Amber Archive Sep 2013: by subject

[AMBER] About T-REMD convergence
- Jason Swails (Mon Sep 16 2013 - 09:19:36 PDT)
- Francesco Pietra (Mon Sep 16 2013 - 08:00:48 PDT)
- Francesco Pietra (Mon Sep 16 2013 - 07:57:48 PDT)
- Carlos Simmerling (Mon Sep 16 2013 - 05:50:07 PDT)
- Jason Swails (Mon Sep 16 2013 - 03:31:59 PDT)
- Francesco Pietra (Mon Sep 16 2013 - 02:17:24 PDT)
[AMBER] Adding an extra non-bonded pair list
- Jason Swails (Fri Sep 20 2013 - 15:27:12 PDT)
- jfloresc.andrew.cmu.edu (Fri Sep 20 2013 - 11:40:11 PDT)
[AMBER] Adding an extra non-bonded pair list (solved)
- jfloresc.andrew.cmu.edu (Wed Sep 25 2013 - 18:17:42 PDT)
[AMBER] Amber Install
- Jason Swails (Wed Sep 04 2013 - 12:04:36 PDT)
- Lindsay Morrison (Wed Sep 04 2013 - 10:45:27 PDT)
[AMBER] AMBER on AWS - Beta testers wanted.
- Ross Walker (Wed Sep 25 2013 - 13:14:11 PDT)
[AMBER] Amber Tools cpptraj woes
- Geoffrey Gray (Mon Sep 09 2013 - 20:32:21 PDT)
- Jason Swails (Mon Sep 09 2013 - 14:17:44 PDT)
- Geoffrey Gray (Mon Sep 09 2013 - 12:59:21 PDT)
- Daniel Roe (Mon Sep 09 2013 - 12:27:21 PDT)
- Geoffrey Gray (Mon Sep 09 2013 - 11:42:54 PDT)
[AMBER] AMBER version
- Mary Varughese (Mon Sep 23 2013 - 16:14:59 PDT)
- David A Case (Mon Sep 23 2013 - 04:47:58 PDT)
- Jason Swails (Mon Sep 23 2013 - 04:27:08 PDT)
- Mary Varughese (Mon Sep 23 2013 - 01:27:28 PDT)
[AMBER] AMBER: the units of the physical quantities
- case (Sat Sep 21 2013 - 06:12:55 PDT)
- hustgt08 (Sat Sep 21 2013 - 05:08:34 PDT)
[AMBER] AmberTools 1.5.2 compilation Error: Return type mismatch of function 'cgalf' at (1) (REAL(8)/REAL(4))
- harry mangalam (Tue Sep 24 2013 - 19:11:26 PDT)
- case (Tue Sep 24 2013 - 18:56:32 PDT)
- Jason Swails (Tue Sep 24 2013 - 16:31:39 PDT)
- harry mangalam (Tue Sep 24 2013 - 12:19:37 PDT)
[AMBER] AmberTools update 17 for CPPTRAJ
- Daniel Roe (Mon Sep 23 2013 - 08:03:06 PDT)
[AMBER] Antechamber
- FyD (Tue Sep 17 2013 - 07:20:58 PDT)
- Jasim, Mahmood (Student) (Tue Sep 17 2013 - 06:44:02 PDT)
- David A Case (Tue Sep 17 2013 - 05:59:43 PDT)
- Jasim, Mahmood (Student) (Tue Sep 17 2013 - 05:09:21 PDT)
- David A Case (Tue Sep 17 2013 - 04:36:33 PDT)
- Jasim, Mahmood (Student) (Tue Sep 17 2013 - 03:58:56 PDT)
- case (Mon Sep 16 2013 - 04:47:48 PDT)
- case (Mon Sep 16 2013 - 04:45:33 PDT)
- Jasim, Mahmood (Student) (Mon Sep 16 2013 - 04:12:23 PDT)
- Jasim, Mahmood (Student) (Mon Sep 16 2013 - 02:34:50 PDT)
- David A Case (Fri Sep 13 2013 - 09:17:24 PDT)
- Jasim, Mahmood (Student) (Fri Sep 13 2013 - 07:50:42 PDT)
- David A Case (Fri Sep 13 2013 - 07:30:10 PDT)
- Jasim, Mahmood (Student) (Fri Sep 13 2013 - 06:15:48 PDT)
[AMBER] antechamber no convergence
- FyD (Wed Sep 18 2013 - 22:29:47 PDT)
- David A Case (Wed Sep 18 2013 - 04:47:07 PDT)
- FyD (Tue Sep 17 2013 - 22:49:12 PDT)
- Jianhui Tian (Tue Sep 17 2013 - 06:53:07 PDT)
- FyD (Tue Sep 17 2013 - 00:11:25 PDT)
- Jianhui Tian (Mon Sep 16 2013 - 12:47:28 PDT)
- Jianhui Tian (Mon Sep 16 2013 - 11:49:20 PDT)
- case (Mon Sep 16 2013 - 07:13:55 PDT)
- Jianhui Tian (Mon Sep 16 2013 - 07:06:09 PDT)
- Jianhui Tian (Fri Sep 13 2013 - 07:18:51 PDT)
- David A Case (Fri Sep 13 2013 - 06:02:45 PDT)
- Jianhui Tian (Thu Sep 12 2013 - 12:05:18 PDT)
[AMBER] Are Amber able to analyze the feature of certain bond?
