Amber Archive Feb 2010: by subject

[AMBER] (no subject)
- Yubo Fan (Tue Feb 16 2010 - 10:23:15 PST)
- Rebeca García Fandiño (Tue Feb 16 2010 - 10:14:45 PST)
- case (Tue Feb 16 2010 - 04:34:33 PST)
- Yubo Fan (Tue Feb 16 2010 - 00:31:46 PST)
- mani grover (Mon Feb 08 2010 - 22:19:15 PST)
[AMBER] 10_12 potential
- aapeters.ncsu.edu (Tue Feb 09 2010 - 06:38:42 PST)
- case (Mon Feb 08 2010 - 18:40:39 PST)
- aapeters.ncsu.edu (Mon Feb 08 2010 - 12:40:11 PST)
- aapeters.ncsu.edu (Mon Feb 08 2010 - 08:54:09 PST)
- case (Mon Feb 08 2010 - 05:19:34 PST)
- aapeters.ncsu.edu (Mon Feb 08 2010 - 00:14:39 PST)
[AMBER] [Fwd: 10_12 potential]
- aapeters.ncsu.edu (Mon Feb 08 2010 - 03:01:35 PST)
[AMBER] About RAMD
- Cojocaru,Vlad (Thu Feb 11 2010 - 13:18:28 PST)
- Francesco Pietra (Thu Feb 11 2010 - 08:57:32 PST)
- Vlad Cojocaru (Thu Feb 11 2010 - 06:57:20 PST)
- gokul algates (Thu Feb 11 2010 - 06:27:32 PST)
[AMBER] About the err of antechamber's tutorial!
- FyD (Fri Feb 05 2010 - 09:27:27 PST)
- David Watson (Fri Feb 05 2010 - 08:00:03 PST)
- David Watson (Fri Feb 05 2010 - 07:25:06 PST)
- Aurum Bai (Fri Feb 05 2010 - 07:07:49 PST)
[AMBER] Add charge on quaternary nitrogen
- Pol Boudard (Fri Feb 05 2010 - 05:40:34 PST)
[AMBER] adding atom types to leapfrc
- Jason Swails (Thu Feb 04 2010 - 07:34:05 PST)
- Francesco Pietra (Thu Feb 04 2010 - 02:50:15 PST)
- Francesco Pietra (Thu Feb 04 2010 - 02:50:41 PST)
- Bill Ross (Wed Feb 03 2010 - 11:11:56 PST)
- Francesco Pietra (Wed Feb 03 2010 - 10:53:00 PST)
[AMBER] Addles and makeDIST_RST
- Titus, Jamie (bairdje) (Thu Feb 04 2010 - 04:58:13 PST)
- case (Wed Feb 03 2010 - 14:45:12 PST)
- Titus, Jamie (bairdje) (Wed Feb 03 2010 - 12:08:20 PST)
[AMBER] Amber 8 sander.f file, force.f file
- gokul algates (Fri Feb 19 2010 - 21:14:34 PST)
[AMBER] AMBER 9 parallel compilation problem on Mac OS X 10.6
- David Watson (Wed Feb 03 2010 - 06:21:11 PST)
- case (Wed Feb 03 2010 - 04:48:43 PST)
- pelaez.usal.es (Wed Feb 03 2010 - 04:15:43 PST)
[AMBER] AMBER MD simulation
- Nancy (Tue Feb 23 2010 - 02:56:50 PST)
[AMBER] AMBER10 build - failing "jar" and "jar_multi" tests
- Mark Dixon (Fri Feb 05 2010 - 07:15:02 PST)
- Jason Swails (Fri Feb 05 2010 - 07:02:57 PST)
- Mark Dixon (Fri Feb 05 2010 - 06:55:29 PST)
[AMBER] Amber11 vs Amber10
- case (Thu Feb 04 2010 - 11:20:16 PST)
- Steve Seibold (Thu Feb 04 2010 - 10:58:59 PST)
[AMBER] AmberTools1.3 installation error
- case (Wed Feb 24 2010 - 11:35:43 PST)
- Bill Ross (Wed Feb 24 2010 - 10:18:52 PST)
- Bill Ross (Wed Feb 24 2010 - 09:58:16 PST)
- Jason Swails (Wed Feb 24 2010 - 09:30:40 PST)
- Anna Dejardin (Wed Feb 24 2010 - 02:38:26 PST)
- Bill Ross (Tue Feb 23 2010 - 10:06:01 PST)
- Anna Dejardin (Tue Feb 23 2010 - 05:45:35 PST)
- Atro Tossavainen (Tue Feb 23 2010 - 05:36:51 PST)
- case (Tue Feb 23 2010 - 05:01:37 PST)
- Anna Dejardin (Tue Feb 23 2010 - 03:23:54 PST)
[AMBER] amoeba--Too many dipole_dipole interactions for allocated
- case (Thu Feb 18 2010 - 14:49:03 PST)
- Dian Jiao (Thu Feb 18 2010 - 12:03:27 PST)
- case (Thu Feb 18 2010 - 08:43:51 PST)
- Dian Jiao (Thu Feb 18 2010 - 08:25:45 PST)
[AMBER] Announcement: Amber MD Workshop 2010 in Duesseldorf, Germany April 26-30th
- xueping chin (Thu Feb 04 2010 - 01:35:07 PST)
- steinbrt.rci.rutgers.edu (Thu Feb 04 2010 - 00:37:17 PST)
- xueping chin (Wed Feb 03 2010 - 15:47:53 PST)
- steinbrt.rci.rutgers.edu (Tue Feb 02 2010 - 02:45:53 PST)
[AMBER] antechamber with carbon monoxide
- Francesco Pietra (Sat Feb 06 2010 - 02:52:54 PST)
[AMBER] Antechamber: imidazole=aromatic, imidazolium=not aromatic?
- Dmitry Mukha (Wed Feb 10 2010 - 00:17:43 PST)
- FyD (Tue Feb 09 2010 - 22:41:34 PST)
- Gabriel Rocklin (Mon Feb 08 2010 - 23:33:17 PST)
[AMBER] are translations applied in the 'average' command of ptraj?
- Thomas Cheatham (Sat Feb 20 2010 - 01:20:01 PST)
- Jose Borreguero (Fri Feb 19 2010 - 16:02:22 PST)
[AMBER] Binding energy calculation using MMPBSA.py: Sander from amber9 complains "mdfil: Error unknown flag: -y"
- Arvind Marathe (Tue Feb 16 2010 - 01:26:14 PST)
- Jason Swails (Mon Feb 15 2010 - 06:40:22 PST)
- Arvind Marathe (Mon Feb 15 2010 - 06:30:04 PST)
[AMBER] Calcium and Phosphate
- Syed Tarique Moin (Wed Feb 17 2010 - 02:29:02 PST)
- sikander azam (Tue Feb 16 2010 - 22:12:22 PST)
[AMBER] ccl4 simulation
- Sandro L. Fornili (Thu Feb 18 2010 - 01:02:52 PST)
- FyD (Wed Feb 17 2010 - 15:10:30 PST)
[AMBER] chamber - psf/pdb from VMD
- Mark Williamson (Fri Feb 19 2010 - 10:41:08 PST)
- Alan (Fri Feb 19 2010 - 00:48:31 PST)
- Balazs Jojart (Thu Feb 18 2010 - 23:27:48 PST)
- Mark Williamson (Thu Feb 18 2010 - 18:12:14 PST)
- Mark Williamson (Thu Feb 18 2010 - 15:08:48 PST)
- Balazs Jojart (Thu Feb 18 2010 - 13:45:18 PST)
[AMBER] Charge protocol for OLP, HYP
- FyD (Sat Feb 27 2010 - 23:27:48 PST)
- FyD (Sat Feb 27 2010 - 23:24:44 PST)
- Emmanuel Baribefe Naziga (Sat Feb 27 2010 - 16:29:55 PST)
- FyD (Sat Feb 27 2010 - 09:10:22 PST)
- Lachele Foley (Lists) (Fri Feb 26 2010 - 10:12:18 PST)
- Emmanuel Baribefe Naziga (Fri Feb 26 2010 - 08:28:22 PST)
- Lachele Foley (Lists) (Fri Feb 26 2010 - 07:56:44 PST)
- Emmanuel Baribefe Naziga (Thu Feb 25 2010 - 09:33:32 PST)
- Lachele Foley (Lists) (Thu Feb 25 2010 - 09:27:15 PST)
- Emmanuel Baribefe Naziga (Wed Feb 24 2010 - 07:36:14 PST)
- Lachele Foley (Lists) (Wed Feb 24 2010 - 06:59:36 PST)
- Carlos Simmerling (Wed Feb 24 2010 - 06:28:17 PST)
- FyD (Wed Feb 24 2010 - 06:20:29 PST)
- Emmanuel Baribefe Naziga (Tue Feb 23 2010 - 17:52:43 PST)
[AMBER] Charges of ASN in all_aminoct03
- FyD (Mon Feb 08 2010 - 08:55:04 PST)
- CR Gregor (Mon Feb 08 2010 - 05:27:20 PST)
[AMBER] compiling amber on intel xeon 5500 series cpu
- Bill Ross (Fri Feb 12 2010 - 14:22:56 PST)
- Max Wang (Fri Feb 12 2010 - 14:10:19 PST)
- Bill Ross (Fri Feb 12 2010 - 12:26:17 PST)
- Max Wang (Fri Feb 12 2010 - 12:16:29 PST)
[AMBER] Converting Gaussian output format to the RESP input format
- imtiaz shafiq (Tue Feb 02 2010 - 00:31:36 PST)
- imtiaz shafiq (Mon Feb 01 2010 - 23:53:06 PST)
- FyD (Mon Feb 01 2010 - 11:25:38 PST)
- Jason Swails (Mon Feb 01 2010 - 07:54:59 PST)
- imtiaz shafiq (Mon Feb 01 2010 - 07:44:45 PST)
[AMBER] deriving charges for use with gaff
- FyD (Sat Feb 20 2010 - 05:39:30 PST)
- Sidney Elmer (Fri Feb 19 2010 - 12:00:06 PST)
[AMBER] design of peptides to stabilize proteins
- Jason Swails (Wed Feb 24 2010 - 09:27:47 PST)
- Simon Becker (Wed Feb 24 2010 - 06:55:24 PST)
[AMBER] deuterate protein atoms by editing the topology file
- Jose Borreguero (Tue Feb 02 2010 - 13:35:24 PST)
- case (Tue Feb 02 2010 - 13:31:41 PST)
- Jose Borreguero (Tue Feb 02 2010 - 12:16:43 PST)
[AMBER] dielectric constant in NMODE
- Jeffrey (Wed Feb 03 2010 - 18:45:26 PST)
[AMBER] Energy Minimization of a Complex
- Dean Cuebas (Sun Feb 07 2010 - 17:53:49 PST)
- MUHAMMAD IMTIA SHAFIQ (Sun Feb 07 2010 - 16:22:57 PST)
[AMBER] enquire of NAB tutorial or any detailed introduction
- case (Sun Feb 21 2010 - 18:28:03 PST)
- xueqin pang (Sun Feb 21 2010 - 06:41:08 PST)
[AMBER] enquiry regarding distance-dependent dielectric constant minimization
- David A. Case (Thu Feb 18 2010 - 04:59:22 PST)
- bharat lakhani (Mon Feb 15 2010 - 23:35:44 PST)
[AMBER] errors in leap
- Bill Ross (Mon Feb 01 2010 - 09:24:50 PST)
- case (Mon Feb 01 2010 - 08:19:13 PST)
- Jason Swails (Mon Feb 01 2010 - 07:32:13 PST)
- Beale, John (Mon Feb 01 2010 - 07:09:06 PST)
[AMBER] failure when doing bugfix patch for amber10 and tools V1.2
- xueqin pang (Thu Feb 04 2010 - 17:45:05 PST)
- Ray Luo (Wed Feb 03 2010 - 10:03:45 PST)
- xueqin pang (Tue Feb 02 2010 - 22:52:56 PST)
[AMBER] Final PDB after Energy minimization
- Carlos Simmerling (Tue Feb 23 2010 - 19:39:15 PST)
- Shaandar Nyamtulga (Tue Feb 23 2010 - 19:03:15 PST)
[AMBER] Fitting Torsional parameters
- Ilyas Yildirim (Wed Feb 17 2010 - 17:36:07 PST)
- stephane acoca (Wed Feb 17 2010 - 08:07:09 PST)
- stephane acoca (Mon Feb 15 2010 - 13:49:24 PST)
- Jason Swails (Mon Feb 15 2010 - 09:42:31 PST)
- Ilyas Yildirim (Mon Feb 15 2010 - 08:07:05 PST)
- stephane acoca (Mon Feb 15 2010 - 07:48:07 PST)
[AMBER] Glycerol Models
- FyD (Wed Feb 17 2010 - 15:02:07 PST)
- Mannan (Wed Feb 17 2010 - 06:50:27 PST)
- FyD (Sat Feb 13 2010 - 00:45:16 PST)
- Mannan (Fri Feb 12 2010 - 00:39:45 PST)
[AMBER] GUI Competition
- Vlad (Wed Feb 24 2010 - 15:21:52 PST)
- case (Wed Feb 24 2010 - 07:53:15 PST)
- Matthew Tessier (Wed Feb 24 2010 - 06:18:20 PST)
[AMBER] helicity of a peptide
- Carlos Simmerling (Wed Feb 24 2010 - 04:45:21 PST)
- Mannan (Wed Feb 24 2010 - 00:56:41 PST)
[AMBER] help
- Billy Miller III (Thu Feb 18 2010 - 05:58:04 PST)
- vaibhav jain (Thu Feb 18 2010 - 05:54:02 PST)
[AMBER] help on minimization
- bharat lakhani (Fri Feb 19 2010 - 05:51:29 PST)
- bharat lakhani (Fri Feb 19 2010 - 05:44:18 PST)
[AMBER] how is better to measure ligand drift against protein in Amber
- Andrew Voronkov (Mon Feb 15 2010 - 06:21:02 PST)
[AMBER] How to construct the methyl-animo acid?
- FyD (Tue Feb 02 2010 - 03:24:24 PST)
- Aurum Bai (Tue Feb 02 2010 - 01:17:02 PST)
[AMBER] how to fix or restraint atoms in molecules
- Jim Miller (Tue Feb 09 2010 - 00:30:20 PST)
[AMBER] how to generate acetone box
- FyD (Wed Feb 17 2010 - 14:47:03 PST)
- parvesh singh (Wed Feb 17 2010 - 03:10:09 PST)
[AMBER] how to identify closest waters to protein surface?
- Jose Borreguero (Sat Feb 20 2010 - 16:24:40 PST)
- Tom Joseph (Sat Feb 20 2010 - 16:01:24 PST)
- Jose Borreguero (Sat Feb 20 2010 - 15:47:54 PST)
[AMBER] How to unsolvate solvated protein?
- Jason Swails (Tue Feb 23 2010 - 21:51:47 PST)
- Bill Ross (Tue Feb 23 2010 - 21:34:52 PST)
- Shaandar Nyamtulga (Tue Feb 23 2010 - 21:17:21 PST)
[AMBER] If this is normal for 3 or 4 sander.MPI jobs appearing on one node
- Carlos Simmerling (Tue Feb 02 2010 - 11:51:57 PST)
- MUHAMMAD IMTIA SHAFIQ (Tue Feb 02 2010 - 11:46:31 PST)
[AMBER] Imaging difficulty
- Hopkins, Robert (Mon Feb 08 2010 - 12:39:59 PST)
[AMBER] Information regarding how to group atoms for ionic liquid
- case (Wed Feb 03 2010 - 10:40:30 PST)
- dhilip kumar ramalingam (Wed Feb 03 2010 - 01:10:31 PST)
[AMBER] Installation error of amber10 after compile Ambertools1.3
- Jason Swails (Sun Feb 28 2010 - 09:07:11 PST)
- Trevor Gokey (Sun Feb 28 2010 - 00:35:08 PST)
- Jason Swails (Sat Feb 27 2010 - 12:46:48 PST)
- albert albert (Sat Feb 27 2010 - 12:37:51 PST)
[AMBER] installation problem
- case (Tue Feb 23 2010 - 04:50:10 PST)
- gunajyoti das (Tue Feb 23 2010 - 00:51:52 PST)
[AMBER] Instaltion parallel amber on macbook pro
- Jason Swails (Sun Feb 28 2010 - 09:01:51 PST)
- Christine Baranski (Sun Feb 28 2010 - 04:15:00 PST)
[AMBER] interaction energy of single residue to its environment
- Carlos Simmerling (Mon Feb 01 2010 - 11:04:16 PST)
- luzhenw1.msu.edu (Mon Feb 01 2010 - 10:49:56 PST)
[AMBER] limit of joining residues
- Jio M (Wed Feb 17 2010 - 06:56:32 PST)
- Bill Ross (Mon Feb 15 2010 - 14:10:00 PST)
- Jio M (Sun Feb 14 2010 - 21:03:49 PST)
- Bill Ross (Sun Feb 14 2010 - 12:10:17 PST)
- Jio M (Sun Feb 14 2010 - 03:42:34 PST)
- Bill Ross (Sat Feb 13 2010 - 11:22:33 PST)
- FyD (Sat Feb 13 2010 - 00:37:50 PST)
- Jio M (Sat Feb 13 2010 - 00:20:58 PST)
- Bill Ross (Thu Feb 11 2010 - 09:46:04 PST)
- FyD (Thu Feb 11 2010 - 02:47:34 PST)
- Jio M (Thu Feb 11 2010 - 00:34:52 PST)
- Bill Ross (Wed Feb 10 2010 - 10:00:43 PST)
- Jio M (Wed Feb 10 2010 - 08:12:58 PST)
- Bill Ross (Mon Feb 08 2010 - 09:32:57 PST)
- Jio M (Mon Feb 08 2010 - 05:38:54 PST)
[AMBER] load pdb into xleap
- case (Fri Feb 05 2010 - 04:27:14 PST)
- Jim Miller (Fri Feb 05 2010 - 01:12:12 PST)
[AMBER] loading parm7 and coords with tLeap?
- Nicholas Musolino (Fri Feb 05 2010 - 08:48:52 PST)
- case (Thu Feb 04 2010 - 19:35:03 PST)
- Nicholas Musolino (Thu Feb 04 2010 - 12:41:10 PST)
[AMBER] mailing list
- manikanthan bhavaraju (Tue Feb 09 2010 - 13:22:45 PST)
[AMBER] makeCHIR_RST and LES
- Titus, Jamie (bairdje) (Fri Feb 19 2010 - 07:40:55 PST)
- Carlos Simmerling (Fri Feb 19 2010 - 06:51:37 PST)
- Titus, Jamie (bairdje) (Wed Feb 17 2010 - 08:34:13 PST)
[AMBER] MM PBSA problem
- Jagdeesh C (Sat Feb 13 2010 - 09:53:32 PST)
- Ray Luo (Sat Feb 13 2010 - 09:31:59 PST)
- Jagdeesh C (Sat Feb 13 2010 - 08:49:19 PST)
[AMBER] mm-pbsa receptor and ligand masking
- Jio M (Fri Feb 19 2010 - 07:52:54 PST)
- Billy Miller III (Fri Feb 19 2010 - 06:32:24 PST)
- Jio M (Fri Feb 19 2010 - 06:07:49 PST)
- Jason Swails (Thu Feb 18 2010 - 16:17:42 PST)
- Workalemhu Berhanu (Thu Feb 18 2010 - 15:38:41 PST)
- Jason Swails (Thu Feb 18 2010 - 13:35:31 PST)
- Billy Miller III (Thu Feb 18 2010 - 13:32:58 PST)
- Workalemhu Berhanu (Thu Feb 18 2010 - 13:26:03 PST)
[AMBER] MM-PBSA: decompose energy error
- Ryan Pavlovicz (Fri Feb 19 2010 - 11:30:54 PST)
[AMBER] mm_pbsa statistics problem
- Marina Grabar (Mon Feb 15 2010 - 04:48:17 PST)
- Ray Luo (Fri Feb 12 2010 - 09:51:27 PST)
- Dwight McGee (Fri Feb 12 2010 - 07:28:55 PST)
- Marina Grabar (Fri Feb 12 2010 - 03:57:24 PST)
- Ray Luo (Thu Feb 11 2010 - 09:20:54 PST)
- Marina Grabar (Thu Feb 11 2010 - 07:22:05 PST)
- Dwight McGee (Thu Feb 11 2010 - 07:09:14 PST)
- Marina Grabar (Thu Feb 11 2010 - 06:51:01 PST)
[AMBER] MMPBSA
- Jason Swails (Mon Feb 01 2010 - 04:38:57 PST)
- Billy Miller III (Mon Feb 01 2010 - 04:24:03 PST)
- s. Bill (Mon Feb 01 2010 - 03:43:11 PST)
[AMBER] mmpbsa error: No data for 0+2 MM BOND 200
- xueqin pang (Mon Feb 01 2010 - 22:46:08 PST)
- Jason Swails (Mon Feb 01 2010 - 20:16:20 PST)
- xueqin pang (Mon Feb 01 2010 - 17:25:55 PST)
[AMBER] MMPBSA.py error
- s. Bill (Thu Feb 11 2010 - 04:14:18 PST)
- Jason Swails (Wed Feb 10 2010 - 16:57:52 PST)
- s. Bill (Wed Feb 10 2010 - 16:40:13 PST)
- s. Bill (Wed Feb 10 2010 - 15:46:34 PST)
[AMBER] mmpbsa.py ion radius
- Jason Swails (Mon Feb 15 2010 - 10:58:08 PST)
- Dian Jiao (Mon Feb 15 2010 - 10:38:16 PST)
- Jason Swails (Mon Feb 15 2010 - 10:29:27 PST)
- s. Bill (Mon Feb 15 2010 - 10:16:29 PST)
- Billy Miller III (Sat Feb 13 2010 - 18:25:08 PST)
- s. Bill (Sat Feb 13 2010 - 18:02:43 PST)
[AMBER] MOL2 Output through LEAP
- case (Tue Feb 02 2010 - 13:28:59 PST)
- FyD (Tue Feb 02 2010 - 13:19:20 PST)
- Jason Swails (Tue Feb 02 2010 - 12:30:21 PST)
- Matthew Tessier (Tue Feb 02 2010 - 12:01:15 PST)
- Jason Swails (Tue Feb 02 2010 - 11:41:19 PST)
- Matthew Tessier (Tue Feb 02 2010 - 11:20:54 PST)
[AMBER] MPICH2 and AMBER9
- Jason Swails (Mon Feb 22 2010 - 12:43:31 PST)
- dxli75 (Mon Feb 22 2010 - 12:37:25 PST)
[AMBER] msd calculation using ptraj diffusion
- hannes.loeffler.stfc.ac.uk (Sat Feb 27 2010 - 05:18:59 PST)
- Monika Sharma (Sat Feb 27 2010 - 01:30:09 PST)
- hannes.loeffler.stfc.ac.uk (Sat Feb 27 2010 - 01:22:20 PST)
- Monika Sharma (Fri Feb 26 2010 - 22:05:39 PST)
[AMBER] multiple intercalating waters
- wong105.llnl.gov (Thu Feb 04 2010 - 11:05:32 PST)
[AMBER] New Bursaries and Plenary Speaker - Molecular Modeling Workshop 2010 in Erlangen, Germany
- Harald Lanig (Thu Feb 18 2010 - 02:39:24 PST)
[AMBER] NMR complex and vlimit exceeded
- Carlos Simmerling (Thu Feb 25 2010 - 13:46:29 PST)
- Michael Durney (Thu Feb 25 2010 - 08:00:50 PST)
[AMBER] Not runing the Nmode!
- Billy Miller III (Thu Feb 25 2010 - 07:52:25 PST)
- Aurum Bai (Thu Feb 25 2010 - 07:02:18 PST)
[AMBER] parallel test error
- Jason Swails (Tue Feb 23 2010 - 07:23:49 PST)
- Nicee (Tue Feb 23 2010 - 01:34:00 PST)
[AMBER] parameters for heme-CO
- FyD (Wed Feb 03 2010 - 06:38:07 PST)
- Francesco Pietra (Tue Feb 02 2010 - 10:51:12 PST)
[AMBER] parmchk lists multiple values of the same parameter
- Jason Swails (Wed Feb 03 2010 - 10:05:05 PST)
- Sidney Elmer (Wed Feb 03 2010 - 09:12:39 PST)
[AMBER] PARMSCAN
- Ross Walker (Sun Feb 21 2010 - 19:50:25 PST)
- Peter Charles Kahuna (Sun Feb 21 2010 - 18:38:14 PST)
- Peter Charles Kahuna (Fri Feb 19 2010 - 19:13:56 PST)
- E.M. (Tue Feb 16 2010 - 20:08:45 PST)
- E.M. (Mon Feb 15 2010 - 19:58:15 PST)
[AMBER] Periodic Boundary in AMBER(PMEMD) GPU Acceleration support ?
- jacky zhao (Sat Feb 27 2010 - 00:42:45 PST)
- Ross Walker (Fri Feb 26 2010 - 21:40:56 PST)
- ZhaoLei (Fri Feb 26 2010 - 19:57:59 PST)
- Hiromasa WATANABE (Thu Feb 25 2010 - 22:40:26 PST)
- Ross Walker (Thu Feb 25 2010 - 22:22:09 PST)
- Hiromasa WATANABE (Thu Feb 25 2010 - 19:05:41 PST)
[AMBER] Perturbed charges and types
- case (Mon Feb 22 2010 - 07:44:22 PST)
- s. Bill (Sun Feb 21 2010 - 08:01:14 PST)
[AMBER] plotting RMS vs. residue number
- Beale, John (Mon Feb 01 2010 - 11:15:39 PST)
[AMBER] plumed and sander.MPI
- Jason Swails (Fri Feb 12 2010 - 15:26:37 PST)
- Giuseppe De Marco (Fri Feb 12 2010 - 10:07:08 PST)
[AMBER] PMEMD compiling errors
- Dian Jiao (Thu Feb 11 2010 - 19:10:46 PST)
- Jason Swails (Thu Feb 11 2010 - 18:10:34 PST)
- Dian Jiao (Thu Feb 11 2010 - 15:56:31 PST)
[AMBER] pmemd.cuda progress
- Ross Walker (Thu Feb 18 2010 - 18:51:51 PST)
- Trevor Gokey (Thu Feb 18 2010 - 16:44:15 PST)
[AMBER] positional restraints of different strengths
- Jose Borreguero (Tue Feb 09 2010 - 05:00:06 PST)
- case (Sat Feb 06 2010 - 08:53:38 PST)
- Jose Borreguero (Sat Feb 06 2010 - 03:33:10 PST)
- Bill Ross (Fri Feb 05 2010 - 16:51:16 PST)
- Jose Borreguero (Fri Feb 05 2010 - 15:55:28 PST)
[AMBER] Problem compiling Amber 10 after applying latest bugfix file
- Sanders, Larry R. (Wed Feb 10 2010 - 12:17:40 PST)
[AMBER] Problem in creating cubic water box
- Sangita Kachhap (Sat Feb 13 2010 - 00:43:54 PST)
- case (Tue Feb 09 2010 - 09:46:12 PST)
- Bill Ross (Mon Feb 08 2010 - 10:21:47 PST)
- Sangita Kachhap (Mon Feb 08 2010 - 09:51:28 PST)
[AMBER] Problem in MM-PBSA
- Jason Swails (Thu Feb 25 2010 - 08:08:34 PST)
- Hyma vathi (Thu Feb 25 2010 - 01:54:48 PST)
[AMBER] Problem in Ptraj
- Jason Swails (Fri Feb 05 2010 - 23:22:19 PST)
- Kshatresh Dutta Dubey (Fri Feb 05 2010 - 22:41:12 PST)
[AMBER] Problem in setting parameters for non standard DG residue:O6-Methylguanine
- case (Mon Feb 01 2010 - 08:04:51 PST)
- Jason Swails (Mon Feb 01 2010 - 04:52:39 PST)
- Carlos Simmerling (Mon Feb 01 2010 - 03:53:36 PST)
- N.R. Jena (Mon Feb 01 2010 - 03:47:47 PST)
[AMBER] problem of chenge of the water box during equilibration
- Sangita Kachhap (Sat Feb 13 2010 - 00:42:32 PST)
- Jason Swails (Wed Feb 10 2010 - 08:54:07 PST)
- Sangita Kachhap (Wed Feb 10 2010 - 08:48:34 PST)
[AMBER] Problem reading PDB residues in AmberTools-1.3
- case (Thu Feb 04 2010 - 19:28:36 PST)
- Hopkins, Robert (Thu Feb 04 2010 - 18:10:04 PST)
[AMBER] Problem with specifying mask for MMPBSA.py script
- Arvind Marathe (Fri Feb 12 2010 - 09:54:45 PST)
- Billy Miller III (Fri Feb 12 2010 - 07:50:44 PST)
- Arvind Marathe (Fri Feb 12 2010 - 07:09:03 PST)
[AMBER] Problem with translate restrt file
- Jason Swails (Sun Feb 28 2010 - 16:32:12 PST)
- Ivan Gladich (Sun Feb 28 2010 - 14:17:45 PST)
- Jason Swails (Sun Feb 28 2010 - 11:07:53 PST)
- Ivan Gladich (Sun Feb 28 2010 - 11:00:06 PST)
[AMBER] Problems with PMEMD compilation
- Alex Rodriguez (Fri Feb 12 2010 - 02:45:09 PST)
[AMBER] Protein + Bilayer Simulations: Role of salt
- Jason Swails (Sun Feb 28 2010 - 16:40:37 PST)
- Lalit Dubey (Sun Feb 28 2010 - 15:35:05 PST)
- Barbault Florent (Sun Feb 28 2010 - 14:16:07 PST)
- Lalit Dubey (Sun Feb 28 2010 - 13:32:05 PST)
[AMBER] Protein Stability in amber mmpbsa tutorial
- MUHAMMAD IMTIA SHAFIQ (Mon Feb 22 2010 - 12:54:54 PST)
[AMBER] ptraj, imaging for NAMD generated dcd files, Error in tokenize
- Monika Sharma (Thu Feb 25 2010 - 05:02:53 PST)
- Hannes Loeffler (Thu Feb 25 2010 - 04:55:08 PST)
- Monika Sharma (Thu Feb 25 2010 - 04:24:20 PST)
- Monika Sharma (Thu Feb 25 2010 - 04:20:16 PST)
[AMBER] ptraj.MPI issue with
- Trevor Gokey (Mon Feb 22 2010 - 17:11:25 PST)
[AMBER] ptraj.MPI issue with "uninterruptible sleep"
- Ross Walker (Mon Feb 22 2010 - 17:37:23 PST)
- Jason Swails (Mon Feb 22 2010 - 16:38:29 PST)
- Trevor Gokey (Mon Feb 22 2010 - 16:04:28 PST)
[AMBER] QM/MM new parameters
- s. Bill (Tue Feb 09 2010 - 14:40:08 PST)
- Ross Walker (Tue Feb 09 2010 - 04:14:38 PST)
- s. Bill (Mon Feb 08 2010 - 15:53:52 PST)
- Adrian Roitberg (Mon Feb 08 2010 - 15:40:10 PST)
- s. Bill (Mon Feb 08 2010 - 15:32:59 PST)
[AMBER] Query about LMOD
- gunajyoti das (Thu Feb 25 2010 - 03:53:31 PST)
[AMBER] Query about xmin
- case (Thu Feb 25 2010 - 05:33:33 PST)
- gunajyoti das (Wed Feb 24 2010 - 23:58:14 PST)
[AMBER] question about how to fix the number of water molecule
- Ilyas Yildirim (Mon Feb 15 2010 - 05:40:14 PST)
- mirage . (Sun Feb 14 2010 - 23:39:29 PST)
[AMBER] Question about transition from AMBER6 to AMBER9
- case (Sat Feb 27 2010 - 08:06:58 PST)
- 坂庭　大輔 (Sat Feb 27 2010 - 07:30:33 PST)
- case (Sat Feb 27 2010 - 06:08:14 PST)
- 坂庭　大輔 (Sat Feb 27 2010 - 02:07:53 PST)
- case (Sat Feb 20 2010 - 19:35:00 PST)
- 坂庭　大輔 (Fri Feb 19 2010 - 02:19:27 PST)
[AMBER] Question of Tutorials-A: the total charge is not integer
- Tom Williams (Sun Feb 07 2010 - 00:00:39 PST)
[AMBER] Question on applying restraints in absolute dG calculations with TI in Amber 10
- steinbrt.rci.rutgers.edu (Thu Feb 25 2010 - 02:15:13 PST)
- Samuel Genheden (Wed Feb 24 2010 - 10:55:19 PST)
- steinbrt.rci.rutgers.edu (Wed Feb 24 2010 - 07:52:36 PST)
- Samuel Genheden (Wed Feb 24 2010 - 04:19:08 PST)
- steinbrt.rci.rutgers.edu (Wed Feb 24 2010 - 03:52:30 PST)
- Samuel Genheden (Wed Feb 24 2010 - 01:03:21 PST)
[AMBER] RDF analysis
- Shaikh Abdul R S Ramaju (Tue Feb 23 2010 - 00:05:58 PST)
[AMBER] RDF with ptraj
- Dian Jiao (Mon Feb 15 2010 - 12:45:00 PST)
[AMBER] Reducing RMS errors in TI calculation
- steinbrt.rci.rutgers.edu (Tue Feb 09 2010 - 23:19:56 PST)
- ET (Tue Feb 09 2010 - 13:02:48 PST)
[AMBER] References of all force fields for citations
- case (Thu Feb 18 2010 - 06:21:33 PST)
- Sushil Mishra (Thu Feb 18 2010 - 06:18:26 PST)
[AMBER] Regarding restraints during minimisation stage 1 in explicit solvent
- Carlos Simmerling (Mon Feb 08 2010 - 03:39:15 PST)
- Asfa Ali (Sun Feb 07 2010 - 21:23:12 PST)
[AMBER] reimaging the trajectory
- Carlos Simmerling (Fri Feb 05 2010 - 03:15:00 PST)
- Shaikh Abdul R S Ramaju (Fri Feb 05 2010 - 02:25:53 PST)
[AMBER] relaxed PES
- eric henon (Wed Feb 17 2010 - 13:19:47 PST)
- Jason Swails (Wed Feb 17 2010 - 12:05:06 PST)
- eric henon (Wed Feb 17 2010 - 11:58:50 PST)
[AMBER] sander compilation
- Jason Swails (Tue Feb 16 2010 - 17:59:45 PST)
- s. Bill (Tue Feb 16 2010 - 17:23:47 PST)
[AMBER] Sander jac benchmark segfaults with non-power of two processors
- Ross Walker (Thu Feb 25 2010 - 09:55:37 PST)
- Manjunath Sripadarao (Wed Feb 24 2010 - 23:05:52 PST)
[AMBER] Script
- Josmar R. da Rocha (Mon Feb 22 2010 - 09:50:03 PST)
- Carlos Simmerling (Sun Feb 21 2010 - 06:15:51 PST)
- Lachele Foley (Lists) (Thu Feb 18 2010 - 07:43:23 PST)
- Beale, John (Thu Feb 18 2010 - 05:15:59 PST)
- Carlos Simmerling (Thu Feb 18 2010 - 04:59:03 PST)
- Beale, John (Thu Feb 18 2010 - 04:47:21 PST)
- Beale, John (Thu Feb 18 2010 - 04:42:50 PST)
- Carlos Simmerling (Thu Feb 18 2010 - 04:40:57 PST)
- Beale, John (Thu Feb 18 2010 - 04:35:26 PST)
[AMBER] Segmentation fault with xleap while loading a leaprc
- Nicolas Sapay (Fri Feb 19 2010 - 06:42:00 PST)
- Bill Ross (Thu Feb 18 2010 - 11:56:53 PST)
- Nicolas Sapay (Thu Feb 18 2010 - 11:48:18 PST)
- Bill Ross (Thu Feb 18 2010 - 10:43:31 PST)
- Nicolas Sapay (Thu Feb 18 2010 - 08:42:59 PST)
- case (Thu Feb 18 2010 - 08:27:55 PST)
- Nicolas Sapay (Thu Feb 18 2010 - 06:29:54 PST)
- case (Thu Feb 18 2010 - 06:07:47 PST)
- Nicolas Sapay (Thu Feb 18 2010 - 05:48:00 PST)
[AMBER] serial compilation of pmemd
- case (Thu Feb 25 2010 - 08:16:59 PST)
- bbalta.itu.edu.tr (Thu Feb 25 2010 - 07:45:00 PST)
[AMBER] Simple question on EM
- Jason Swails (Wed Feb 24 2010 - 20:06:40 PST)
- Shaandar Nyamtulga (Wed Feb 24 2010 - 19:42:03 PST)
[AMBER] Simple question on EM again
- MQO.Carlos Javier Nunez Aguero (Thu Feb 25 2010 - 22:17:00 PST)
- Jason Swails (Thu Feb 25 2010 - 20:31:30 PST)
- Bill Ross (Thu Feb 25 2010 - 20:21:46 PST)
- Jason Swails (Thu Feb 25 2010 - 19:54:45 PST)
- Shaandar Nyamtulga (Thu Feb 25 2010 - 19:00:39 PST)
- Carlos Simmerling (Thu Feb 25 2010 - 05:12:00 PST)
- MQO.Carlos Javier Nunez Aguero (Wed Feb 24 2010 - 23:12:01 PST)
- Jason Swails (Wed Feb 24 2010 - 22:56:32 PST)
- Shaandar Nyamtulga (Wed Feb 24 2010 - 21:24:41 PST)
[AMBER] sleap crash with single water molecule and amoeba
- case (Tue Feb 16 2010 - 09:19:04 PST)
- Neil Henson (Tue Feb 16 2010 - 08:20:22 PST)
- Alan (Tue Feb 16 2010 - 04:17:47 PST)
- case (Mon Feb 15 2010 - 13:14:15 PST)
- Neil Henson (Mon Feb 08 2010 - 06:14:45 PST)
[AMBER] Small Molecule Parameters
- MUHAMMAD IMTIA SHAFIQ (Thu Feb 11 2010 - 13:51:59 PST)
- Bill Ross (Thu Feb 11 2010 - 11:05:32 PST)
- imtiaz shafiq (Thu Feb 11 2010 - 10:44:18 PST)
[AMBER] softcore TI lambda values of 0 and 1
- steinbrt.rci.rutgers.edu (Sun Feb 07 2010 - 02:01:55 PST)
- Hugh Heldenbrand (Fri Feb 05 2010 - 12:49:05 PST)
[AMBER] Solvating a protein - tleap works where sleap does not?
- Ben Roberts (Mon Feb 01 2010 - 07:10:56 PST)
[AMBER] strange behavior in QMMM simulation
- M. L. Dodson (Sun Feb 14 2010 - 06:19:00 PST)
- case (Sat Feb 13 2010 - 19:28:38 PST)
- M. L. Dodson (Sat Feb 13 2010 - 12:21:06 PST)
- M. L. Dodson (Thu Feb 11 2010 - 12:35:25 PST)
[AMBER] swiss cheese water shell
- Ross Walker (Sat Feb 27 2010 - 14:03:20 PST)
- Mark M Huntress (Sat Feb 27 2010 - 13:46:07 PST)
- Peter Schmidtke (Sat Feb 27 2010 - 12:34:11 PST)
- Nicholas Musolino (Sat Feb 27 2010 - 06:08:54 PST)
- Barbault Florent (Sat Feb 27 2010 - 03:48:29 PST)
- Mark M Huntress (Fri Feb 26 2010 - 21:40:25 PST)
[AMBER] Test log
- Jason Swails (Mon Feb 01 2010 - 13:24:43 PST)
- s. Bill (Mon Feb 01 2010 - 12:41:28 PST)
- case (Mon Feb 01 2010 - 10:49:22 PST)
- s. Bill (Mon Feb 01 2010 - 09:48:10 PST)
[AMBER] TEST_FAILURES
- sikander azam (Tue Feb 16 2010 - 04:55:09 PST)
- Ross Walker (Thu Feb 04 2010 - 12:48:05 PST)
- Jason Swails (Thu Feb 04 2010 - 07:41:54 PST)
- sikander azam (Thu Feb 04 2010 - 05:37:44 PST)
[AMBER] TI calculation of absolute dG with restraint and energy decomposition
- Samuel Genheden (Sat Feb 20 2010 - 03:11:01 PST)
- Hannes Kopitz (Fri Feb 19 2010 - 07:33:47 PST)
- Samuel Genheden (Fri Feb 19 2010 - 01:10:45 PST)
[AMBER] tleap command for disulfide bonds: for chain A and Chain B ???
- Anselm Horn (Wed Feb 03 2010 - 01:17:40 PST)
- Jason Swails (Tue Feb 02 2010 - 23:50:16 PST)
- case (Tue Feb 02 2010 - 20:32:11 PST)
- Siddharth Rastogi (Tue Feb 02 2010 - 17:19:28 PST)
[AMBER] trajectory alignment to a reference frame
- Thomas Cheatham III (Thu Feb 25 2010 - 12:39:13 PST)
- Oliver Kuhn (Wed Feb 24 2010 - 07:17:39 PST)
[AMBER] trouble with cooling down a system
- Carlos Simmerling (Tue Feb 23 2010 - 03:08:18 PST)
- Nancy (Tue Feb 23 2010 - 02:56:49 PST)
[AMBER] trouble with cooling down the system
- Carlos Simmerling (Tue Feb 23 2010 - 03:10:16 PST)
- song_jianing_hi (Tue Feb 23 2010 - 02:43:39 PST)
[AMBER] Tutorial for Glycoprotein simulation
- Siddharth Rastogi (Tue Feb 02 2010 - 16:56:28 PST)
- Lachele Foley (Lists) (Mon Feb 01 2010 - 06:34:15 PST)
[AMBER] use tleap through stdin
- Peter Schmidtke (Thu Feb 25 2010 - 06:47:29 PST)
- case (Thu Feb 25 2010 - 06:31:16 PST)
- Peter Schmidtke (Tue Feb 23 2010 - 09:41:04 PST)
[AMBER] VDW parameter for Cobalt and Nickel
- Raja Pandian (Mon Feb 01 2010 - 06:17:21 PST)
[AMBER] Virtual waters
- Fernando Martín García (Thu Feb 18 2010 - 05:35:45 PST)
- David A. Case (Thu Feb 18 2010 - 04:37:35 PST)
- Fernando Martín García (Wed Feb 17 2010 - 23:39:09 PST)
- case (Wed Feb 17 2010 - 09:45:45 PST)
- Fernando Martín García (Wed Feb 17 2010 - 02:59:05 PST)
[AMBER] VMD and Amber coordinates
- Bill Ross (Tue Feb 16 2010 - 13:19:35 PST)
- InSuk Joung (Tue Feb 16 2010 - 10:52:12 PST)
- Rebeca García Fandiño (Tue Feb 16 2010 - 10:25:25 PST)
[AMBER] What is the ".ac" files as input of respgen and how to generate it?
- Aurum Bai (Thu Feb 04 2010 - 21:42:37 PST)
[AMBER] xmin_verbosity
- case (Sat Feb 27 2010 - 06:16:25 PST)
- gunajyoti das (Sat Feb 27 2010 - 05:40:59 PST)
Antechamber: imidazole=aromatic, imidazolium=not aromatic?
- Niel Henriksen (Wed Feb 24 2010 - 17:42:36 PST)
- Gabriel Rocklin (Fri Feb 19 2010 - 15:51:24 PST)
- Alan (Fri Feb 19 2010 - 00:42:08 PST)
- Gabriel Rocklin (Thu Feb 18 2010 - 15:21:27 PST)
- Gabriel Rocklin (Mon Feb 15 2010 - 15:21:45 PST)
- Gabriel Rocklin (Wed Feb 10 2010 - 11:23:24 PST)
ODP: [AMBER] help
- lina (Thu Feb 18 2010 - 06:06:22 PST)
- MASLYK, MACIEJ MARCIN (Thu Feb 18 2010 - 05:58:58 PST)
Problem compiling Amber 10 after applying latest bugfix file
- Sanders, Larry R. (Thu Feb 11 2010 - 06:35:06 PST)
Problem reading PDB residues in AmberTools-1.3
- Hopkins, Robert (Fri Feb 05 2010 - 10:51:25 PST)
- case (Fri Feb 05 2010 - 10:44:41 PST)
- Hopkins, Robert (Fri Feb 05 2010 - 07:37:09 PST)
Question of Tutorials-A: the total charge is not integer
- Ross Walker (Sun Feb 07 2010 - 02:02:40 PST)
SOS: make CYX bond using xleap
- Jason Swails (Thu Feb 25 2010 - 18:34:53 PST)

Amber Archive Feb 2010 by subject