMBER: acetone box
- parvesh singh (Wed Sep 17 2008 - 04:09:01 PDT)
AMBER: adding new potential function
- Harianto Tjong (Wed Sep 17 2008 - 12:12:34 PDT)
AMBER: amber 10 parallel cpu utlization
- Ross Walker (Mon Sep 15 2008 - 19:09:37 PDT)
- meandme meandme (Mon Sep 15 2008 - 10:30:49 PDT)
AMBER: amber 9 install
- chen bents (Wed Sep 17 2008 - 00:44:46 PDT)
- Ye Mei (Tue Sep 16 2008 - 20:26:07 PDT)
- chen bents (Tue Sep 16 2008 - 20:14:47 PDT)
AMBER: Amber GB problems on PMEMD !!
- Ross Walker (Thu Sep 25 2008 - 08:23:44 PDT)
- Andreas Svrcek-Seiler (Thu Sep 25 2008 - 08:12:59 PDT)
- Sampath Koppole (Thu Sep 25 2008 - 06:02:42 PDT)
- Robert Duke (Thu Sep 25 2008 - 05:22:06 PDT)
- Sampath Koppole (Thu Sep 25 2008 - 02:09:30 PDT)
AMBER: amber minimisation
- David A. Case (Mon Sep 08 2008 - 05:59:26 PDT)
- Carlos Simmerling (Mon Sep 08 2008 - 05:40:44 PDT)
- Majeed Shaik (Mon Sep 08 2008 - 05:32:17 PDT)
AMBER: Amber on Infiniband clusters: SDR vs DDR cables?
- Sasha Buzko (Thu Sep 25 2008 - 16:06:44 PDT)
AMBER: Amber10 Compilation
- Ross Walker (Wed Sep 10 2008 - 05:31:47 PDT)
- Anthony Cruz (Tue Sep 09 2008 - 07:26:04 PDT)
AMBER: AMBER10 Compilation (SGI Altix)
- Anthony Cruz (Tue Sep 16 2008 - 09:56:45 PDT)
- Ross Walker (Mon Sep 15 2008 - 19:15:54 PDT)
- Anthony Cruz (Mon Sep 15 2008 - 11:21:49 PDT)
AMBER: AMBER9 Compilation
- chen bents (Tue Sep 16 2008 - 18:25:59 PDT)
AMBER: AMBER9 installation problen with open mpi
- Ross Walker (Wed Sep 03 2008 - 08:35:43 PDT)
- saurabh agrawal (Wed Sep 03 2008 - 07:55:31 PDT)
- Vlad Cojocaru (Tue Sep 02 2008 - 05:00:33 PDT)
- saurabh agrawal (Tue Sep 02 2008 - 04:41:55 PDT)
AMBER: Announcement of ACS COMP Division CCG and HP award deadlines for Spring 2009 meeting
- Carlos Simmerling (Mon Sep 15 2008 - 09:39:58 PDT)
AMBER: Another problem when trying to compile Sander in debug mode
- Ben Roberts (Mon Sep 08 2008 - 08:49:52 PDT)
AMBER: antechamber cannot generate prep files
- moitrayee.mbu.iisc.ernet.in (Thu Sep 04 2008 - 04:47:17 PDT)
AMBER: binding energy: high ELE
- CHAMI F. (Thu Sep 11 2008 - 10:24:23 PDT)
- David A. Case (Thu Sep 11 2008 - 08:42:56 PDT)
- CHAMI F. (Wed Sep 10 2008 - 08:15:40 PDT)
AMBER: bis(trifluoromethylsulfonyl)imide (Tf2N)
- David Watson (Sun Sep 21 2008 - 09:01:04 PDT)
- babak minoofar (Sun Sep 21 2008 - 07:34:39 PDT)
AMBER: Buckingham potential
- Adrian Roitberg (Tue Sep 30 2008 - 08:14:53 PDT)
- Diddo Diddens (Tue Sep 30 2008 - 08:01:57 PDT)
- Andreas Svrcek-Seiler (Tue Sep 30 2008 - 07:47:27 PDT)
- Diddo Diddens (Tue Sep 30 2008 - 07:16:47 PDT)
AMBER: Ca ions not recognized
- Peterson, Matthew W. (Tue Sep 30 2008 - 07:08:16 PDT)
- Cristina Sisu (Tue Sep 30 2008 - 07:00:24 PDT)
AMBER: Changes in the Amber web site
- Carlos Simmerling (Mon Sep 08 2008 - 08:14:33 PDT)
- Majeed Shaik (Mon Sep 08 2008 - 08:07:21 PDT)
- David A. Case (Mon Sep 08 2008 - 06:25:41 PDT)
AMBER: cluster for running amber10
- Ross Walker (Tue Sep 30 2008 - 08:25:09 PDT)
- Guillermo Mulliert Carlín (Tue Sep 30 2008 - 08:14:07 PDT)
AMBER: Comment: constant pH, non-integer charge -> weird error
- Markus Kaukonen (Sun Sep 14 2008 - 00:51:58 PDT)
AMBER: compilation problem
- Atro Tossavainen (Sat Sep 27 2008 - 12:18:13 PDT)
- David A. Case (Sat Sep 27 2008 - 05:29:53 PDT)
- Manikandan Chandrasekaran (Fri Sep 26 2008 - 20:51:50 PDT)
- David A. Case (Fri Sep 26 2008 - 09:06:46 PDT)
- Atro Tossavainen (Thu Sep 25 2008 - 12:32:06 PDT)
- David A. Case (Mon Sep 22 2008 - 05:19:47 PDT)
- john smith (Mon Sep 22 2008 - 04:59:17 PDT)
- David A. Case (Fri Sep 12 2008 - 05:04:59 PDT)
- john smith (Thu Sep 11 2008 - 22:51:22 PDT)
- David A. Case (Tue Sep 02 2008 - 07:32:45 PDT)
- Vlad Cojocaru (Tue Sep 02 2008 - 03:16:13 PDT)
- john smith (Tue Sep 02 2008 - 03:03:14 PDT)
AMBER: Compiling Amber10 PMEMD with MVAPICH, InfiniBand support
- Pablo Englebienne (Thu Sep 25 2008 - 12:07:48 PDT)
- Robert Duke (Wed Sep 24 2008 - 12:39:30 PDT)
- Pablo Englebienne (Wed Sep 24 2008 - 12:04:46 PDT)
AMBER: Constant pH simulation force field
- David A. Case (Sat Sep 27 2008 - 05:10:39 PDT)
- Soonmin Jang (Sat Sep 27 2008 - 02:13:51 PDT)
AMBER: coordinate file question
- Robert Hanson (Tue Sep 30 2008 - 10:24:47 PDT)
- Ross Walker (Tue Sep 30 2008 - 06:55:57 PDT)
- Robert Hanson (Tue Sep 30 2008 - 06:30:21 PDT)
- Ross Walker (Mon Sep 29 2008 - 20:33:10 PDT)
- Robert Hanson (Mon Sep 29 2008 - 20:16:25 PDT)
AMBER: Cutoff list exceeds largest sphere in unit cell
- Majeed Shaik (Thu Sep 11 2008 - 04:49:09 PDT)
- Ross Walker (Wed Sep 10 2008 - 13:08:53 PDT)
- Majeed Shaik (Wed Sep 10 2008 - 10:42:58 PDT)
- Majeed Shaik (Wed Sep 10 2008 - 10:44:52 PDT)
- Ross Walker (Wed Sep 10 2008 - 09:01:18 PDT)
- Majeed Shaik (Wed Sep 10 2008 - 07:54:58 PDT)
AMBER: D2O
- Nicolas Lux Fawzi (Mon Sep 15 2008 - 09:54:17 PDT)
- Chih-Ying Lin (Thu Sep 11 2008 - 17:51:03 PDT)
- Adrian Roitberg (Thu Sep 11 2008 - 08:20:07 PDT)
- Carlos Simmerling (Thu Sep 11 2008 - 07:44:06 PDT)
- Chih-Ying Lin (Thu Sep 11 2008 - 07:32:03 PDT)
- Carlos Simmerling (Tue Sep 09 2008 - 16:09:41 PDT)
- Chih-Ying Lin (Tue Sep 09 2008 - 12:59:13 PDT)
- David A. Case (Tue Sep 09 2008 - 11:21:37 PDT)
- Carlos Simmerling (Tue Sep 09 2008 - 11:08:37 PDT)
- Chih-Ying Lin (Tue Sep 09 2008 - 10:00:59 PDT)
AMBER: Dihedral Drive
- Ilyas Yildirim (Sat Sep 20 2008 - 01:07:07 PDT)
- Hashem Taha (Sat Sep 20 2008 - 00:31:13 PDT)
AMBER: Dihedral: ptraj
- Carlos Simmerling (Thu Sep 18 2008 - 02:32:38 PDT)
- waqasuddin.khan.iccs.edu (Thu Sep 18 2008 - 02:14:50 PDT)
- Carlos Simmerling (Thu Sep 18 2008 - 02:04:24 PDT)
- waqasuddin.khan.iccs.edu (Wed Sep 17 2008 - 23:39:33 PDT)
AMBER: Emperical Valence Bond
- sai kumar ramadugu (Tue Sep 09 2008 - 14:46:25 PDT)
AMBER: energy decomposition with sander?
- Yongmei Pan (Mon Sep 08 2008 - 14:32:32 PDT)
AMBER: energy terms in hybrid REMD calculation
- Ye Mei (Mon Sep 29 2008 - 02:28:13 PDT)
AMBER: error when using tleap with leaprc.ff02EP
- Ross Walker (Fri Sep 05 2008 - 09:06:13 PDT)
- Yongmei Pan (Fri Sep 05 2008 - 08:49:38 PDT)
AMBER: error while running REMD in amber9
- Carlos Simmerling (Thu Sep 25 2008 - 11:28:17 PDT)
- priya priya (Thu Sep 25 2008 - 11:04:26 PDT)
- Carlos Simmerling (Thu Sep 25 2008 - 10:51:58 PDT)
- priya priya (Thu Sep 25 2008 - 10:44:13 PDT)
- Carlos Simmerling (Thu Sep 25 2008 - 09:55:35 PDT)
- priya priya (Thu Sep 25 2008 - 09:49:28 PDT)
- Carlos Simmerling (Wed Sep 24 2008 - 11:27:22 PDT)
- priya priya (Wed Sep 24 2008 - 10:53:09 PDT)
AMBER: Error: PB bomb in pb_reslist(): maxnbr too small
- Rajendra P. OJHA (Thu Sep 18 2008 - 07:34:15 PDT)
AMBER: ESURF - SASA - isolate residues
- Deepangi Pandit (Fri Sep 05 2008 - 07:23:23 PDT)
AMBER: EVB allocation problem
- sai kumar ramadugu (Fri Sep 12 2008 - 09:08:41 PDT)
AMBER: Explanation of the energy unit ?
- Marek Malý (Wed Sep 10 2008 - 03:24:17 PDT)
- David A. Case (Mon Sep 08 2008 - 13:51:50 PDT)
- Carlos Simmerling (Mon Sep 08 2008 - 13:16:16 PDT)
- Marek Malý (Mon Sep 08 2008 - 13:19:47 PDT)
- Marek Malý (Mon Sep 08 2008 - 13:15:43 PDT)
- Gustavo Seabra (Mon Sep 08 2008 - 12:07:28 PDT)
- Carlos Simmerling (Mon Sep 08 2008 - 11:51:49 PDT)
- Marek Malý (Mon Sep 08 2008 - 12:02:37 PDT)
- Carlos Simmerling (Mon Sep 08 2008 - 07:56:48 PDT)
- Marek Malý (Mon Sep 08 2008 - 08:01:10 PDT)
- David A. Case (Sun Sep 07 2008 - 15:12:22 PDT)
- Marek Malý (Sat Sep 06 2008 - 07:29:06 PDT)
AMBER: Failure of antechamber in amber10
- Francesco Pietra (Sun Sep 14 2008 - 07:18:49 PDT)
AMBER: fix for POL3 heating problem?
- Grange Hermitage (Mon Sep 22 2008 - 02:35:02 PDT)
AMBER: Harmonic restraint between two atoms
- Adrian Roitberg (Fri Sep 26 2008 - 11:42:55 PDT)
- greddy1.umd.edu (Fri Sep 26 2008 - 11:37:34 PDT)
AMBER: help can amber couple part of the system to different heat bath?
- Jose Borreguero (Thu Sep 18 2008 - 14:09:27 PDT)
- Jose Borreguero (Thu Sep 18 2008 - 14:09:23 PDT)
AMBER: help... structure factors from amber trajectories?
- Jose Borreguero (Thu Sep 04 2008 - 10:35:57 PDT)
AMBER: help...ptraj does not output bounding box info
- Jose Borreguero (Wed Sep 03 2008 - 11:28:02 PDT)
- Carlos Simmerling (Wed Sep 03 2008 - 10:53:33 PDT)
- Jose Borreguero (Wed Sep 03 2008 - 10:26:57 PDT)
- Carlos Simmerling (Wed Sep 03 2008 - 09:23:28 PDT)
- Bill Ross (Wed Sep 03 2008 - 09:22:18 PDT)
- Jose Borreguero (Wed Sep 03 2008 - 09:12:30 PDT)
- Carlos Simmerling (Wed Sep 03 2008 - 08:41:48 PDT)
- Jose Borreguero (Wed Sep 03 2008 - 08:39:41 PDT)
AMBER: help...sander "segmentation fault" after 2hours of minimization
- Ross Walker (Fri Sep 05 2008 - 10:02:30 PDT)
- Jose Borreguero (Fri Sep 05 2008 - 09:26:23 PDT)
- Ross Walker (Fri Sep 05 2008 - 09:07:27 PDT)
- Jose Borreguero (Fri Sep 05 2008 - 08:43:39 PDT)
- Ross Walker (Fri Sep 05 2008 - 08:23:42 PDT)
- David A. Case (Fri Sep 05 2008 - 08:20:40 PDT)
- Jose Borreguero (Fri Sep 05 2008 - 08:06:42 PDT)
AMBER: Help...which commands in ptraj does clustering by RMSD?
- Jose Borreguero (Thu Sep 11 2008 - 15:01:02 PDT)
- Sasha Buzko (Thu Sep 11 2008 - 14:48:14 PDT)
- Jose Borreguero (Thu Sep 11 2008 - 14:12:00 PDT)
- Sasha Buzko (Thu Sep 11 2008 - 13:39:44 PDT)
- Jose Borreguero (Thu Sep 11 2008 - 13:28:49 PDT)
AMBER: how to enlarge the TIP3PBOX size
- David A. Case (Fri Sep 26 2008 - 09:06:37 PDT)
- Qiuting Hong (Fri Sep 26 2008 - 00:28:53 PDT)
- Ross Walker (Thu Sep 25 2008 - 07:55:38 PDT)
- Ross Walker (Wed Sep 24 2008 - 23:40:21 PDT)
- waqasuddin.khan.iccs.edu (Wed Sep 24 2008 - 23:01:57 PDT)
- Carlos Simmerling (Wed Sep 24 2008 - 16:01:44 PDT)
- Qiuting Hong (Wed Sep 24 2008 - 15:56:10 PDT)
AMBER: How to set up a water slab in Amber?
- Zhao, Zhen (zhaozh) (Tue Sep 30 2008 - 14:23:06 PDT)
AMBER: Hydrogen bond energies in explicit solvent.
- Carlos Simmerling (Mon Sep 15 2008 - 09:24:07 PDT)
- Waqas Nasir (Mon Sep 15 2008 - 09:17:04 PDT)
- Carlos Simmerling (Mon Sep 15 2008 - 08:54:25 PDT)
- Waqas Nasir (Mon Sep 15 2008 - 08:47:00 PDT)
- Carlos Simmerling (Mon Sep 15 2008 - 08:01:41 PDT)
- Waqas Nasir (Mon Sep 15 2008 - 07:56:34 PDT)
AMBER: increasing temperature smoothly
- Germain Vallverdu (Mon Sep 22 2008 - 02:00:19 PDT)
- David A. Case (Mon Sep 22 2008 - 04:44:02 PDT)
- Germain Vallverdu (Mon Sep 22 2008 - 04:31:56 PDT)
- Ross Walker (Fri Sep 19 2008 - 11:29:31 PDT)
- David A. Case (Fri Sep 19 2008 - 09:49:46 PDT)
- Germain Vallverdu (Fri Sep 19 2008 - 08:17:56 PDT)
AMBER: Install problems
- David A. Case (Tue Sep 09 2008 - 12:53:18 PDT)
- M. L. Dodson (Tue Sep 09 2008 - 11:41:07 PDT)
- Mark Williamson (Tue Sep 09 2008 - 11:16:38 PDT)
- David A. Case (Tue Sep 09 2008 - 04:37:16 PDT)
- Mark Williamson (Mon Sep 08 2008 - 16:56:35 PDT)
- Gustavo Seabra (Mon Sep 08 2008 - 11:58:02 PDT)
- Marisa Frechero (Mon Sep 08 2008 - 11:35:08 PDT)
AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10?
- David A. Case (Mon Sep 22 2008 - 04:25:38 PDT)
- cgji (Sat Sep 20 2008 - 09:22:07 PDT)
AMBER: Is there a way to cluster frames of a trajectory?
- Sasha Buzko (Mon Sep 08 2008 - 15:11:04 PDT)
- Carlos Simmerling (Mon Sep 08 2008 - 13:46:45 PDT)
- Sasha Buzko (Mon Sep 08 2008 - 13:34:22 PDT)
AMBER: Is there any way I can extract the potential energy of the solute with the solvent instead of the total energy in Amber?
- Barbault Florent (Sat Sep 20 2008 - 13:40:34 PDT)
- Zhao, Zhen (zhaozh) (Sat Sep 20 2008 - 13:01:59 PDT)
AMBER: Leap atoms CL and OXT do not have a type
- Bill Ross (Tue Sep 30 2008 - 11:11:12 PDT)
- Francesco Pietra (Tue Sep 30 2008 - 03:05:13 PDT)
- Bill Ross (Mon Sep 29 2008 - 15:03:28 PDT)
- Francesco Pietra (Mon Sep 29 2008 - 13:13:05 PDT)
- Bill Ross (Mon Sep 29 2008 - 11:38:46 PDT)
- Francesco Pietra (Sat Sep 27 2008 - 12:31:51 PDT)
- Carlos Simmerling (Sat Sep 27 2008 - 11:21:19 PDT)
- Francesco Pietra (Sat Sep 27 2008 - 11:11:49 PDT)
- Carlos Simmerling (Sat Sep 27 2008 - 10:07:03 PDT)
- David A. Case (Sat Sep 27 2008 - 09:29:23 PDT)
- Francesco Pietra (Sat Sep 27 2008 - 08:36:47 PDT)
- David A. Case (Sat Sep 27 2008 - 07:12:40 PDT)
- Carlos Simmerling (Sat Sep 27 2008 - 06:56:22 PDT)
- Francesco Pietra (Sat Sep 27 2008 - 06:46:10 PDT)
AMBER: Location of vdw radii and partial charges for ff99SB
- Carlos Simmerling (Mon Sep 29 2008 - 07:58:45 PDT)
- Ross Walker (Mon Sep 29 2008 - 07:51:44 PDT)
- Charles Letner, Ph.D. (Mon Sep 29 2008 - 06:08:27 PDT)
AMBER: matrix correl
- Steve Seibold (Wed Sep 03 2008 - 11:40:28 PDT)
AMBER: MD at a given pH
- David A. Case (Sat Sep 27 2008 - 04:53:56 PDT)
- Beale, John (Fri Sep 26 2008 - 09:44:32 PDT)
AMBER: MD goes wrong
- Ross Walker (Tue Sep 23 2008 - 21:33:43 PDT)
- Adrian Roitberg (Tue Sep 23 2008 - 20:19:19 PDT)
- baohua zhang (Tue Sep 23 2008 - 19:17:57 PDT)
AMBER: MD simulation crashed
- Carlos Simmerling (Wed Sep 17 2008 - 06:27:59 PDT)
- Aust, Susanne (Wed Sep 17 2008 - 06:10:17 PDT)
AMBER: Minimizaton stops after Ncyc steps only
- Carlos Simmerling (Mon Sep 15 2008 - 10:23:00 PDT)
- mon_sharma.research.iiit.ac.in (Mon Sep 15 2008 - 09:34:22 PDT)
AMBER: MM-PBSA problem : Missing PBCAV for PB
- Carra, Claudio (JSC-SK)[USRA] (Tue Sep 30 2008 - 09:49:26 PDT)
AMBER: MM-PBSA/NMODE in Amber 10
- Daniel Oehme (Mon Sep 22 2008 - 00:13:55 PDT)
- Daniel Oehme (Mon Sep 15 2008 - 18:23:26 PDT)
- Peterson, Matthew W. (MPETERSON) (Mon Sep 15 2008 - 13:37:41 PDT)
AMBER: MM_PBSA - SASA - Question
- Deepangi Pandit (Tue Sep 02 2008 - 19:10:13 PDT)
AMBER: mm_pbsa error : Scale paremeter for PBSA
- Ray Luo (Fri Sep 05 2008 - 10:45:12 PDT)
- CHAMI F. (Fri Sep 05 2008 - 10:26:46 PDT)
AMBER: MM_PBSA snapshot statistic calc problem
- Peterson, Matthew W. (Mon Sep 29 2008 - 14:25:57 PDT)
- Vasu Chandrasekaran (Mon Sep 29 2008 - 12:08:15 PDT)
- haixiao jin (Fri Sep 26 2008 - 23:40:20 PDT)
AMBER: mmpbsa
- Hannes Kopitz (Wed Sep 03 2008 - 02:15:19 PDT)
- Henrik Öberg (Wed Sep 03 2008 - 00:30:43 PDT)
- Hannes Kopitz (Tue Sep 02 2008 - 11:15:47 PDT)
- Matthew Peterson (Tue Sep 02 2008 - 06:57:24 PDT)
- Henrik Öberg (Tue Sep 02 2008 - 07:18:56 PDT)
- Neha Gandhi (Tue Sep 02 2008 - 05:49:33 PDT)
- Henrik Öberg (Tue Sep 02 2008 - 04:36:55 PDT)
AMBER: MMPBSA error
- Cristina Sisu (Tue Sep 23 2008 - 03:30:38 PDT)
AMBER: mmpbsa errors in redoing the tutorial A3:MMPBSA
- haixiao jin (Sat Sep 27 2008 - 00:45:06 PDT)
AMBER: mmpbsa molsurf.c error
- parvesh singh (Mon Sep 22 2008 - 02:26:29 PDT)
- David A. Case (Wed Sep 17 2008 - 05:10:40 PDT)
- Ilyas Yildirim (Thu Sep 04 2008 - 17:45:58 PDT)
- Ilyas Yildirim (Wed Sep 03 2008 - 16:56:59 PDT)
AMBER: molecule drift out of water box?
- Ilyas Yildirim (Sun Sep 21 2008 - 19:52:17 PDT)
- Qiuting Hong (Sun Sep 21 2008 - 18:43:38 PDT)
- Ilyas Yildirim (Sun Sep 21 2008 - 13:45:45 PDT)
- Qiuting Hong (Sun Sep 21 2008 - 13:22:19 PDT)
- Ilyas Yildirim (Fri Sep 19 2008 - 17:00:03 PDT)
- Qiuting Hong (Fri Sep 19 2008 - 16:39:42 PDT)
AMBER: mulliken charges in QM/MM calculation
- Ross Walker (Sun Sep 14 2008 - 01:44:00 PDT)
- Barbault Florent (Sun Sep 14 2008 - 01:26:25 PDT)
AMBER: multiple heat baths in a single simulation?
- Jose Borreguero (Sun Sep 21 2008 - 16:09:41 PDT)
AMBER: NAB parameter: wcons
- David A. Case (Wed Sep 10 2008 - 05:19:32 PDT)
- ramu.vt.edu (Mon Sep 08 2008 - 14:06:54 PDT)
AMBER: Need help... High energies for complex...
- Lachele Foley (Lists) (Tue Sep 09 2008 - 07:09:06 PDT)
- Waqas Nasir (Tue Sep 09 2008 - 07:06:18 PDT)
- Carlos Simmerling (Tue Sep 09 2008 - 06:56:00 PDT)
- Carlos Simmerling (Tue Sep 09 2008 - 06:46:19 PDT)
- Waqas Nasir (Tue Sep 09 2008 - 06:16:29 PDT)
- Carlos Simmerling (Mon Sep 08 2008 - 09:45:51 PDT)
- Waqas Nasir (Mon Sep 08 2008 - 09:06:26 PDT)
- Carlos Simmerling (Fri Sep 05 2008 - 03:07:01 PDT)
- Waqas Nasir (Fri Sep 05 2008 - 02:15:59 PDT)
- Carlos Simmerling (Thu Sep 04 2008 - 09:21:42 PDT)
- Waqas Nasir (Thu Sep 04 2008 - 09:14:35 PDT)
- Carlos Simmerling (Thu Sep 04 2008 - 08:41:38 PDT)
- Waqas Nasir (Thu Sep 04 2008 - 08:22:55 PDT)
- David A. Case (Thu Sep 04 2008 - 07:36:37 PDT)
- Carlos Simmerling (Thu Sep 04 2008 - 07:35:02 PDT)
- Carlos Simmerling (Thu Sep 04 2008 - 07:33:32 PDT)
- Waqas Nasir (Thu Sep 04 2008 - 07:12:21 PDT)
- Carlos Simmerling (Thu Sep 04 2008 - 03:39:48 PDT)
- Waqas Nasir (Thu Sep 04 2008 - 03:38:53 PDT)
- Waqas Nasir (Thu Sep 04 2008 - 03:08:49 PDT)
- Neha Gandhi (Wed Sep 03 2008 - 05:41:16 PDT)
- Carlos Simmerling (Wed Sep 03 2008 - 05:04:07 PDT)
- Waqas Nasir (Wed Sep 03 2008 - 04:45:20 PDT)
- Carlos Simmerling (Wed Sep 03 2008 - 04:27:06 PDT)
- Waqas Nasir (Wed Sep 03 2008 - 04:20:01 PDT)
AMBER: nmode units
- Arturas Ziemys (Thu Sep 04 2008 - 08:22:41 PDT)
- David A. Case (Thu Sep 04 2008 - 07:58:22 PDT)
- Arturas Ziemys (Thu Sep 04 2008 - 07:26:57 PDT)
- Chris Moth (Wed Sep 03 2008 - 16:10:19 PDT)
- Arturas Ziemys (Wed Sep 03 2008 - 15:28:44 PDT)
AMBER: nmode/nab entropy calculations memory issues
- Andreas Svrcek-Seiler (Tue Sep 16 2008 - 08:50:11 PDT)
- chaitanya koppisetty (Tue Sep 16 2008 - 07:58:01 PDT)
AMBER: nmode/nab entropy calculations without hydrogens
- chaitanya koppisetty (Wed Sep 17 2008 - 00:47:58 PDT)
AMBER: No bond and angle parameters for - -?????
- Lachele Foley (Lists) (Thu Sep 04 2008 - 07:03:08 PDT)
- Waqas Nasir (Thu Sep 04 2008 - 03:15:37 PDT)
AMBER: Nonbonded FE parameter missing in frcmod.
- moitrayee.mbu.iisc.ernet.in (Thu Sep 11 2008 - 10:16:34 PDT)
- David A. Case (Thu Sep 11 2008 - 10:19:53 PDT)
- moitrayee.mbu.iisc.ernet.in (Thu Sep 11 2008 - 05:22:58 PDT)
AMBER: parallel amber 10 sander.MPI (low cpu utilization)
- meandme meandme (Mon Sep 15 2008 - 10:27:06 PDT)
AMBER: PMEMD and sander.MPI
- Robert Duke (Tue Sep 09 2008 - 07:14:52 PDT)
- Germain Vallverdu (Tue Sep 09 2008 - 06:50:40 PDT)
AMBER: PMEMD installation problem.
- Cenk \(Jenk\) Andac (Mon Sep 08 2008 - 05:46:19 PDT)
- Robert Duke (Mon Sep 08 2008 - 05:20:15 PDT)
- Cenk \(Jenk\) Andac (Mon Sep 08 2008 - 02:16:38 PDT)
- Ross Walker (Mon Sep 08 2008 - 01:21:17 PDT)
- Cenk \(Jenk\) Andac (Sun Sep 07 2008 - 23:58:42 PDT)
AMBER: Position: Postdoctoral Fellow
- Willy Valdivia-Granda (Mon Sep 22 2008 - 08:50:48 PDT)
AMBER: Preparing peptides with D-amino acids
- Carlos Simmerling (Tue Sep 09 2008 - 18:14:34 PDT)
- David Watson (Tue Sep 09 2008 - 18:04:44 PDT)
- Carlos Simmerling (Tue Sep 09 2008 - 17:26:20 PDT)
- Carlos Simmerling (Tue Sep 09 2008 - 17:28:08 PDT)
- David Watson (Tue Sep 09 2008 - 17:06:58 PDT)
AMBER: Problem compiling Amber with Intel 10 compilers - "undefined reference" errors
- Ben Roberts (Tue Sep 09 2008 - 10:38:56 PDT)
- Ben Roberts (Mon Sep 08 2008 - 14:24:30 PDT)
- David A. Case (Mon Sep 08 2008 - 14:09:53 PDT)
- Ben Roberts (Mon Sep 08 2008 - 08:43:47 PDT)
AMBER: Problem in EVB and Trajectory analysis
- sai kumar ramadugu (Fri Sep 05 2008 - 14:20:17 PDT)
AMBER: problem in installing parallel version of amber10 with lam
- Shibasish Chowdhury (Tue Sep 16 2008 - 03:37:06 PDT)
- Ross Walker (Mon Sep 15 2008 - 19:02:48 PDT)
- Shibasish Chowdhury (Sun Sep 14 2008 - 21:20:12 PDT)
AMBER: Problem In Paralklel Amber
- Ross Walker (Mon Sep 29 2008 - 07:35:50 PDT)
- Ranga Swamy (Sun Sep 28 2008 - 22:23:57 PDT)
- Carlos Simmerling (Fri Sep 26 2008 - 04:52:00 PDT)
- Ranga Swamy (Fri Sep 26 2008 - 04:10:13 PDT)
AMBER: Problem of "Too many dipole-dipole interactions allocated" when using amoeba.
- Zhao, Zhen (zhaozh) (Tue Sep 23 2008 - 07:11:23 PDT)
- Tom Darden (Mon Sep 22 2008 - 13:51:53 PDT)
- Zhao, Zhen (zhaozh) (Mon Sep 22 2008 - 12:02:27 PDT)
AMBER: problem of use MPICHI2 to run RMED on amber10
- Carlos Simmerling (Tue Sep 30 2008 - 14:33:12 PDT)
- xwu.purdue.edu (Tue Sep 30 2008 - 14:29:19 PDT)
- Carlos Simmerling (Tue Sep 30 2008 - 14:09:59 PDT)
- xwu.purdue.edu (Tue Sep 30 2008 - 14:03:08 PDT)
- Carlos Simmerling (Tue Sep 30 2008 - 13:45:58 PDT)
- xwu.purdue.edu (Tue Sep 30 2008 - 13:31:24 PDT)
AMBER: problem when running energy minimization with polarizable potential
- Yongmei Pan (Tue Sep 09 2008 - 13:36:33 PDT)
- David A. Case (Tue Sep 09 2008 - 11:32:27 PDT)
- Yongmei Pan (Mon Sep 08 2008 - 08:32:30 PDT)
AMBER: problem with editing with xleap
- David A. Case (Wed Sep 17 2008 - 04:30:55 PDT)
- moitrayee.mbu.iisc.ernet.in (Tue Sep 16 2008 - 08:50:38 PDT)
AMBER: problem with parmchck
- aneesh cna (Tue Sep 30 2008 - 10:10:28 PDT)
AMBER: problem with traj and strip waters
- Carlos Simmerling (Thu Sep 18 2008 - 07:22:30 PDT)
- Steve Seibold (Thu Sep 18 2008 - 07:13:38 PDT)
- David A. Case (Thu Sep 18 2008 - 06:34:18 PDT)
- Carlos Simmerling (Thu Sep 18 2008 - 06:19:17 PDT)
- Steve Seibold (Thu Sep 18 2008 - 06:08:21 PDT)
AMBER: problems with ptraj and strip waters
- Gustavo Seabra (Thu Sep 18 2008 - 16:18:44 PDT)
- Carlos Simmerling (Thu Sep 18 2008 - 14:29:56 PDT)
- Steve Seibold (Thu Sep 18 2008 - 14:19:25 PDT)
AMBER: ptraj & imaging of velocities
- Lars Skjærven (Tue Sep 02 2008 - 06:15:49 PDT)
- FyD (Tue Sep 02 2008 - 06:06:08 PDT)
AMBER: ptraj and netcdf with AmberTools1.2 ?
- Lars Skjærven (Mon Sep 01 2008 - 02:11:23 PDT)
AMBER: QM/MM
- Chih-Ying Lin (Fri Sep 05 2008 - 15:33:23 PDT)
AMBER: Question
- Carlos Simmerling (Wed Sep 17 2008 - 04:18:19 PDT)
- Beale, John (Wed Sep 17 2008 - 04:14:15 PDT)
AMBER: question about dihedral angles
- Ilyas Yildirim (Mon Sep 15 2008 - 08:10:55 PDT)
- Harry (Yicun) Ni (Mon Sep 15 2008 - 07:41:31 PDT)
AMBER: Question: GAFF
- Chih-Ying Lin (Fri Sep 05 2008 - 14:33:14 PDT)
AMBER: RDF: Segmentation fault
- Sergey Samsonov (Wed Sep 10 2008 - 01:13:29 PDT)
AMBER: replica exchange with amber9
- Carlos Simmerling (Tue Sep 23 2008 - 15:52:04 PDT)
- greddy1.umd.edu (Tue Sep 23 2008 - 15:44:24 PDT)
AMBER: resp and 99999
- Ross Walker (Fri Sep 05 2008 - 07:31:51 PDT)
- Markus Kaukonen (Thu Sep 04 2008 - 23:13:10 PDT)
AMBER: RMSD restraint in umbrella sampling
- Carlos Simmerling (Thu Sep 18 2008 - 14:23:01 PDT)
- nurith.rice.edu (Thu Sep 18 2008 - 13:36:24 PDT)
AMBER: Single point energy calculations with explicit solvent.
- Carlos Simmerling (Thu Sep 18 2008 - 05:55:00 PDT)
- Waqas Nasir (Thu Sep 18 2008 - 05:48:47 PDT)
AMBER: solvate without translating
- Ross Walker (Thu Sep 25 2008 - 07:55:53 PDT)
- Ross Walker (Wed Sep 24 2008 - 23:46:52 PDT)
- Anuradha Mittal (Wed Sep 24 2008 - 12:38:31 PDT)
AMBER: solvent interaction in active site
- Carlos Simmerling (Mon Sep 01 2008 - 06:49:20 PDT)
- S.Sundar Raman (Mon Sep 01 2008 - 07:28:10 PDT)
AMBER: Some Problems With the Installation of Ambertools
- David A. Case (Sat Sep 20 2008 - 05:38:55 PDT)
- Manikandan Chandrasekaran (Fri Sep 19 2008 - 12:49:41 PDT)
- David A. Case (Thu Sep 18 2008 - 11:35:27 PDT)
- Manikandan Chandrasekaran (Thu Sep 18 2008 - 09:43:39 PDT)
- David A. Case (Thu Sep 18 2008 - 04:10:12 PDT)
- Atro Tossavainen (Thu Sep 18 2008 - 01:06:57 PDT)
- Manikandan Chandrasekaran (Wed Sep 17 2008 - 16:21:06 PDT)
AMBER: steered MD
- Germain Vallverdu (Wed Sep 10 2008 - 05:10:49 PDT)
- Adrian Roitberg (Wed Sep 10 2008 - 04:31:19 PDT)
- David A. Case (Wed Sep 10 2008 - 04:30:27 PDT)
- Carlos Simmerling (Wed Sep 10 2008 - 04:23:51 PDT)
- Germain Vallverdu (Wed Sep 10 2008 - 04:17:10 PDT)
- Carlos Simmerling (Wed Sep 10 2008 - 03:32:02 PDT)
- Germain Vallverdu (Wed Sep 10 2008 - 03:26:31 PDT)
AMBER: Temperature regulation
- julliane Yoneda (Tue Sep 16 2008 - 16:34:52 PDT)
- julliane Yoneda (Tue Sep 16 2008 - 16:36:01 PDT)
- Myunggi Yi (Tue Sep 16 2008 - 14:28:21 PDT)
- Carlos Simmerling (Tue Sep 16 2008 - 11:22:55 PDT)
- julliane Yoneda (Tue Sep 16 2008 - 11:05:27 PDT)
- Carlos Simmerling (Mon Sep 15 2008 - 18:07:57 PDT)
- julliane Yoneda (Mon Sep 15 2008 - 17:48:50 PDT)
AMBER: Test error in installing amber 10 using four threads on a single-cpu machine
- David A. Case (Sun Sep 07 2008 - 15:07:14 PDT)
- haixiao jin (Sun Sep 07 2008 - 06:26:31 PDT)
- David A. Case (Sun Sep 07 2008 - 05:50:57 PDT)
- haixiao jin (Sun Sep 07 2008 - 02:42:10 PDT)
AMBER: The forming of micelle
- Chih-Ying Lin (Tue Sep 23 2008 - 17:07:47 PDT)
- Chih-Ying Lin (Mon Sep 22 2008 - 12:02:30 PDT)
- Adrian Roitberg (Mon Sep 22 2008 - 11:20:50 PDT)
- Chih-Ying Lin (Mon Sep 22 2008 - 11:06:24 PDT)
AMBER: The forming of micelle (CMC)
- Gustavo Seabra (Wed Sep 24 2008 - 15:00:45 PDT)
- Chih-Ying Lin (Wed Sep 24 2008 - 11:02:22 PDT)
AMBER: The size of the simulation box and the # of solute / water molecules?
- Chih-Ying Lin (Mon Sep 22 2008 - 12:19:06 PDT)
AMBER: tleap and Zn parameter
- Ross Walker (Wed Sep 03 2008 - 08:31:26 PDT)
- David A. Case (Tue Sep 02 2008 - 13:41:21 PDT)
- David A. Case (Mon Sep 01 2008 - 06:53:26 PDT)
- Aust, Susanne (Mon Sep 01 2008 - 01:14:53 PDT)
AMBER: to prepare pdb file fro unusual amino acid.
- priya priya (Thu Sep 25 2008 - 09:40:07 PDT)
- Ross Walker (Thu Sep 25 2008 - 07:55:21 PDT)
- Ross Walker (Wed Sep 24 2008 - 23:36:08 PDT)
- waqasuddin.khan.iccs.edu (Wed Sep 24 2008 - 22:55:51 PDT)
- FyD (Wed Sep 24 2008 - 11:36:03 PDT)
- Hakkim Boy (Wed Sep 24 2008 - 07:41:33 PDT)
- priya priya (Wed Sep 24 2008 - 01:03:06 PDT)
AMBER: top and crd files without hydrogen
- Waqas Nasir (Tue Sep 16 2008 - 03:32:42 PDT)
- Carlos Simmerling (Tue Sep 16 2008 - 03:04:36 PDT)
- Waqas Nasir (Tue Sep 16 2008 - 02:18:08 PDT)
AMBER: unsubscribe amber
- steinbrt.scripps.edu (Mon Sep 29 2008 - 07:57:50 PDT)
AMBER: Using AMBER forces
- Germain Vallverdu (Tue Sep 09 2008 - 06:48:32 PDT)
AMBER: who can give a sample input file regarding the energy decomposition with sander?
- David A. Case (Mon Sep 08 2008 - 14:31:50 PDT)
- Yongmei Pan (Mon Sep 08 2008 - 13:41:37 PDT)
AMBER: xleap and Sirius on ubuntu 8.04
- Sasha Buzko (Thu Sep 11 2008 - 20:22:38 PDT)
- Gustavo Seabra (Thu Sep 11 2008 - 20:13:58 PDT)
- alsarraj (Thu Sep 11 2008 - 19:45:54 PDT)
AMBER: xleap fails to savemol2
- Mark Williamson (Mon Sep 22 2008 - 11:43:35 PDT)
- alsarraj (Fri Sep 19 2008 - 13:59:44 PDT)
- alsarraj (Thu Sep 18 2008 - 13:15:20 PDT)
- FyD (Thu Sep 04 2008 - 12:45:49 PDT)
AMBER: XLF problem in compiling AMBER8 on IBM PPC64 SUSE
- liu junjun (Tue Sep 30 2008 - 12:17:26 PDT)
- liu junjun (Tue Sep 30 2008 - 11:48:11 PDT)
- Jed W Pitera (Tue Sep 30 2008 - 11:56:18 PDT)
- Ross Walker (Tue Sep 30 2008 - 11:18:44 PDT)
- liu junjun (Tue Sep 30 2008 - 11:07:09 PDT)
AW: AMBER: tleap and Zn parameter
- Aust, Susanne (Wed Sep 03 2008 - 00:18:28 PDT)
- Aust, Susanne (Mon Sep 01 2008 - 23:46:23 PDT)
Personal favor
- fatima.chami.durham.ac.uk (Mon Sep 01 2008 - 04:29:46 PDT)
reaction coordinate in umbrella sampling
- Jerome.GOLEBIOWSKI.unice.fr (Tue Sep 23 2008 - 00:33:43 PDT)
- Sudha Mani Karra (Mon Sep 22 2008 - 08:00:42 PDT)
reference paper - pls help
- Ross Walker (Fri Sep 05 2008 - 09:37:24 PDT)

Amber Archive Sep 2008 by subject