- X Sun (Fri Sep 06 2013 - 20:09:24 PDT)
[AMBER] Assigning atom type.
- Jason Swails (Sat Sep 14 2013 - 21:09:22 PDT)
- Sanjib Paul (Fri Sep 13 2013 - 06:52:35 PDT)
[AMBER] atomic fluctuation and average structure
- Mary Varughese (Mon Sep 09 2013 - 21:03:28 PDT)
- Daniel Roe (Mon Sep 09 2013 - 19:48:43 PDT)
- Mary Varughese (Mon Sep 09 2013 - 17:55:54 PDT)
[AMBER] Average Conformations from trajectory
- Daniel Roe (Thu Sep 05 2013 - 07:11:06 PDT)
- Covington, Cody Lance (Thu Sep 05 2013 - 06:33:39 PDT)
[AMBER] best Generalized Born solvation model for intrinsically disordered peptides
- Carlos Simmerling (Thu Sep 05 2013 - 09:01:49 PDT)
- Thomas Evangelidis (Thu Sep 05 2013 - 08:36:58 PDT)
- Daniel Roe (Thu Sep 05 2013 - 07:48:46 PDT)
- Hai Nguyen (Tue Sep 03 2013 - 13:55:21 PDT)
- Thomas Evangelidis (Tue Sep 03 2013 - 13:35:24 PDT)
- Hai Nguyen (Tue Sep 03 2013 - 12:49:58 PDT)
- Hai Nguyen (Tue Sep 03 2013 - 12:48:04 PDT)
- Thomas Evangelidis (Tue Sep 03 2013 - 05:03:19 PDT)
- Carlos Simmerling (Tue Sep 03 2013 - 04:56:09 PDT)
- Thomas Evangelidis (Mon Sep 02 2013 - 13:48:12 PDT)
[AMBER] Calculate average property
- Bill Ross (Fri Sep 20 2013 - 21:37:16 PDT)
- Daniel Roe (Tue Sep 17 2013 - 08:08:48 PDT)
- Jason Swails (Tue Sep 17 2013 - 07:24:16 PDT)
- Gargi Borgohai (Tue Sep 17 2013 - 04:05:39 PDT)
- Gargi Borgohai (Tue Sep 17 2013 - 04:03:42 PDT)
[AMBER] CHAMBER VDW energy in PBC
- Ross Walker (Tue Sep 03 2013 - 11:05:41 PDT)
- Jun Feng (Tue Sep 03 2013 - 10:54:03 PDT)
[AMBER] CHAMBER: dihe energy in c36 vs c22
- Jun Feng (Tue Sep 03 2013 - 14:32:19 PDT)
[AMBER] Changing the Lennard Jones potential
- Jason Swails (Sun Sep 29 2013 - 04:58:23 PDT)
- Pengzhi Zhang (Sat Sep 28 2013 - 15:44:25 PDT)
[AMBER] compile ambertools 13 with -nofftw3
- sunyeping (Sat Sep 14 2013 - 10:23:21 PDT)
[AMBER] compile ambertools with -nofftw3
- case (Mon Sep 02 2013 - 06:27:16 PDT)
- sunyeping (Sun Sep 01 2013 - 20:37:44 PDT)
[AMBER] Constraint failure in RATTLE algorithm occurs during NAMD simulation with amber force field
- case (Sun Sep 01 2013 - 09:35:43 PDT)
- sunyeping (Sun Sep 01 2013 - 07:31:07 PDT)
[AMBER] Convert DCD to MDCRD, lose PBC.
- Bill Ross (Wed Sep 04 2013 - 17:57:44 PDT)
- Jason Swails (Wed Sep 04 2013 - 16:33:15 PDT)
- X Sun (Wed Sep 04 2013 - 17:22:21 PDT)
- Thomas Cheatham (Wed Sep 04 2013 - 13:57:56 PDT)
- X Sun (Wed Sep 04 2013 - 14:54:18 PDT)
[AMBER] Coordinate of excess charge (proton)
- Adrian Roitberg (Mon Sep 23 2013 - 14:51:41 PDT)
- Fabrício Bracht (Mon Sep 23 2013 - 14:48:04 PDT)
[AMBER] CORRECTION: Oct 22 deadline for ACS COMP Division Awards for Spring 2014 meeting
- Carlos Simmerling (Wed Sep 25 2013 - 12:34:32 PDT)
[AMBER] Cpptraj bug - low priority
- Sorensen, Jesper (Mon Sep 16 2013 - 08:41:52 PDT)
- Daniel Roe (Mon Sep 16 2013 - 07:31:01 PDT)
- Sorensen, Jesper (Mon Sep 16 2013 - 00:23:07 PDT)
[AMBER] CPPtraj not producing outputs
- Jason Swails (Wed Sep 18 2013 - 09:09:02 PDT)
- Neha Sikka (Wed Sep 18 2013 - 08:51:29 PDT)
[AMBER] cpptraj removes velocities upon imaging
- Daniel Roe (Thu Sep 05 2013 - 10:45:23 PDT)
[AMBER] cytidine triphosphate
- Hallel Freedman (Thu Sep 26 2013 - 23:24:00 PDT)
- FyD (Thu Sep 26 2013 - 23:17:58 PDT)
- Hallel Freedman (Thu Sep 26 2013 - 13:39:17 PDT)
- FyD (Thu Sep 26 2013 - 13:24:04 PDT)
- Hallel Freedman (Thu Sep 26 2013 - 11:46:32 PDT)
[AMBER] deltaG binding obtained from AmberTools 12 and 13 are different
- Adrian Roitberg (Tue Sep 03 2013 - 19:09:13 PDT)
- Xioling Chuang (Tue Sep 03 2013 - 19:06:50 PDT)
- Jason Swails (Tue Sep 03 2013 - 08:06:20 PDT)
- Xioling Chuang (Tue Sep 03 2013 - 06:44:35 PDT)
- Jason Swails (Tue Sep 03 2013 - 05:05:26 PDT)
- Xioling Chuang (Tue Sep 03 2013 - 02:04:50 PDT)
- Jason Swails (Mon Sep 02 2013 - 09:12:23 PDT)
- Xioling Chuang (Mon Sep 02 2013 - 06:18:58 PDT)
[AMBER] Difference between atomtype s6 and sy?
- David A Case (Fri Sep 13 2013 - 06:06:05 PDT)
- X Sun (Mon Sep 09 2013 - 21:16:08 PDT)
[AMBER] Different MMPBSA results in the use of sander and pmemd
- Jason Swails (Wed Sep 11 2013 - 06:34:21 PDT)
- 千语千寻 (Wed Sep 11 2013 - 06:16:23 PDT)
- Jason Swails (Tue Sep 10 2013 - 04:06:06 PDT)
- 千语千寻 (Mon Sep 09 2013 - 20:44:58 PDT)
- wmsmith.uci.edu (Mon Sep 09 2013 - 10:13:26 PDT)
- Jason Swails (Mon Sep 09 2013 - 09:39:36 PDT)
- 千语千寻 (Mon Sep 09 2013 - 02:49:35 PDT)
[AMBER] Distance restraint using com keyword
- Sun (Mon Sep 02 2013 - 07:27:50 PDT)
[AMBER] DMPC GAFF lipid membrane is freezing at 303 K.
- Subbarao Kanchi (Fri Sep 27 2013 - 11:22:02 PDT)
- Subbarao Kanchi (Tue Sep 24 2013 - 12:30:09 PDT)
- jojartb.jgypk.u-szeged.hu (Tue Sep 24 2013 - 11:02:48 PDT)
- Subbarao Kanchi (Tue Sep 24 2013 - 10:19:06 PDT)
- Ross Walker (Tue Sep 24 2013 - 09:35:40 PDT)
- Subbarao Kanchi (Tue Sep 24 2013 - 01:56:16 PDT)
- Subbarao Kanchi (Sun Sep 22 2013 - 02:48:28 PDT)
- Subbarao Kanchi (Sat Sep 21 2013 - 00:16:02 PDT)
[AMBER] energetics of displacing water molecules from protein binding sites
- Changqing Yan (Mon Sep 23 2013 - 21:09:51 PDT)
[AMBER] entropy
- kirtana S (Mon Sep 30 2013 - 12:52:08 PDT)
- Daniel Roe (Mon Sep 30 2013 - 11:58:03 PDT)
- kirtana S (Mon Sep 30 2013 - 10:58:52 PDT)
- Daniel Roe (Mon Sep 30 2013 - 08:59:26 PDT)
- kirtana S (Sun Sep 29 2013 - 17:17:07 PDT)
[AMBER] Erro in the Thermodynamic Intergration using soft core potentials"
- David A Case (Mon Sep 30 2013 - 09:15:01 PDT)
- Daniel Roe (Mon Sep 30 2013 - 09:07:20 PDT)
- 冉挺 (Mon Sep 30 2013 - 06:18:07 PDT)
- David A Case (Mon Sep 30 2013 - 05:01:34 PDT)
- 冉挺 (Sun Sep 29 2013 - 19:02:28 PDT)
[AMBER] error in installing ambertools 1.5
- David A Case (Wed Sep 11 2013 - 04:58:02 PDT)
- Kumud Agarwal (Wed Sep 11 2013 - 00:08:08 PDT)
[AMBER] error in leap -- Glycam residue building
- Lachele Foley (Tue Sep 10 2013 - 12:55:17 PDT)
- lara lara (Tue Sep 10 2013 - 12:29:47 PDT)
[AMBER] Error in QM/MM calculations
- Cuiyl (Fri Sep 27 2013 - 04:45:58 PDT)
- Jason Swails (Fri Sep 27 2013 - 04:03:53 PDT)
- Cuiyl (Thu Sep 26 2013 - 20:05:14 PDT)
- Cuiyl (Thu Sep 26 2013 - 19:00:00 PDT)
[AMBER] Error with NVT and NPT Simulations
- Jason Swails (Tue Sep 10 2013 - 10:46:46 PDT)
- Ross Walker (Tue Sep 10 2013 - 10:41:44 PDT)
- Brian Radak (Tue Sep 10 2013 - 10:25:33 PDT)
- Daniel Roe (Mon Sep 09 2013 - 14:42:24 PDT)
- Kyler L Cook (Mon Sep 09 2013 - 13:28:29 PDT)
[AMBER] For format correction after generating solvent file.
- David A Case (Fri Sep 06 2013 - 08:17:14 PDT)
- Daniel Roe (Fri Sep 06 2013 - 07:59:30 PDT)
- Krati Sharma (Fri Sep 06 2013 - 07:33:05 PDT)
- David A Case (Fri Sep 06 2013 - 05:23:34 PDT)
- Krati Sharma (Fri Sep 06 2013 - 03:35:04 PDT)
- Daniel Roe (Thu Sep 05 2013 - 20:34:58 PDT)
- Krati Sharma (Thu Sep 05 2013 - 20:25:19 PDT)
[AMBER] Force constant in umbrella sampling
- Adrian Roitberg (Wed Sep 04 2013 - 13:08:47 PDT)
- Fabrício Bracht (Wed Sep 04 2013 - 13:02:59 PDT)
[AMBER] Forcefield for lipopeptides
- Prasanna Venkatesh D (Mon Sep 09 2013 - 20:10:59 PDT)
- Jason Swails (Mon Sep 09 2013 - 07:24:39 PDT)
- Prasanna Venkatesh D (Mon Sep 09 2013 - 01:28:00 PDT)
[AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K.
- Subbarao Kanchi (Mon Sep 30 2013 - 11:14:01 PDT)
- Subbarao Kanchi (Wed Sep 11 2013 - 03:23:14 PDT)
[AMBER] Generating periodic box parameters for a pdb file already solvated
- Sajeewa Pemasinghe (Thu Sep 26 2013 - 04:38:52 PDT)
- Jason Swails (Thu Sep 26 2013 - 03:45:33 PDT)
- Sajeewa Pemasinghe (Wed Sep 25 2013 - 22:54:22 PDT)
[AMBER] Generating topology files for two proteins in a single input pdb
- George Green (Mon Sep 30 2013 - 08:01:04 PDT)
- David A Case (Mon Sep 30 2013 - 04:53:43 PDT)
- George Green (Sun Sep 29 2013 - 14:26:37 PDT)
[AMBER] glycam - leap error
- lara lara (Mon Sep 16 2013 - 07:57:58 PDT)
- Karl N. Kirschner (Fri Sep 13 2013 - 07:09:45 PDT)
- Lachele Foley (Thu Sep 12 2013 - 14:44:50 PDT)
- Lachele Foley (Thu Sep 12 2013 - 11:10:11 PDT)
- lara lara (Thu Sep 12 2013 - 10:31:16 PDT)
[AMBER] GTX 600/700 benchmarks
- Parker de Waal (Sun Sep 08 2013 - 17:03:35 PDT)
[AMBER] hbond analysis
- Mary Varughese (Mon Sep 09 2013 - 07:26:32 PDT)
- Jason Swails (Mon Sep 09 2013 - 05:15:21 PDT)
- Mary Varughese (Sun Sep 08 2013 - 19:22:56 PDT)
- Daniel Roe (Sat Sep 07 2013 - 09:16:29 PDT)
- Mary Varughese (Sat Sep 07 2013 - 00:19:29 PDT)
[AMBER] hbond in Ambertools
- Daniel Roe (Thu Sep 05 2013 - 07:20:21 PDT)
- Shesh Nath (Thu Sep 05 2013 - 02:09:36 PDT)
- Neha Gandhi (Thu Sep 05 2013 - 00:31:47 PDT)
[AMBER] HEATING run using SANDER
- case (Tue Sep 24 2013 - 18:59:20 PDT)
- Sourav Purohit (Tue Sep 24 2013 - 12:30:12 PDT)
[AMBER] Help on MMPBSA script
- Jason Swails (Tue Sep 24 2013 - 07:35:53 PDT)
- R R S Pissurlenkar (Tue Sep 24 2013 - 05:59:21 PDT)
[AMBER] help to run restricted MD
- Brian Radak (Mon Sep 30 2013 - 08:32:15 PDT)
- Fengxue Li (Mon Sep 30 2013 - 07:17:23 PDT)
[AMBER] help with RESP tutorial using antechambe
- Anselm Horn (Tue Sep 24 2013 - 01:30:58 PDT)
- Fengxue Li (Tue Sep 24 2013 - 00:44:19 PDT)
[AMBER] help with RESP tutorial using antechamber and gaussian
- FyD (Sun Sep 22 2013 - 23:29:30 PDT)
- Fengxue Li (Sun Sep 22 2013 - 19:29:59 PDT)
[AMBER] histidine_residue
- Jason Swails (Fri Sep 27 2013 - 09:09:22 PDT)
- Shomesankar Bhunia (Fri Sep 27 2013 - 08:38:51 PDT)
- Concha, Monica (Fri Sep 27 2013 - 06:10:51 PDT)
- Shomesankar Bhunia (Fri Sep 27 2013 - 03:10:28 PDT)
- Shomesankar Bhunia (Fri Sep 27 2013 - 02:24:07 PDT)
[AMBER] How do I read a trail file in the format of NetCDF with VMD ?
- Jason Swails (Thu Sep 26 2013 - 03:43:44 PDT)
- Yanyan ZHU (Thu Sep 26 2013 - 02:00:40 PDT)
[AMBER] How do I use MMPBSA.py for namd .dcd file?
- Jason Swails (Mon Sep 23 2013 - 19:16:06 PDT)
- sudipta (Mon Sep 23 2013 - 17:11:02 PDT)
- Jason Swails (Mon Sep 23 2013 - 16:56:23 PDT)
- sudipta (Mon Sep 23 2013 - 16:53:09 PDT)
- sudipta (Mon Sep 23 2013 - 16:36:08 PDT)
- Jason Swails (Mon Sep 23 2013 - 11:31:44 PDT)
- sudipta (Mon Sep 23 2013 - 08:59:29 PDT)
- Jason Swails (Mon Sep 23 2013 - 04:04:30 PDT)
- Jason Swails (Mon Sep 23 2013 - 03:59:04 PDT)
- sudipta (Sun Sep 22 2013 - 20:26:18 PDT)
- Daniel Roe (Sun Sep 22 2013 - 19:53:56 PDT)
- sudipta (Sun Sep 22 2013 - 16:13:56 PDT)
- sudipta (Sun Sep 22 2013 - 07:46:44 PDT)
- Jason Swails (Mon Sep 16 2013 - 10:24:30 PDT)
- sudipta (Mon Sep 16 2013 - 10:05:28 PDT)
- Jason Swails (Mon Sep 16 2013 - 09:20:39 PDT)
- sudipta (Mon Sep 16 2013 - 08:25:20 PDT)
- Jason Swails (Mon Sep 16 2013 - 06:59:24 PDT)
- sudipta (Mon Sep 16 2013 - 05:39:25 PDT)
- Jason Swails (Mon Sep 16 2013 - 02:51:22 PDT)
- Sarah Witzke (Mon Sep 16 2013 - 00:10:56 PDT)
- sudipta (Sun Sep 15 2013 - 21:45:01 PDT)
- sudipta (Sat Sep 14 2013 - 19:28:10 PDT)
- Jason Swails (Sat Sep 14 2013 - 16:18:25 PDT)
- sudipta (Sat Sep 14 2013 - 11:55:36 PDT)
- sudipta (Fri Sep 13 2013 - 20:51:29 PDT)
- Ross Walker (Fri Sep 13 2013 - 10:31:18 PDT)
- sudipta (Fri Sep 13 2013 - 10:20:11 PDT)
- Jason Swails (Fri Sep 13 2013 - 08:53:55 PDT)
- Daniel Roe (Fri Sep 13 2013 - 08:35:37 PDT)
- sudipta (Fri Sep 13 2013 - 08:28:43 PDT)
- Daniel Roe (Fri Sep 13 2013 - 08:14:37 PDT)
- sudipta (Fri Sep 13 2013 - 07:45:50 PDT)
[AMBER] How to choose ntc value?
- Jason Swails (Sat Sep 14 2013 - 20:53:55 PDT)
- X Sun (Sat Sep 14 2013 - 10:55:08 PDT)
[AMBER] How to do clustering analysis by ptraj?
- Biao Ma (Wed Sep 25 2013 - 19:18:29 PDT)
- Jason Swails (Wed Sep 25 2013 - 10:22:56 PDT)
- Daniel Roe (Wed Sep 25 2013 - 07:36:02 PDT)
- Biao Ma (Tue Sep 24 2013 - 22:04:55 PDT)
- Daniel Roe (Tue Sep 24 2013 - 09:18:38 PDT)
- Biao Ma (Tue Sep 24 2013 - 01:30:51 PDT)
- Thomas Cheatham (Fri Sep 20 2013 - 10:42:07 PDT)
- Biao Ma (Thu Sep 19 2013 - 23:56:34 PDT)
- Thomas Cheatham (Tue Sep 17 2013 - 09:50:49 PDT)
- Biao Ma (Tue Sep 17 2013 - 00:43:33 PDT)
[AMBER] How to get the prmtop and inpcrd files of melamine in Amber?
- Jason Swails (Mon Sep 09 2013 - 06:22:29 PDT)
- 张明焜 (Mon Sep 09 2013 - 00:20:08 PDT)
- David A Case (Fri Sep 06 2013 - 05:31:05 PDT)
- Jason Swails (Fri Sep 06 2013 - 04:58:06 PDT)
- 张明焜 (Thu Sep 05 2013 - 20:52:05 PDT)
[AMBER] how to use commands “sequence”, “set”, “add”, “bond”, “ impose” or someothers necessary to add a –H and a –OH to the GLY
- Jason Swails (Tue Sep 24 2013 - 04:04:52 PDT)
- 张明焜 (Mon Sep 23 2013 - 23:53:36 PDT)
[AMBER] How to use makeDIST_RST without MAPping?
- Jan-Philip Gehrcke (Mon Sep 23 2013 - 08:43:36 PDT)
- David A Case (Mon Sep 23 2013 - 09:15:34 PDT)
[AMBER] Hydrogen bond analysis problem
- Daniel Roe (Fri Sep 20 2013 - 08:50:09 PDT)
- Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Fri Sep 20 2013 - 02:04:45 PDT)
- Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Thu Sep 19 2013 - 07:46:47 PDT)
- Daniel Roe (Thu Sep 19 2013 - 07:42:50 PDT)
- Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Thu Sep 19 2013 - 07:28:51 PDT)
- Daniel Roe (Thu Sep 19 2013 - 07:15:56 PDT)
- Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Wed Sep 18 2013 - 23:22:05 PDT)
- Daniel Roe (Wed Sep 18 2013 - 08:16:51 PDT)
- Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Wed Sep 18 2013 - 02:50:06 PDT)
[AMBER] issue running AMBER on double sockets hexa cores
- Jan-Philip Gehrcke (Wed Sep 18 2013 - 08:15:02 PDT)
- Pascal Bonnet (Wed Sep 18 2013 - 08:00:23 PDT)
- Ross Walker (Mon Sep 16 2013 - 15:54:25 PDT)
- case (Mon Sep 16 2013 - 14:32:55 PDT)
- Pascal Bonnet (Mon Sep 16 2013 - 11:42:12 PDT)
[AMBER] Issue with intramolecular pairwise-residue energy decomposition
- Jason Swails (Mon Sep 09 2013 - 06:32:45 PDT)
- rohitarora10.gmail.com (Mon Sep 09 2013 - 00:33:23 PDT)
[AMBER] issues with MMPBSA and explicit waters
- Alfredo Quevedo (Tue Sep 03 2013 - 11:17:28 PDT)
- Jason Swails (Tue Sep 03 2013 - 11:12:15 PDT)
- Jason Swails (Tue Sep 03 2013 - 07:59:44 PDT)
- Alfredo Quevedo (Tue Sep 03 2013 - 07:09:05 PDT)
- Jason Swails (Mon Sep 02 2013 - 09:08:57 PDT)
- Alfredo Quevedo (Mon Sep 02 2013 - 07:39:19 PDT)
[AMBER] Jobs hanging on parallel CUDA without producing output
- Nils Oberhauser (Thu Sep 26 2013 - 08:26:30 PDT)
- Jason Swails (Thu Sep 26 2013 - 02:40:07 PDT)
- Nils Oberhauser (Wed Sep 25 2013 - 23:58:49 PDT)
- Ross Walker (Mon Sep 23 2013 - 09:35:32 PDT)
- Jason Swails (Mon Sep 23 2013 - 04:36:38 PDT)
- Nils Oberhauser (Mon Sep 23 2013 - 03:12:59 PDT)
[AMBER] make error in installing sander.APBS
- Robert Konecny (Thu Sep 05 2013 - 11:33:11 PDT)
- Asmita Gupta (Thu Sep 05 2013 - 11:22:42 PDT)
- Daniel Roe (Thu Sep 05 2013 - 10:50:46 PDT)
- Robert Konecny (Thu Sep 05 2013 - 10:48:22 PDT)
- Asmita Gupta (Thu Sep 05 2013 - 10:40:34 PDT)
- Daniel Roe (Thu Sep 05 2013 - 10:33:26 PDT)
- Asmita Gupta (Thu Sep 05 2013 - 10:25:29 PDT)
- Jason Swails (Thu Sep 05 2013 - 08:57:23 PDT)
- Asmita Gupta (Thu Sep 05 2013 - 08:27:47 PDT)
- Daniel Roe (Thu Sep 05 2013 - 07:21:47 PDT)
- Asmita Gupta (Wed Sep 04 2013 - 23:35:34 PDT)
[AMBER] Minimization terminates with unknown reason
- Jason Swails (Mon Sep 02 2013 - 14:44:58 PDT)
- Xiaoquan Sun (Mon Sep 02 2013 - 13:59:18 PDT)
[AMBER] missing loop
- Bill Ross (Mon Sep 09 2013 - 20:54:17 PDT)
- Vlad Cojocaru (Wed Sep 04 2013 - 09:31:21 PDT)
- Wong, Sergio E. (Wed Sep 04 2013 - 09:08:38 PDT)
- Sergio R Aragon (Tue Sep 03 2013 - 14:58:16 PDT)
- Fabian Glaser (Tue Sep 03 2013 - 07:05:53 PDT)
[AMBER] mmP(G)BSA correlation time
- Adrian Roitberg (Thu Sep 05 2013 - 12:38:12 PDT)
- psu4.uic.edu (Thu Sep 05 2013 - 12:13:16 PDT)
[AMBER] mmpbsa number of atoms issues
- Ayesha Fatima (Sat Sep 14 2013 - 22:42:35 PDT)
- Jason Swails (Sat Sep 14 2013 - 21:05:31 PDT)
- Ayesha Fatima (Sat Sep 14 2013 - 03:44:31 PDT)
[AMBER] MMPBSA.py EPB problem with idecomp=3
- Ray Luo, Ph.D. (Fri Sep 06 2013 - 11:14:37 PDT)
- Ryan Pavlovicz (Thu Sep 05 2013 - 16:17:02 PDT)
[AMBER] MMPBSA.py PB error
- Aronica, Pietro (Mon Sep 30 2013 - 07:44:52 PDT)
- Jason Swails (Mon Sep 30 2013 - 07:44:34 PDT)
- Aronica, Pietro (Mon Sep 30 2013 - 07:27:38 PDT)
[AMBER] MMPBSA.py: energy decomposition
- Kshatresh Dutta Dubey (Mon Sep 16 2013 - 01:01:11 PDT)
[AMBER] MMPBSA/GBSA error
- Ray Luo, Ph.D. (Wed Sep 25 2013 - 20:25:41 PDT)
- Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Wed Sep 25 2013 - 18:41:35 PDT)
- Ray Luo, Ph.D. (Wed Sep 25 2013 - 14:45:35 PDT)
- Ray Luo, Ph.D. (Fri Sep 20 2013 - 12:05:53 PDT)
- Jason Swails (Fri Sep 20 2013 - 11:22:57 PDT)
- Jason Swails (Fri Sep 20 2013 - 03:41:46 PDT)
- Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Thu Sep 19 2013 - 22:25:41 PDT)
- wmsmith.uci.edu (Thu Sep 19 2013 - 18:05:08 PDT)
- Jason Swails (Thu Sep 19 2013 - 12:08:17 PDT)
- Jason Swails (Thu Sep 19 2013 - 12:06:44 PDT)
- Ray Luo, Ph.D. (Thu Sep 19 2013 - 11:49:00 PDT)
- Jason Swails (Thu Sep 19 2013 - 11:16:57 PDT)
- Ray Luo, Ph.D. (Thu Sep 19 2013 - 09:14:22 PDT)
- Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Thu Sep 19 2013 - 08:18:35 PDT)
- Jason Swails (Thu Sep 19 2013 - 08:07:00 PDT)
- Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Thu Sep 19 2013 - 07:54:07 PDT)
- Jason Swails (Thu Sep 19 2013 - 07:49:17 PDT)
- Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Thu Sep 19 2013 - 06:56:11 PDT)
- Jason Swails (Thu Sep 19 2013 - 03:41:25 PDT)
- Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Thu Sep 19 2013 - 01:15:28 PDT)
- Jason Swails (Wed Sep 18 2013 - 04:08:36 PDT)
- Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Wed Sep 18 2013 - 00:27:47 PDT)
[AMBER] mpi4py building error during AmberTools 13 install
- sunyeping (Sat Sep 14 2013 - 10:18:23 PDT)
[AMBER] namd-l: MMPBSA calculation using NAMD
- sunyeping (Sun Sep 15 2013 - 23:35:03 PDT)
- Aron Broom (Sun Sep 15 2013 - 22:52:39 PDT)
- sunyeping (Sun Sep 15 2013 - 21:56:31 PDT)
[AMBER] NAMD_AMBER_MD
- Shomesankar Bhunia (Fri Sep 27 2013 - 20:14:53 PDT)
- Jason Swails (Fri Sep 27 2013 - 08:55:51 PDT)
- Shomesankar Bhunia (Fri Sep 27 2013 - 08:42:49 PDT)
[AMBER] NaN problem with GTX680
- Jason Swails (Tue Sep 03 2013 - 05:21:35 PDT)
- JAVAD MAHMOUDZADEH (Tue Sep 03 2013 - 05:18:20 PDT)
- Jason Swails (Tue Sep 03 2013 - 04:50:49 PDT)
- David A Case (Tue Sep 03 2013 - 04:43:14 PDT)
- JAVAD MAHMOUDZADEH (Tue Sep 03 2013 - 00:12:05 PDT)
[AMBER] No torsion terms for N-Cg-Cg-Ng
- Lachele Foley (Thu Sep 26 2013 - 07:10:57 PDT)
- sunita gupta (Thu Sep 26 2013 - 00:08:32 PDT)
[AMBER] Norleucine Parameters
- Adam (Tue Sep 24 2013 - 12:16:46 PDT)
[AMBER] November 11 deadline for ACS COMP Division Awards for Spring 2014 meeting
- Carlos Simmerling (Wed Sep 25 2013 - 10:17:35 PDT)
[AMBER] Number of residues in a solvent box
- Brian Radak (Thu Sep 26 2013 - 10:35:29 PDT)
- Chinthaka Ratnaweera (Thu Sep 26 2013 - 09:53:27 PDT)
[AMBER] Oct 22nd deadline for ACS COMP division awards for Spring national meeting
- Carlos Simmerling (Fri Sep 27 2013 - 06:41:27 PDT)
[AMBER] openmp on 64core/AMD vs MPI over IB on multiple nodes
- harry mangalam (Wed Sep 25 2013 - 14:51:03 PDT)
- harry mangalam (Wed Sep 25 2013 - 14:04:17 PDT)
- Jason Swails (Wed Sep 25 2013 - 13:19:07 PDT)
- harry mangalam (Wed Sep 25 2013 - 12:42:06 PDT)
[AMBER] passing a new argument to sander on command line
- Jason Swails (Mon Sep 30 2013 - 10:49:05 PDT)
- Kepa K. Burusco (Mon Sep 30 2013 - 10:07:32 PDT)
- Jason Swails (Mon Sep 30 2013 - 09:28:18 PDT)
- Kepa K. Burusco (Mon Sep 30 2013 - 08:56:10 PDT)
[AMBER] Path Setting
- Aldo Segura (Wed Sep 11 2013 - 13:07:41 PDT)
- arundhati dutta (Wed Sep 11 2013 - 12:27:47 PDT)
[AMBER] PCA analysis and porcupine plots
- Soma Ghosh (Sat Sep 21 2013 - 05:39:10 PDT)
- wmsmith.uci.edu (Fri Sep 20 2013 - 09:15:13 PDT)
- Soma Ghosh (Thu Sep 19 2013 - 23:56:01 PDT)
- monica.imtech.res.in (Thu Sep 19 2013 - 23:22:07 PDT)
- Soma Ghosh (Thu Sep 19 2013 - 22:58:54 PDT)
[AMBER] Predicting druggable hotspots
- anu chandra (Sun Sep 29 2013 - 22:54:36 PDT)
[AMBER] Probelm with antechamber for resp charge derivation
- David A Case (Wed Sep 25 2013 - 04:33:08 PDT)
- FyD (Wed Sep 25 2013 - 02:27:42 PDT)
- Fengxue Li (Tue Sep 24 2013 - 20:23:37 PDT)
[AMBER] Problem in antechamber execution
- David A Case (Wed Sep 25 2013 - 04:37:48 PDT)
- FyD (Wed Sep 25 2013 - 02:36:52 PDT)
- Tanmoy Paul (Tue Sep 24 2013 - 22:55:34 PDT)
[AMBER] problem in installation
- case (Sat Sep 21 2013 - 06:07:52 PDT)
- esther nehu (Sat Sep 21 2013 - 02:58:42 PDT)
[AMBER] problem in installing AmberTools13
- Vijay Manickam Achari (Tue Sep 03 2013 - 08:11:23 PDT)
- Jason Swails (Tue Sep 03 2013 - 05:11:17 PDT)
- Vijay Manickam Achari (Tue Sep 03 2013 - 01:21:09 PDT)
- Jan-Philip Gehrcke (Tue Sep 03 2013 - 01:12:07 PDT)
- Vijay Manickam Achari (Mon Sep 02 2013 - 23:36:50 PDT)
[AMBER] problem in running AMBER12 in GPU
- Jan-Philip Gehrcke (Wed Sep 11 2013 - 07:32:06 PDT)
- David A Case (Wed Sep 11 2013 - 07:31:28 PDT)
- Sanjib Paul (Wed Sep 11 2013 - 07:14:01 PDT)
- Jan-Philip Gehrcke (Wed Sep 11 2013 - 07:13:07 PDT)
- Sanjib Paul (Wed Sep 11 2013 - 07:04:22 PDT)
- Jan-Philip Gehrcke (Wed Sep 11 2013 - 06:38:26 PDT)
- Sanjib Paul (Wed Sep 11 2013 - 06:28:26 PDT)
- Jason Swails (Wed Sep 04 2013 - 07:56:20 PDT)
- Sanjib Paul (Wed Sep 04 2013 - 07:21:56 PDT)
- Jason Swails (Tue Sep 03 2013 - 09:08:44 PDT)
- Sanjib Paul (Tue Sep 03 2013 - 08:01:24 PDT)
[AMBER] problem installin amber9 in ubuntu 12.04
- Jason Swails (Sat Aug 31 2013 - 22:01:54 PDT)
[AMBER] Problem passing cuda tests.
- Ross Walker (Mon Sep 02 2013 - 10:25:59 PDT)
- Szymon Murawski (Mon Sep 02 2013 - 06:36:06 PDT)
[AMBER] problem running antechamber - amber Version 10
- FyD (Wed Sep 25 2013 - 08:02:51 PDT)
- Daniel Roe (Wed Sep 25 2013 - 07:43:21 PDT)
- Concha, Monica (Wed Sep 25 2013 - 07:17:03 PDT)
[AMBER] problem with addIons in tleap
- Fengxue Li (Fri Sep 27 2013 - 06:50:22 PDT)
[AMBER] problem with antechamber in ambertools 13
- FyD (Wed Sep 04 2013 - 08:33:55 PDT)
- Rodrigo Salazar (Wed Sep 04 2013 - 07:59:22 PDT)
- David A Case (Wed Sep 04 2013 - 05:41:51 PDT)
- FyD (Wed Sep 04 2013 - 05:35:41 PDT)
- