Amber Archive Feb 2012: by subject

: about using MMPBSA Tan and Luo method in AMBER 11: discrepancy in ECAVITY values
- Holger Gohlke (Sat Feb 04 2012 - 01:34:53 PST)
[AMBER-Developers] [AMBER] Issues with hydrogens using glycam force field in Amber 10
- David A Case (Mon Feb 20 2012 - 06:13:48 PST)
[AMBER-Developers] [AMBER] Radii issue with mbondi2 + leaprc.parmCHI_YIL.bsc for RNA
- David A Case (Mon Feb 20 2012 - 06:07:17 PST)
[AMBER] 2D PMFs with multiple constraints
- Aron Broom (Tue Feb 28 2012 - 09:47:57 PST)
- Adrian Roitberg (Tue Feb 28 2012 - 07:30:24 PST)
- Sampson C.M. (Tue Feb 28 2012 - 07:28:00 PST)
[AMBER] [Contact q4md] HF/6-31++g(2d, 2p) option for anionic fragments in GLYCAM06
- FyD (Sat Feb 25 2012 - 00:26:19 PST)
[AMBER] [Fwd: Problems with ff99SB force field reading]
- vladanstefanovic.kg.ac.rs (Fri Feb 03 2012 - 01:23:15 PST)
- David A Case (Thu Feb 02 2012 - 10:46:55 PST)
- Jason Swails (Thu Feb 02 2012 - 08:40:17 PST)
- vladanstefanovic.kg.ac.rs (Thu Feb 02 2012 - 08:05:59 PST)
[AMBER] [Fwd: Protonated state of GLU, CYS]
- Ngo Son Tung (Wed Feb 22 2012 - 07:47:46 PST)
- Jason Swails (Tue Feb 21 2012 - 20:01:44 PST)
- Ngo Son Tung (Tue Feb 21 2012 - 05:57:58 PST)
- David A Case (Tue Feb 21 2012 - 05:19:04 PST)
- Ngo Son Tung (Tue Feb 21 2012 - 02:11:43 PST)
[AMBER] [q4md-fft] a question about double bond in R.E.D
- FyD (Sun Feb 12 2012 - 00:04:52 PST)
[AMBER] [q4md-fft] How to show charge values using Jmol?
- FyD (Fri Feb 24 2012 - 23:26:14 PST)
- FyD (Fri Feb 24 2012 - 23:09:44 PST)
[AMBER] a general question about membrane simulation
- Albert (Mon Feb 06 2012 - 05:11:34 PST)
[AMBER] a question about double bond in R.E.D
- Albert (Sat Feb 11 2012 - 21:52:02 PST)
[AMBER] about Ewald error estimate
- case (Sun Feb 12 2012 - 04:41:12 PST)
- leila karami (Sun Feb 12 2012 - 00:02:56 PST)
- case (Sat Feb 11 2012 - 09:05:43 PST)
- leila karami (Wed Feb 08 2012 - 04:19:55 PST)
[AMBER] About the source file regarding SMD calculations
- Mo Chen (Tue Feb 28 2012 - 18:38:10 PST)
- Aron Broom (Tue Feb 28 2012 - 18:32:22 PST)
- Mo Chen (Tue Feb 28 2012 - 15:08:57 PST)
[AMBER] about using MMPBSA Tan and Luo method in AMBER 11: discrepancy in ECAVITY values
- Fulle.uni-duesseldorf.de (Fri Feb 03 2012 - 09:26:08 PST)
- Therese Malliavin (Wed Feb 01 2012 - 00:48:36 PST)
[AMBER] Amber 11/12 and Kepler
- Ross Walker (Tue Feb 14 2012 - 09:18:01 PST)
- filip fratev (Tue Feb 14 2012 - 08:25:20 PST)
[AMBER] Amber 12
- David A Case (Thu Feb 16 2012 - 05:31:28 PST)
- Artem Zhmurov (Wed Feb 15 2012 - 23:45:11 PST)
[AMBER] Amber 12 & Amoeba
- Jason Swails (Sun Feb 12 2012 - 20:54:09 PST)
- Ismail, Mohd F. (Sun Feb 12 2012 - 20:18:47 PST)
[AMBER] AMBER minimization
- David A Case (Thu Feb 09 2012 - 08:34:06 PST)
- Olena Dobrovolska (Thu Feb 09 2012 - 03:04:52 PST)
- David A. Case (Wed Feb 08 2012 - 10:31:38 PST)
- Olena Dobrovolska (Wed Feb 08 2012 - 10:12:01 PST)
- David A. Case (Wed Feb 08 2012 - 05:38:27 PST)
- Olena Dobrovolska (Wed Feb 08 2012 - 04:19:21 PST)
- David A. Case (Tue Feb 07 2012 - 16:56:54 PST)
- Olena Dobrovolska (Tue Feb 07 2012 - 08:19:43 PST)
[AMBER] AMBER QM/MM Coordinate resetting (SHAKE) cannot be accomplished
- Marc van der Kamp (Mon Feb 13 2012 - 01:27:58 PST)
- tonghf (Sun Feb 12 2012 - 21:08:26 PST)
[AMBER] AMBER11 installation
- Hirdesh Kumar (Thu Feb 02 2012 - 22:39:53 PST)
- Jason Swails (Thu Feb 02 2012 - 22:19:47 PST)
- rameshwar prajapati (Thu Feb 02 2012 - 22:13:56 PST)
- Hirdesh Kumar (Thu Feb 02 2012 - 21:53:43 PST)
[AMBER] Amber11 Installation Error
- case (Sat Feb 04 2012 - 07:07:08 PST)
- Hirdesh Kumar (Sat Feb 04 2012 - 00:35:26 PST)
[AMBER] Announcement: 2012 summer intern position at GSK
- Guanglei Cui (Fri Feb 10 2012 - 13:13:27 PST)
- Ganesh Kamath (Fri Feb 10 2012 - 13:05:19 PST)
- Guanglei Cui (Fri Feb 10 2012 - 12:59:32 PST)
[AMBER] ante-MMPBSA error message:additional OXT atom
- Jason Swails (Tue Feb 07 2012 - 08:42:18 PST)
- Shuyi Cao (Tue Feb 07 2012 - 08:25:42 PST)
- Jason Swails (Mon Feb 06 2012 - 20:27:13 PST)
- Shuyi Cao (Mon Feb 06 2012 - 18:40:47 PST)
- liu junjun (Mon Feb 06 2012 - 18:35:48 PST)
- Shuyi Cao (Mon Feb 06 2012 - 18:03:51 PST)
[AMBER] Antechamber
- David A Case (Mon Feb 20 2012 - 05:41:03 PST)
- Beale, John (Mon Feb 20 2012 - 02:04:32 PST)
[AMBER] antechamber doesn't create mol2 file
- FyD (Fri Feb 10 2012 - 00:03:26 PST)
- FyD (Fri Feb 03 2012 - 00:04:42 PST)
- FyD (Tue Jan 31 2012 - 22:17:03 PST)
[AMBER] Any references on studying energy landscape of a protein by AMBER
- Jason Swails (Fri Feb 03 2012 - 11:23:24 PST)
- Catein Catherine (Fri Feb 03 2012 - 01:34:49 PST)
[AMBER] ATP minimization
- FyD (Tue Feb 28 2012 - 06:37:16 PST)
- Sangita Kachhap (Tue Feb 28 2012 - 03:20:03 PST)
- FyD (Mon Feb 27 2012 - 00:22:15 PST)
- Sangita Kachhap (Sun Feb 26 2012 - 09:16:57 PST)
- FyD (Wed Feb 22 2012 - 10:22:38 PST)
- Sangita Kachhap (Wed Feb 22 2012 - 10:15:59 PST)
- FyD (Wed Feb 22 2012 - 09:49:59 PST)
- Sangita Kachhap (Wed Feb 22 2012 - 09:32:04 PST)
[AMBER] bad atom type
- Osman, Roman (Wed Feb 29 2012 - 09:11:45 PST)
- Jason Swails (Tue Feb 28 2012 - 17:53:34 PST)
- Osman, Roman (Tue Feb 28 2012 - 16:08:40 PST)
- Dwight McGee (Tue Feb 28 2012 - 15:33:31 PST)
- Osman, Roman (Tue Feb 28 2012 - 14:59:05 PST)
[AMBER] bond breaking
- Jason Swails (Sun Feb 12 2012 - 13:02:13 PST)
- amir abbasi (Sun Feb 12 2012 - 10:38:26 PST)
[AMBER] building wrapped DNA in NAB
- David A Case (Wed Feb 15 2012 - 13:31:42 PST)
- David A Case (Wed Feb 15 2012 - 12:32:04 PST)
[AMBER] Calculate the volume of a protein from the trajectory
- surasak chunsrivirot (Wed Feb 29 2012 - 02:15:24 PST)
- Tyler Luchko (Tue Feb 28 2012 - 10:07:52 PST)
- Mark Williamson (Tue Feb 28 2012 - 06:34:19 PST)
- Cannon, John F. (Tue Feb 28 2012 - 06:31:21 PST)
- George M Giambasu (Tue Feb 28 2012 - 06:30:58 PST)
- Brian Radak (Tue Feb 28 2012 - 06:24:24 PST)
- surasak chunsrivirot (Mon Feb 27 2012 - 23:41:08 PST)
[AMBER] Calculating Binding Energy
- Aron Broom (Mon Feb 20 2012 - 07:43:26 PST)
- Ravleen, KAUR (Mon Feb 20 2012 - 03:06:02 PST)
[AMBER] Calculation of backbone torsion angles
- Rajendra P. OJHA (Mon Feb 27 2012 - 22:48:01 PST)
- Carlos Simmerling (Mon Feb 27 2012 - 04:23:17 PST)
- souvik sur (Mon Feb 27 2012 - 04:10:49 PST)
[AMBER] Change the residue number in pdb file
- David A Case (Wed Feb 15 2012 - 07:42:19 PST)
- Jan-Philip Gehrcke (Wed Feb 15 2012 - 06:46:51 PST)
- Olena Dobrovolska (Wed Feb 15 2012 - 05:46:27 PST)
[AMBER] Charge calculation using RESP: MCPB
- kanika singal (Tue Feb 07 2012 - 08:45:54 PST)
- Martin Peters (Tue Feb 07 2012 - 06:07:54 PST)
- kanika singal (Mon Feb 06 2012 - 04:06:04 PST)
[AMBER] Charges
- David A Case (Tue Feb 21 2012 - 05:11:59 PST)
- Beale, John (Tue Feb 21 2012 - 02:11:32 PST)
[AMBER] Clustering and minimization
- Bernhard (Tue Feb 28 2012 - 08:07:35 PST)
[AMBER] Comaring energy values after restart
- Daniel Roe (Sun Feb 26 2012 - 05:52:11 PST)
- Dilraj LAMA (Sun Feb 26 2012 - 02:36:08 PST)
- Jason Swails (Sat Feb 25 2012 - 14:32:37 PST)
- case (Sat Feb 25 2012 - 06:26:11 PST)
- Daniel Roe (Sat Feb 25 2012 - 05:23:57 PST)
- Dilraj LAMA (Sat Feb 25 2012 - 00:32:33 PST)
[AMBER] compilation of amber 11 + amber tools 1.5 with intel 12.1.2
- Jan-Philip Gehrcke (Mon Feb 06 2012 - 03:18:43 PST)
- Vlad Cojocaru (Mon Feb 06 2012 - 02:58:59 PST)
- Vlad Cojocaru (Mon Feb 06 2012 - 02:13:41 PST)
[AMBER] Compile Amber 11 with IPP instead of OpenMPI
- David A Case (Tue Feb 07 2012 - 04:49:51 PST)
- David A Case (Tue Feb 07 2012 - 04:48:16 PST)
- Yubo Fan (Mon Feb 06 2012 - 19:37:57 PST)
[AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint."
- Jan-Philip Gehrcke (Mon Feb 20 2012 - 11:17:49 PST)
- David A Case (Thu Feb 16 2012 - 06:33:07 PST)
[AMBER] Constant Temperature
- amir abbasi (Fri Feb 24 2012 - 13:05:32 PST)
- Daniel Roe (Fri Feb 24 2012 - 12:54:05 PST)
- amir abbasi (Fri Feb 24 2012 - 12:48:29 PST)
- Aron Broom (Fri Feb 24 2012 - 12:39:06 PST)
- David A Case (Fri Feb 24 2012 - 12:37:41 PST)
- Jason Swails (Fri Feb 24 2012 - 12:25:12 PST)
- amir abbasi (Fri Feb 24 2012 - 11:35:22 PST)
[AMBER] Cosine content of PCA analysis
- Fernando Martín García (Tue Feb 28 2012 - 02:35:38 PST)
- Catein Catherine (Tue Feb 28 2012 - 00:58:12 PST)
[AMBER] CUDA version for Amber 11?
- Scott Le Grand (Mon Feb 27 2012 - 11:37:15 PST)
- Mettu, Ramgopal (Mon Feb 27 2012 - 11:24:13 PST)
- Scott Le Grand (Mon Feb 27 2012 - 10:15:41 PST)
- Jan-Philip Gehrcke (Mon Feb 27 2012 - 08:58:32 PST)
- Ross Walker (Mon Feb 27 2012 - 08:48:03 PST)
- Ross Walker (Mon Feb 27 2012 - 08:44:27 PST)
- Jan-Philip Gehrcke (Mon Feb 27 2012 - 07:57:39 PST)
- Scott Le Grand (Mon Feb 27 2012 - 07:45:11 PST)
- Mettu, Ramgopal (Mon Feb 27 2012 - 07:37:34 PST)
- Scott Le Grand (Fri Feb 24 2012 - 09:16:22 PST)
- Mettu, Ramgopal (Fri Feb 24 2012 - 08:36:39 PST)
- Ismail, Mohd F. (Fri Feb 24 2012 - 06:24:15 PST)
- Mettu, Ramgopal (Thu Feb 23 2012 - 20:45:48 PST)
- Ross Walker (Thu Feb 23 2012 - 20:37:53 PST)
- Mettu, Ramgopal (Thu Feb 23 2012 - 20:22:54 PST)
- Ross Walker (Thu Feb 23 2012 - 15:34:49 PST)
- Mettu, Ramgopal (Thu Feb 23 2012 - 14:09:35 PST)
[AMBER] cygwin-ambertools
- David A Case (Mon Feb 06 2012 - 05:14:09 PST)
- Алексей Раевский (Mon Feb 06 2012 - 00:08:39 PST)
[AMBER] deletion of hydrogen atoms of pdb file
- Jason Swails (Tue Feb 21 2012 - 20:05:11 PST)
- David A Case (Tue Feb 21 2012 - 05:27:13 PST)
- Atila Petrosian (Tue Feb 21 2012 - 02:37:44 PST)
[AMBER] Deprotonated Tyrosine
- Irene Newhouse (Sun Feb 05 2012 - 16:14:14 PST)
- Markus Kaukonen (Sun Feb 05 2012 - 11:37:29 PST)
- FyD (Sun Feb 05 2012 - 11:15:05 PST)
- Thomas Exner (Sun Feb 05 2012 - 03:21:49 PST)
- FyD (Sun Feb 05 2012 - 02:13:16 PST)
- Barbault Florent (Sun Feb 05 2012 - 00:33:07 PST)
- Albert (Sun Feb 05 2012 - 00:16:17 PST)
- FyD (Sun Feb 05 2012 - 00:04:46 PST)
- Aron Broom (Sat Feb 04 2012 - 08:45:00 PST)
- Thomas Exner (Sat Feb 04 2012 - 07:35:21 PST)
[AMBER] dicrepancy of percentage nonbonded calculation between 2 and 1 node
- setyanto md (Tue Feb 14 2012 - 21:43:14 PST)
- David A Case (Mon Feb 13 2012 - 04:59:03 PST)
- setyanto md (Mon Feb 13 2012 - 02:31:31 PST)
[AMBER] Does AMBER ignore CONECT information in pdb input?
- Chinh Su Tran To (Tue Feb 07 2012 - 02:58:00 PST)
- steinbrt.rci.rutgers.edu (Tue Feb 07 2012 - 01:00:00 PST)
- Chinh Su Tran To (Mon Feb 06 2012 - 21:25:59 PST)
- Chinh Su Tran To (Mon Feb 06 2012 - 21:24:36 PST)
- Jason Swails (Mon Feb 06 2012 - 20:32:52 PST)
- Aron Broom (Mon Feb 06 2012 - 20:18:26 PST)
- Chinh Su Tran To (Mon Feb 06 2012 - 20:05:04 PST)
[AMBER] Electrostatic calculation using Amber partial charge.
- BERGY (Thu Feb 23 2012 - 20:23:13 PST)
- David A Case (Thu Feb 23 2012 - 06:08:26 PST)
- SENTHIL KUMAR (Wed Feb 22 2012 - 23:56:01 PST)
[AMBER] Embed Shell Scripting in ptraj script
- g t (Wed Feb 29 2012 - 04:59:32 PST)
- Ismail, Mohd F. (Tue Feb 28 2012 - 10:03:24 PST)
- Thomas Cheatham III (Tue Feb 28 2012 - 09:54:14 PST)
- Adrian Roitberg (Tue Feb 28 2012 - 09:53:27 PST)
- Ismail, Mohd F. (Tue Feb 28 2012 - 09:48:13 PST)
[AMBER] energy decomposition for the surface term
- Junmei Wang (Tue Feb 14 2012 - 19:17:33 PST)
[AMBER] Enquiry about MM/PBSA energy
- Jason Swails (Mon Feb 27 2012 - 08:27:00 PST)
- Catein Catherine (Sun Feb 26 2012 - 23:17:48 PST)
[AMBER] Entropy analysis
- Amir Abbasi (Fri Feb 17 2012 - 12:56:46 PST)
[AMBER] Error during extending the simulations...
- Jason Swails (Mon Feb 06 2012 - 14:55:07 PST)
- Rajendra Sharma (Sun Feb 05 2012 - 18:06:16 PST)
[AMBER] error in .rst file creation
- David A Case (Fri Feb 03 2012 - 05:58:30 PST)
- Daniel Roe (Fri Feb 03 2012 - 05:28:06 PST)
- abinayar.imsc.res.in (Fri Feb 03 2012 - 03:51:22 PST)
[AMBER] Error in running energy minimization
- David A Case (Thu Feb 09 2012 - 08:32:38 PST)
- DEBOSTUTI GHOSHDASTIDAR (Thu Feb 09 2012 - 02:42:53 PST)
- Brian Radak (Wed Feb 08 2012 - 05:54:48 PST)
- DEBOSTUTI GHOSHDASTIDAR (Wed Feb 08 2012 - 02:18:47 PST)
- David A Case (Mon Feb 06 2012 - 05:26:30 PST)
- DEBOSTUTI GHOSHDASTIDAR (Mon Feb 06 2012 - 03:12:11 PST)
[AMBER] error in tleap execution of loadpdb
- molguin.miners.utep.edu (Wed Feb 08 2012 - 21:02:57 PST)
- Aron Broom (Tue Feb 07 2012 - 22:33:16 PST)
- molguin.miners.utep.edu (Tue Feb 07 2012 - 22:09:48 PST)
[AMBER] errors on testing pbsa
- Yubo Fan (Tue Feb 21 2012 - 08:26:17 PST)
[AMBER] fail to compile Amber 9 with intel/10.1 + openmpi/1.2.4
- Jason Swails (Fri Feb 03 2012 - 16:09:09 PST)
- Yubo Fan (Fri Feb 03 2012 - 13:13:23 PST)
- Daniel Roe (Fri Feb 03 2012 - 10:11:26 PST)
- Yubo Fan (Fri Feb 03 2012 - 08:03:51 PST)
[AMBER] Faking Vacuum Simulations with a GPU
- Aron Broom (Sat Feb 25 2012 - 21:44:36 PST)
- David A Case (Thu Feb 23 2012 - 11:09:57 PST)
- Aron Broom (Tue Feb 21 2012 - 06:56:03 PST)
[AMBER] ff03.r1 issue
- David A Case (Wed Feb 15 2012 - 07:40:00 PST)
- Aron Broom (Wed Feb 15 2012 - 05:43:08 PST)
- Dmitry Mukha (Wed Feb 15 2012 - 01:31:55 PST)
[AMBER] force field Hydroxide ion
- Brian Radak (Mon Feb 06 2012 - 11:09:58 PST)
- iccy liu (Mon Feb 06 2012 - 10:59:25 PST)
[AMBER] Force Field Parameterization -- Torsion Potentials
- Ryan Pavlovicz (Fri Feb 10 2012 - 14:26:25 PST)
- Ryan Pavlovicz (Fri Feb 10 2012 - 14:18:44 PST)
- Ryan Pavlovicz (Fri Feb 10 2012 - 10:10:38 PST)
- FyD (Thu Feb 09 2012 - 03:59:50 PST)
- Karl N. Kirschner (Thu Feb 09 2012 - 01:25:48 PST)
- Lorenzo Gontrani (Thu Feb 09 2012 - 00:47:43 PST)
- Ryan Pavlovicz (Wed Feb 08 2012 - 09:14:45 PST)
- Karl N. Kirschner (Wed Feb 08 2012 - 05:11:55 PST)
- Ryan Pavlovicz (Tue Feb 07 2012 - 07:40:05 PST)
[AMBER] format plotmtv and plotmtv for ubuntu 11.04
- Jason Swails (Wed Feb 29 2012 - 14:10:33 PST)
- setyanto md (Thu Feb 16 2012 - 19:17:08 PST)
[AMBER] Fwd: [q4md-fft] Constraint during geometry optimization
- FyD (Sun Feb 05 2012 - 11:21:06 PST)
[AMBER] Fwd: about using MMPBSA Tan and Luo method in AMBER 11: discrepancy in ECAVITY values
- Jason Swails (Thu Feb 02 2012 - 15:35:40 PST)
- Qin Cai (Thu Feb 02 2012 - 12:49:51 PST)
- Qin Cai (Thu Feb 02 2012 - 12:33:57 PST)
- Ray Luo, Ph.D. (Wed Feb 01 2012 - 09:49:57 PST)
[AMBER] Fwd: errors on testing pbsa
- Qin Cai (Tue Feb 21 2012 - 14:47:43 PST)
- Jason Swails (Tue Feb 21 2012 - 14:43:06 PST)
- Ray Luo, Ph.D. (Tue Feb 21 2012 - 10:32:02 PST)
[AMBER] Fwd: NMODE list index out of range error
- Jason Swails (Thu Feb 09 2012 - 12:20:03 PST)
- Sangeetha B (Wed Feb 08 2012 - 06:35:30 PST)
- Jason Swails (Tue Feb 07 2012 - 12:05:16 PST)
- Jason Swails (Tue Feb 07 2012 - 08:51:16 PST)
- Sangeetha B (Tue Feb 07 2012 - 03:52:42 PST)
[AMBER] Fwd: Residue Decomposition Sander Error
- Hirdesh Kumar (Thu Feb 09 2012 - 20:33:37 PST)
[AMBER] Fwd: restraints in igb simulation
- M. L. Dodson (Fri Feb 17 2012 - 21:27:23 PST)
[AMBER] G09 incompatibility with ANTECHAMBER for RESP charges
- FyD (Fri Feb 17 2012 - 23:47:13 PST)
- lfelberg.uchicago.edu (Fri Feb 17 2012 - 08:25:58 PST)
[AMBER] Generating topology files for non standard amino acid residue
- Aron Broom (Tue Feb 14 2012 - 19:25:44 PST)
- Matthew D Antalek (Tue Feb 14 2012 - 11:44:05 PST)
- FyD (Tue Feb 14 2012 - 08:10:21 PST)
- Aron Broom (Tue Feb 14 2012 - 05:43:15 PST)
- Matthew D Antalek (Mon Feb 13 2012 - 20:55:34 PST)
- Matthew D Antalek (Sun Feb 12 2012 - 20:00:45 PST)
- Aron Broom (Sun Feb 12 2012 - 19:50:33 PST)
- Jason Swails (Sun Feb 12 2012 - 19:40:31 PST)
- Aron Broom (Sun Feb 12 2012 - 19:09:28 PST)
- Matthew D Antalek (Sun Feb 12 2012 - 18:41:19 PST)
[AMBER] GFP chromophore 1EMB.pdb(detail)
- FyD (Fri Feb 17 2012 - 22:56:20 PST)
- Yasuo Kurita (Fri Feb 17 2012 - 03:25:16 PST)
[AMBER] GFP Chromophore 1EMB.pdb,
- FyD (Thu Feb 16 2012 - 05:43:02 PST)
- David A Case (Thu Feb 16 2012 - 05:30:26 PST)
- Yasuo Kurita (Wed Feb 15 2012 - 22:59:17 PST)
[AMBER] GL4 at C-terminal
- kurisaki (Sun Feb 05 2012 - 16:47:38 PST)
- kurisaki (Sun Feb 05 2012 - 16:43:48 PST)
- FyD (Sun Feb 05 2012 - 11:26:58 PST)
- Jason Swails (Sun Feb 05 2012 - 10:16:57 PST)
- kurisaki (Sun Feb 05 2012 - 04:56:36 PST)
[AMBER] Help with solvating organic molecule with input .prmtop file
- Jason Swails (Wed Feb 29 2012 - 14:04:03 PST)
- David A Case (Wed Feb 29 2012 - 05:04:25 PST)
- Andy Ballard (Tue Feb 28 2012 - 07:55:42 PST)
[AMBER] How to calculate conformational entropy for a protein using AMBER?
- Catein Catherine (Sun Feb 05 2012 - 19:38:01 PST)
[AMBER] How to calculate cosine content of PCA analysis?
- Catein Catherine (Tue Feb 28 2012 - 00:58:54 PST)
[AMBER] how to cite ambertool
- David A Case (Wed Feb 29 2012 - 05:07:11 PST)
- setyanto md (Tue Feb 28 2012 - 20:59:10 PST)
[AMBER] How to convert mdcrd for GROMACS analysis?
- Francesco Oteri (Tue Feb 28 2012 - 01:21:18 PST)
- Lorenzo Gontrani (Tue Feb 28 2012 - 01:20:05 PST)
- Catein Catherine (Tue Feb 28 2012 - 01:01:11 PST)
[AMBER] How to create a script to add two integers in bash
- Mariano Rech (Thu Feb 09 2012 - 12:45:34 PST)
- Jason Swails (Thu Feb 09 2012 - 12:16:00 PST)
- Lachele Foley (Lists) (Thu Feb 09 2012 - 12:06:57 PST)
- shenna shearin (Thu Feb 09 2012 - 11:26:09 PST)
[AMBER] How to handle with two Zn2+ when calculates the free binding energy by mmpbsa.py in metalloprotein
- JiYuan Liu (Thu Feb 16 2012 - 06:16:51 PST)
- JiYuan Liu (Thu Feb 16 2012 - 05:56:11 PST)
[AMBER] How to set the existing waters to be the cap molecules?
- David A. Case (Tue Feb 07 2012 - 17:06:18 PST)
- liu junjun (Mon Feb 06 2012 - 18:29:05 PST)
- David A Case (Mon Feb 06 2012 - 11:35:40 PST)
- liu junjun (Mon Feb 06 2012 - 06:22:49 PST)
[AMBER] HTML page explaining mm_pbsa.pl error messages available
- Adrian Roitberg (Mon Feb 06 2012 - 09:17:05 PST)
- Nadine Homeyer (Mon Feb 06 2012 - 08:50:25 PST)
[AMBER] implicit and explicit
- amir abbasi (Tue Feb 28 2012 - 05:34:06 PST)
[AMBER] installation
- subrata paul (Mon Feb 13 2012 - 06:32:15 PST)
- David A Case (Mon Feb 13 2012 - 04:51:05 PST)
- subrata paul (Sun Feb 12 2012 - 20:56:51 PST)
- case (Sat Feb 11 2012 - 09:02:43 PST)
- subrata paul (Fri Feb 10 2012 - 21:11:06 PST)
- David A Case (Fri Feb 10 2012 - 05:48:18 PST)
- subrata paul (Thu Feb 09 2012 - 21:33:12 PST)
- David A Case (Thu Feb 09 2012 - 08:29:36 PST)
- subrata paul (Wed Feb 08 2012 - 20:58:09 PST)
- David A. Case (Wed Feb 08 2012 - 08:30:00 PST)
- subrata paul (Wed Feb 08 2012 - 05:01:56 PST)
[AMBER] ions
- Carlos Romero (Fri Feb 24 2012 - 14:45:27 PST)
- David A Case (Fri Feb 24 2012 - 04:47:39 PST)
- Carlos Romero (Thu Feb 23 2012 - 22:32:33 PST)
- case (Thu Feb 23 2012 - 18:51:29 PST)
- Carlos Romero (Mon Feb 20 2012 - 18:21:31 PST)
[AMBER] Is there a membrane tutorial for Amber?
- Ross Walker (Tue Feb 28 2012 - 09:43:24 PST)
- David A Case (Tue Feb 28 2012 - 04:57:12 PST)
- Vlad Cojocaru (Mon Feb 27 2012 - 22:59:28 PST)
- Arthur Roberts (Mon Feb 27 2012 - 14:34:28 PST)
[AMBER] is there any tools that can convert Desmond .cms to Amber format?
- Albert (Tue Feb 28 2012 - 11:06:55 PST)
[AMBER] Issue with mmpbsa
- Bill Miller III (Fri Feb 24 2012 - 12:49:58 PST)
- Nick Rakowski (Tue Feb 21 2012 - 23:43:05 PST)
- Jason Swails (Tue Feb 21 2012 - 14:41:24 PST)
- Nick Rakowski (Tue Feb 21 2012 - 05:58:22 PST)
[AMBER] Issues with hydrogens using glycam force field in Amber 10
- Bill Ross (Tue Feb 21 2012 - 09:07:23 PST)
- Lachele Foley (Lists) (Mon Feb 20 2012 - 09:00:21 PST)
- Lachele Foley (Lists) (Mon Feb 20 2012 - 08:08:43 PST)
- tommaso.casalini.mail.polimi.it (Mon Feb 20 2012 - 06:54:30 PST)
- tommaso.casalini.mail.polimi.it (Sat Feb 18 2012 - 07:03:07 PST)
- tommaso.casalini.mail.polimi.it (Sat Feb 18 2012 - 03:57:52 PST)
- Lachele Foley (Lists) (Fri Feb 17 2012 - 19:07:37 PST)
- Karl N. Kirschner (Fri Feb 17 2012 - 17:18:11 PST)
- tommaso.casalini.mail.polimi.it (Fri Feb 17 2012 - 09:09:46 PST)
- Lachele Foley (Lists) (Fri Feb 17 2012 - 08:04:25 PST)
- tommaso.casalini.mail.polimi.it (Fri Feb 17 2012 - 03:35:00 PST)
[AMBER] iwrap concern
- David A Case (Wed Feb 15 2012 - 05:23:49 PST)
- Dilraj LAMA (Wed Feb 15 2012 - 01:14:29 PST)
[AMBER] Ligands fly away from binding pocket
- Aron Broom (Sun Feb 19 2012 - 20:16:36 PST)
- tian zhu (Sun Feb 19 2012 - 15:30:35 PST)
[AMBER] loading of fullerene2160
- FyD (Mon Feb 06 2012 - 06:27:19 PST)
- gargi borgohai (Mon Feb 06 2012 - 05:15:50 PST)
[AMBER] makeDIST_RST command problem
- Olena Dobrovolska (Thu Feb 02 2012 - 08:13:42 PST)
[AMBER] MD simulation of protein with Calcium ion in explicit solvent
- Aron Broom (Wed Feb 15 2012 - 07:34:49 PST)
- Brian Radak (Wed Feb 15 2012 - 07:22:54 PST)
- Aron Broom (Wed Feb 15 2012 - 07:17:46 PST)
- Quentin Delettre (Wed Feb 15 2012 - 07:02:27 PST)
[AMBER] md sticking!
- Ross Walker (Tue Feb 28 2012 - 09:45:57 PST)
- amir abbasi (Tue Feb 28 2012 - 05:56:51 PST)
- amir abbasi (Sun Feb 26 2012 - 03:21:40 PST)
- case (Sat Feb 25 2012 - 08:42:39 PST)
- amir abbasi (Sat Feb 25 2012 - 07:41:13 PST)
- case (Sat Feb 25 2012 - 06:33:37 PST)
- amir abbasi (Sat Feb 25 2012 - 05:38:53 PST)
[AMBER] md stopping in TI calculation
- steinbrt.rci.rutgers.edu (Tue Feb 14 2012 - 04:07:24 PST)
- leila karami (Tue Feb 14 2012 - 01:12:08 PST)
- steinbrt.rci.rutgers.edu (Tue Feb 14 2012 - 00:28:33 PST)
- leila karami (Mon Feb 13 2012 - 23:23:52 PST)
- David A Case (Mon Feb 13 2012 - 11:12:42 PST)
- steinbrt.rci.rutgers.edu (Mon Feb 13 2012 - 03:32:21 PST)
- leila karami (Mon Feb 13 2012 - 02:21:18 PST)
- case (Sun Feb 12 2012 - 18:45:55 PST)
- leila karami (Sun Feb 12 2012 - 06:17:24 PST)
- leila karami (Sun Feb 12 2012 - 06:07:46 PST)
- case (Sun Feb 12 2012 - 04:45:52 PST)
- leila karami (Sun Feb 12 2012 - 04:11:06 PST)
[AMBER] Mixing GAFF and OPLS force field
- Guoxiong Su (Wed Feb 22 2012 - 12:19:15 PST)
- FyD (Wed Feb 22 2012 - 00:12:12 PST)
- Thomas Schlesier (Tue Feb 21 2012 - 09:17:46 PST)
- FyD (Tue Feb 21 2012 - 09:14:47 PST)
- Guoxiong Su (Tue Feb 21 2012 - 08:55:53 PST)
- Guoxiong Su (Tue Feb 21 2012 - 08:31:10 PST)
- FyD (Tue Feb 21 2012 - 08:27:25 PST)
- Thomas Schlesier (Tue Feb 21 2012 - 06:38:48 PST)
- Guoxiong Su (Mon Feb 20 2012 - 13:56:20 PST)
[AMBER] mm_pbsa error: Flag "RADII" not found in PARM file
- Jason Swails (Wed Feb 29 2012 - 13:59:09 PST)
- g t (Wed Feb 29 2012 - 04:32:06 PST)
[AMBER] mmpbsa
- Sel Ercan (Sun Feb 05 2012 - 13:25:03 PST)
- Jason Swails (Sun Feb 05 2012 - 10:08:34 PST)
- case (Sun Feb 05 2012 - 09:44:27 PST)
- Sel Ercan (Sat Feb 04 2012 - 17:05:08 PST)
[AMBER] MMPBSA entropy calculations ASSERTion ' ier == 0 ' failed in nmode.f at line 114. ?
- David A Case (Mon Feb 06 2012 - 11:31:06 PST)
- Ake Sandgren (Mon Feb 06 2012 - 05:40:20 PST)
- David A Case (Mon Feb 06 2012 - 05:10:58 PST)
- Urszula Uciechowska (Sun Feb 05 2012 - 12:50:54 PST)
[AMBER] MMPBSA problem
- mish (Wed Feb 01 2012 - 00:49:18 PST)
- Urszula Uciechowska (Wed Feb 01 2012 - 00:02:35 PST)
- Sushil Mishra (Tue Jan 31 2012 - 23:53:00 PST)
- Urszula Uciechowska (Tue Jan 31 2012 - 23:36:18 PST)
- mish (Tue Jan 31 2012 - 22:41:30 PST)
- Urszula Uciechowska (Tue Jan 31 2012 - 22:26:33 PST)
[AMBER] MMPBSA query
- David A Case (Mon Feb 13 2012 - 05:04:14 PST)
- Soumya Lipsa Rath (Mon Feb 13 2012 - 04:20:31 PST)
[AMBER] MMPBSA results and huge SD
- Jason Swails (Tue Feb 14 2012 - 15:56:02 PST)
- Cenk \(Jenk\) Andac (Tue Feb 14 2012 - 07:38:40 PST)
- mish (Tue Feb 14 2012 - 02:47:18 PST)
- Urszula Uciechowska (Tue Feb 14 2012 - 02:04:28 PST)
- mish (Tue Feb 14 2012 - 01:26:20 PST)
- Urszula Uciechowska (Tue Feb 14 2012 - 01:14:21 PST)
[AMBER] MMPBSA.py troubleshooting
- Bill Miller III (Fri Feb 24 2012 - 12:45:52 PST)
- Åge Skjevik (Thu Feb 23 2012 - 09:49:13 PST)
[AMBER] Multiple frcmod files in tleap: Do parameters come from the last frcmod file loaded?
- Jason Swails (Wed Feb 01 2012 - 19:35:50 PST)
- FyD (Wed Feb 01 2012 - 12:39:30 PST)
- Joel Dockray (Wed Feb 01 2012 - 11:16:49 PST)
[AMBER] mutation of the one base pair by leap
- Vlad Cojocaru (Thu Feb 23 2012 - 23:00:25 PST)
- case (Thu Feb 23 2012 - 18:48:47 PST)
- leila karami (Tue Feb 21 2012 - 02:01:16 PST)
[AMBER] NAB+fortran
- David A. Case (Thu Feb 09 2012 - 08:44:56 PST)
- Daniel Hollas (Mon Feb 06 2012 - 03:20:09 PST)
[AMBER] need KDO prep file
- Lachele Foley (Lists) (Mon Feb 06 2012 - 11:59:26 PST)
- FyD (Thu Feb 02 2012 - 23:42:57 PST)
- Lachele Foley (Lists) (Thu Feb 02 2012 - 16:43:02 PST)
- Camille Sultana (Thu Feb 02 2012 - 13:53:27 PST)
- Lachele Foley (Lists) (Thu Feb 02 2012 - 09:11:22 PST)
- FyD (Wed Feb 01 2012 - 23:34:59 PST)
- Lachele Foley (Lists) (Wed Feb 01 2012 - 17:16:59 PST)
- Camille Sultana (Wed Feb 01 2012 - 17:14:58 PST)
- Camille Sultana (Wed Feb 01 2012 - 17:06:22 PST)
[AMBER] NMODE list index out of range error
- Sangeetha B (Wed Feb 01 2012 - 20:18:27 PST)
[AMBER] NVT and NPT simulation
- Brian Radak (Mon Feb 20 2012 - 06:30:42 PST)
- Daniel Roe (Sat Feb 18 2012 - 07:47:28 PST)
- Aron Broom (Sat Feb 18 2012 - 06:11:43 PST)
- Atila Petrosian (Sat Feb 18 2012 - 03:39:40 PST)
- Atila Petrosian (Sat Feb 18 2012 - 03:02:31 PST)
[AMBER] other makeDIST_RST issues
- David A Case (Fri Feb 10 2012 - 11:33:41 PST)
- Thomas Pochapsky (Fri Feb 10 2012 - 08:27:58 PST)
- David A Case (Wed Feb 01 2012 - 09:24:49 PST)
- Thomas Pochapsky (Wed Feb 01 2012 - 08:34:24 PST)
[AMBER] p2n file connectivity issue
- Steven M. Graham (Wed Feb 08 2012 - 08:00:48 PST)
[AMBER] parm.frosst parameters
- Jason Swails (Tue Feb 14 2012 - 15:13:10 PST)
- thomas.fox.boehringer-ingelheim.com (Tue Feb 14 2012 - 07:49:18 PST)
- Cen Gao (Wed Feb 08 2012 - 19:22:44 PST)
- Guanglei Cui (Wed Feb 08 2012 - 07:30:07 PST)
- David A. Case (Tue Feb 07 2012 - 16:57:04 PST)
- Jason Swails (Tue Feb 07 2012 - 10:32:45 PST)
- Guanglei Cui (Tue Feb 07 2012 - 10:16:17 PST)
- case (Sun Feb 05 2012 - 06:11:48 PST)
- thomas.fox.boehringer-ingelheim.com (Wed Feb 01 2012 - 07:32:24 PST)
[AMBER] partial atomic charges
- Mary Varughese (Tue Feb 21 2012 - 10:42:11 PST)
- FyD (Tue Feb 21 2012 - 08:30:04 PST)
- David A Case (Tue Feb 21 2012 - 05:06:46 PST)
- Mary Varughese (Tue Feb 21 2012 - 01:40:54 PST)
[AMBER] per-residue RMSF without B-factor, what is the unit of these values, could be as large as 5000?
- Jason Swails (Tue Feb 07 2012 - 21:27:04 PST)
- Catein Catherine (Mon Feb 06 2012 - 23:48:11 PST)
[AMBER] pmemd test failure when compiling with intel 12.1.2
- Vlad Cojocaru (Mon Feb 06 2012 - 11:43:52 PST)
- David A Case (Mon Feb 06 2012 - 11:37:51 PST)
- Vlad Cojocaru (Mon Feb 06 2012 - 08:17:42 PST)
- Jason Swails (Mon Feb 06 2012 - 08:04:27 PST)
- Vlad Cojocaru (Mon Feb 06 2012 - 07:22:52 PST)
[AMBER] PMEMD.CUDA.MPI PME tests/Benchmarks
- Scott Le Grand (Tue Feb 07 2012 - 11:31:21 PST)
- Martin Peters (Tue Feb 07 2012 - 08:05:34 PST)
- Scott Le Grand (Tue Feb 07 2012 - 07:52:49 PST)
- Ross Walker (Tue Feb 07 2012 - 06:45:53 PST)
- Martin Peters (Tue Feb 07 2012 - 01:07:23 PST)
- Ross Walker (Fri Feb 03 2012 - 16:15:15 PST)
- Martin Peters (Fri Feb 03 2012 - 07:08:46 PST)
[AMBER] Polarization and normal Ewald Summation
- David A Case (Thu Feb 23 2012 - 08:30:30 PST)
- Volker Lesch (Thu Feb 23 2012 - 06:06:15 PST)
[AMBER] potential of mean force
- M. L. Dodson (Sun Feb 26 2012 - 14:17:06 PST)
- kirtana S (Sun Feb 26 2012 - 12:46:55 PST)
- M. L. Dodson (Sun Feb 26 2012 - 05:46:51 PST)
- kirtana S (Sat Feb 25 2012 - 22:05:17 PST)
- Aron Broom (Wed Feb 15 2012 - 14:43:54 PST)
- Ben Roberts (Wed Feb 15 2012 - 14:41:25 PST)
- kirtana S (Wed Feb 15 2012 - 14:34:27 PST)
[AMBER] Problem building octahedral coordinated ligands in LEaP
- Jesper Sørensen (Mon Feb 20 2012 - 12:50:21 PST)
- Cannon, John F. (Mon Feb 20 2012 - 12:30:27 PST)
- Jesper Sørensen (Mon Feb 20 2012 - 10:38:54 PST)
- Tom Joseph (Mon Feb 20 2012 - 10:21:48 PST)
- Cannon, John F. (Mon Feb 20 2012 - 08:27:38 PST)
[AMBER] problem in getting required snapshots
- Daniel Roe (Tue Feb 21 2012 - 04:20:04 PST)
- Aron Broom (Mon Feb 20 2012 - 13:26:14 PST)
- Adrian Roitberg (Mon Feb 20 2012 - 13:09:16 PST)
- Mahendra B Thapa (Mon Feb 20 2012 - 13:05:28 PST)
[AMBER] problem in output file of the awk script in tutorial A6
- David A Case (Thu Feb 23 2012 - 11:07:44 PST)
- shahab shariati (Thu Feb 23 2012 - 07:21:02 PST)
[AMBER] Problem with ampdb and ptraj
- David A Case (Tue Feb 14 2012 - 04:55:51 PST)
- Andrianopsyah Mas Jaya Putra (Mon Feb 13 2012 - 21:33:38 PST)
[AMBER] problem with atom type
- David A Case (Tue Feb 21 2012 - 05:00:43 PST)
- pancham lal gupta (Mon Feb 20 2012 - 09:09:37 PST)
- David A Case (Mon Feb 20 2012 - 05:36:00 PST)
- pancham lal gupta (Sun Feb 19 2012 - 23:50:58 PST)
[AMBER] Problem with leaprc.ff99SB file sourcing
- David A. Case (Wed Feb 08 2012 - 08:53:46 PST)
- vladanstefanovic.kg.ac.rs (Wed Feb 08 2012 - 07:22:44 PST)
- David A. Case (Wed Feb 08 2012 - 05:52:26 PST)
- vladanstefanovic.kg.ac.rs (Wed Feb 08 2012 - 02:11:57 PST)
[AMBER] Problem with rst file retrieval
- David A Case (Thu Feb 16 2012 - 05:32:26 PST)
- komal soni (Thu Feb 16 2012 - 03:01:01 PST)
[AMBER] Problem with vector principal
- Daniel Roe (Tue Feb 21 2012 - 21:42:51 PST)
- fatima chami (Tue Feb 21 2012 - 14:41:41 PST)
- fatima chami (Tue Feb 21 2012 - 14:34:21 PST)
[AMBER] Problems about dihedral restraint in umbrella sampling
- jylu (Mon Feb 06 2012 - 22:44:10 PST)
[AMBER] Problems in ions in Amber11
- Bill Ross (Thu Feb 02 2012 - 15:42:50 PST)
- Thomas Cheatham III (Thu Feb 02 2012 - 15:35:38 PST)
- TAEJIN KIM (Thu Feb 02 2012 - 15:23:06 PST)
- InSuk Joung (Wed Feb 01 2012 - 11:19:05 PST)
- TAEJIN KIM (Wed Feb 01 2012 - 11:11:30 PST)
[AMBER] Protonated state of GLU, CYS
- Ngo Son Tung (Mon Feb 20 2012 - 07:11:45 PST)
[AMBER] Ptraj - Multimodel PDB Segmentation Fault...
- Daniel Roe (Fri Feb 03 2012 - 05:23:04 PST)
- Cihan Aydin (Thu Feb 02 2012 - 20:12:03 PST)
[AMBER] ptraj analysis
- Daniel Roe (Tue Feb 14 2012 - 07:56:31 PST)
- Giachetti Andrea - CERM (Tue Feb 14 2012 - 07:40:06 PST)
- Daniel Roe (Tue Feb 14 2012 - 07:24:11 PST)
- Giachetti Andrea - CERM (Tue Feb 14 2012 - 06:54:25 PST)
[AMBER] PTRAJ H-bond analysis for protein and ligand
- Swati Adlakha (Tue Feb 28 2012 - 05:44:18 PST)
[AMBER] ptraj to make NMR structure ensemble
- Charles Johnson (Fri Feb 03 2012 - 11:26:55 PST)
[AMBER] QM/MM atoms
- Fernando Martín García (Wed Feb 22 2012 - 07:55:34 PST)
[AMBER] query on .inpcrd file format
- Marc van der Kamp (Tue Feb 07 2012 - 01:55:24 PST)
- abinayar.imsc.res.in (Tue Feb 07 2012 - 01:25:00 PST)
[AMBER] Query on Antechmaber Charge distribution
- David A Case (Tue Feb 14 2012 - 04:49:33 PST)
- Dilraj LAMA (Tue Feb 14 2012 - 00:13:53 PST)
[AMBER] R: Faking Vacuum Simulations with a GPU
- Aron Broom (Tue Feb 21 2012 - 07:55:58 PST)
- Giovanni Pavan (Tue Feb 21 2012 - 07:17:20 PST)
[AMBER] Radii issue with mbondi2 + leaprc.parmCHI_YIL.bsc for RNA
- Mike NG (Fri Feb 17 2012 - 11:49:01 PST)
- Ilyas Yildirim (Fri Feb 17 2012 - 09:06:15 PST)
- Niel Henriksen (Fri Feb 17 2012 - 08:12:46 PST)
- Mike NG (Fri Feb 17 2012 - 07:47:44 PST)
- Jason Swails (Fri Feb 17 2012 - 04:49:11 PST)
- Hai Nguyen (Thu Feb 16 2012 - 20:38:56 PST)
[AMBER] regarding QM/MM simulation
- jani vinod (Sun Feb 05 2012 - 03:52:31 PST)
- Adrian Roitberg (Fri Feb 03 2012 - 05:02:39 PST)
- Marc van der Kamp (Fri Feb 03 2012 - 04:29:26 PST)
- jani vinod (Fri Feb 03 2012 - 03:32:03 PST)
[AMBER] Release of the R.E.D. III.5 tools
- FyD (Wed Feb 22 2012 - 02:46:40 PST)
[AMBER] Restart file for pmemd not showing all information
- Aron Broom (Tue Feb 14 2012 - 19:33:47 PST)
- filip fratev (Tue Feb 14 2012 - 19:15:16 PST)
- case (Tue Feb 14 2012 - 18:52:58 PST)
- filip fratev (Tue Feb 14 2012 - 17:28:31 PST)
- David A Case (Tue Feb 14 2012 - 12:04:56 PST)
- Aron Broom (Tue Feb 14 2012 - 09:40:59 PST)
- Ismail, Mohd F. (Tue Feb 14 2012 - 09:33:26 PST)
- Sasha Perkins (Tue Feb 14 2012 - 08:54:23 PST)
- filip fratev (Tue Feb 14 2012 - 08:38:57 PST)
[AMBER] restraining membrane diffusion
- Jose Borreguero (Wed Feb 22 2012 - 12:09:00 PST)
[AMBER] restraints in igb simulation
- Aron Broom (Fri Feb 17 2012 - 21:25:56 PST)
- M. L. Dodson (Fri Feb 17 2012 - 21:23:20 PST)
- Danny Xu (Fri Feb 17 2012 - 20:43:58 PST)
- Aron Broom (Fri Feb 17 2012 - 19:04:46 PST)
- M. L. Dodson (Fri Feb 17 2012 - 16:03:06 PST)
- Danny Xu (Fri Feb 17 2012 - 15:44:32 PST)
- Danny Xu (Fri Feb 17 2012 - 15:39:56 PST)
- Aron Broom (Fri Feb 17 2012 - 15:38:25 PST)
- Danny Xu (Fri Feb 17 2012 - 15:34:46 PST)
- Daniel Roe (Fri Feb 17 2012 - 09:03:09 PST)
- Aron Broom (Fri Feb 17 2012 - 05:24:13 PST)
- Jason Swails (Fri Feb 17 2012 - 04:52:07 PST)
- Danny Xu (Thu Feb 16 2012 - 22:21:39 PST)
[AMBER] RNA/Protein Interaction
- Vlad Cojocaru (Mon Feb 06 2012 - 02:14:44 PST)
- Amir Abbasi (Mon Feb 06 2012 - 02:05:27 PST)
- amirhossein taghavi (Sun Feb 05 2012 - 07:13:19 PST)
- amir abbasi (Sat Feb 04 2012 - 13:53:39 PST)
[AMBER] Rupture of GlcNAc C-H bonds with AMBER8
- Lachele Foley (Lists) (Wed Feb 15 2012 - 18:53:21 PST)
- Sebastian Enck (Wed Feb 15 2012 - 15:37:54 PST)
- Aron Broom (Tue Feb 14 2012 - 19:30:57 PST)
- case (Tue Feb 14 2012 - 19:08:05 PST)
- Lachele Foley (Lists) (Tue Feb 14 2012 - 17:44:56 PST)
- Sebastian Enck (Tue Feb 14 2012 - 17:16:27 PST)
- Lachele Foley (Lists) (Tue Feb 14 2012 - 10:25:59 PST)
- Sebastian Enck (Tue Feb 14 2012 - 09:09:10 PST)
[AMBER] same simulation using different random seeds on GPU
- Jason Swails (Sun Feb 26 2012 - 10:09:18 PST)
- Oliver Kuhn (Sun Feb 26 2012 - 02:09:18 PST)
- Oliver Kuhn (Fri Feb 24 2012 - 09:22:50 PST)
- Ross Walker (Fri Feb 24 2012 - 09:01:59 PST)
- Aron Broom (Fri Feb 24 2012 - 08:53:10 PST)
- Oliver Kuhn (Fri Feb 24 2012 - 08:50:29 PST)
- Cannon, John F. (Fri Feb 24 2012 - 08:43:11 PST)
- Oliver Kuhn (Fri Feb 24 2012 - 08:37:16 PST)
[AMBER] Sander with NMROPT
- Carlos Simmerling (Tue Feb 07 2012 - 09:28:33 PST)
- Jason Swails (Tue Feb 07 2012 - 08:46:46 PST)
- Rahul Banerjee (Tue Feb 07 2012 - 07:19:54 PST)
[AMBER] SD unit
- Bill Miller III (Thu Feb 09 2012 - 04:20:09 PST)
- Urszula Uciechowska (Thu Feb 09 2012 - 02:49:55 PST)
[AMBER] simulation in lipid
- rukman kesh (Tue Feb 28 2012 - 21:38:44 PST)
[AMBER] Simulation set up
- John S (Sun Feb 26 2012 - 01:04:17 PST)
[AMBER] simulation without solvent
- David A Case (Tue Feb 14 2012 - 04:46:43 PST)
- steinbrt.rci.rutgers.edu (Tue Feb 14 2012 - 00:31:29 PST)
- Atila Petrosian (Tue Feb 14 2012 - 00:19:37 PST)
[AMBER] strip and use of distance-based mask
- Nanna Holmgaard List (Wed Feb 29 2012 - 12:41:06 PST)
- Daniel Roe (Wed Feb 29 2012 - 09:23:19 PST)
- Nanna Holmgaard List (Wed Feb 29 2012 - 08:32:48 PST)
- Daniel Roe (Wed Feb 29 2012 - 06:10:06 PST)
- Nanna Holmgaard List (Tue Feb 28 2012 - 22:42:29 PST)
- Daniel Roe (Tue Feb 28 2012 - 14:48:36 PST)
- Nanna Holmgaard List (Tue Feb 28 2012 - 11:52:02 PST)
[AMBER] Stripping hydrogens etc. from the prmtop?
- Jason Swails (Tue Feb 07 2012 - 21:17:54 PST)
- Cihan Aydin (Tue Feb 07 2012 - 17:41:38 PST)
- David A. Case (Tue Feb 07 2012 - 17:03:22 PST)
- Cihan Aydin (Tue Feb 07 2012 - 12:43:01 PST)
[AMBER] Test if MD converged or not.
- Carlos Simmerling (Mon Feb 27 2012 - 04:03:34 PST)
- Catein Catherine (Sun Feb 26 2012 - 23:08:02 PST)
[AMBER] The charge of metal center is not integer which handled with MCPB
- FyD (Mon Feb 20 2012 - 23:35:39 PST)
- JiYuan Liu (Mon Feb 20 2012 - 22:15:41 PST)
[AMBER] TI: error in reading namelist cntrl
- steinbrt.rci.rutgers.edu (Tue Feb 07 2012 - 07:32:06 PST)
- leila karami (Tue Feb 07 2012 - 06:05:51 PST)
- steinbrt.rci.rutgers.edu (Tue Feb 07 2012 - 05:13:57 PST)
- leila karami (Tue Feb 07 2012 - 04:59:42 PST)
- steinbrt.rci.rutgers.edu (Tue Feb 07 2012 - 04:44:55 PST)
- leila karami (Tue Feb 07 2012 - 04:09:36 PST)
- steinbrt.rci.rutgers.edu (Tue Feb 07 2012 - 02:36:50 PST)
- leila karami (Tue Feb 07 2012 - 01:33:05 PST)
- steinbrt.rci.rutgers.edu (Tue Feb 07 2012 - 01:04:09 PST)
- leila karami (Tue Feb 07 2012 - 00:08:32 PST)
- leila karami (Mon Feb 06 2012 - 10:13:27 PST)
- Jason Swails (Mon Feb 06 2012 - 07:57:36 PST)
- leila karami (Mon Feb 06 2012 - 07:36:18 PST)
[AMBER] TI_All non-softcore atoms must be identical in both systems
- steinbrt.rci.rutgers.edu (Mon Feb 20 2012 - 00:31:45 PST)
- leila karami (Sun Feb 19 2012 - 07:42:29 PST)
- steinbrt.rci.rutgers.edu (Sun Feb 19 2012 - 07:03:55 PST)
- leila karami (Sun Feb 19 2012 - 06:20:34 PST)
- steinbrt.rci.rutgers.edu (Sun Feb 19 2012 - 05:05:55 PST)
- leila karami (Sun Feb 19 2012 - 03:52:18 PST)
[AMBER] tLEaP
- FyD (Wed Feb 01 2012 - 09:20:20 PST)
- David A Case (Wed Feb 01 2012 - 05:53:03 PST)
- Алексей Раевский (Wed Feb 01 2012 - 02:38:05 PST)
[AMBER] tleap: added ions are in close vicinity to protein
- Hirdesh Kumar (Tue Feb 07 2012 - 04:59:39 PST)
- David A Case (Tue Feb 07 2012 - 04:53:55 PST)
- Hirdesh Kumar (Mon Feb 06 2012 - 21:27:45 PST)
[AMBER] To account for the protonation states of amino acids at a constant pH
- Jason Swails (Fri Feb 17 2012 - 04:56:08 PST)
- Aron Broom (Wed Feb 15 2012 - 21:22:36 PST)
- abinayar.imsc.res.in (Wed Feb 15 2012 - 21:01:37 PST)
- David A Case (Wed Feb 15 2012 - 12:34:54 PST)
- abinayar.imsc.res.in (Wed Feb 15 2012 - 03:49:01 PST)
[AMBER] unit for SD in MMPBSa
- Urszula Uciechowska (Thu Feb 09 2012 - 00:33:22 PST)
[AMBER] Use of tabulated potentials in Amber ?
- Adrian Roitberg (Thu Feb 23 2012 - 09:09:24 PST)
- Marek Maly (Thu Feb 23 2012 - 08:53:50 PST)
[AMBER] use Restrain mask function in PMEMD
- David A Case (Mon Feb 13 2012 - 04:53:54 PST)
- Muhammad Khaled Tumbi (Mon Feb 13 2012 - 01:15:49 PST)
[AMBER] using AMBER in GPU & MPI environment
- Jason Swails (Tue Feb 14 2012 - 16:03:09 PST)
- 홍종희 (Mon Feb 13 2012 - 23:45:46 PST)
[AMBER] Using Antechamber in order to make prmtop and inpcrd
- Aditya Setiajid (Sun Feb 26 2012 - 23:39:58 PST)
- Muhammad Aditya Setiajid (Wed Feb 22 2012 - 03:41:19 PST)
- FyD (Wed Feb 22 2012 - 01:11:01 PST)
- Aditya Setiajid (Tue Feb 21 2012 - 22:51:38 PST)
- FyD (Tue Feb 21 2012 - 22:10:59 PST)
- Aditya Setiajid (Tue Feb 21 2012 - 20:20:56 PST)
[AMBER] Water models in prmtop files
- David A Case (Tue Feb 14 2012 - 12:06:55 PST)
- Brian Radak (Tue Feb 14 2012 - 08:46:35 PST)
- Peter Eastman (Mon Feb 13 2012 - 15:42:33 PST)
- David A Case (Mon Feb 13 2012 - 13:22:37 PST)
- Peter Eastman (Mon Feb 13 2012 - 11:33:09 PST)
[AMBER] what do reprocessing steps do in md simulation?
- Irene Newhouse (Wed Feb 08 2012 - 09:12:39 PST)
- khaled bodoor (Wed Feb 08 2012 - 04:13:55 PST)
[AMBER] when will Amber 12 be released?
- Ross Walker (Tue Feb 28 2012 - 13:50:38 PST)
- Albert (Tue Feb 28 2012 - 10:10:21 PST)
- Ross Walker (Tue Feb 28 2012 - 09:41:08 PST)
- Albert (Tue Feb 28 2012 - 05:07:58 PST)
- Scott Brozell (Tue Feb 28 2012 - 01:47:02 PST)
- Albert (Tue Feb 28 2012 - 01:09:10 PST)
[AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW
- JiYuan Liu (Tue Feb 28 2012 - 01:16:04 PST)
[AMBER] wrapping first molecule.. again
- Dmitry Mukha (Tue Feb 21 2012 - 00:09:41 PST)
- Aron Broom (Mon Feb 20 2012 - 12:40:00 PST)
- Dmitry Mukha (Mon Feb 20 2012 - 10:54:52 PST)
- Jan-Philip Gehrcke (Mon Feb 20 2012 - 10:52:11 PST)
- Aron Broom (Mon Feb 20 2012 - 10:37:55 PST)
- Dmitry Mukha (Mon Feb 20 2012 - 09:46:36 PST)
calculation of spectral density
- David A Case (Mon Feb 20 2012 - 06:40:58 PST)
- Mahendra B Thapa (Thu Feb 16 2012 - 12:11:34 PST)
p2n file connectivity issue
- FyD (Wed Feb 08 2012 - 10:02:44 PST)
problem in getting required snapshots
- Mahendra B Thapa (Fri Feb 24 2012 - 09:11:46 PST)
rmsd input file
- Sel Ercan (Wed Feb 01 2012 - 02:47:36 PST)

Amber Archive Feb 2012 by subject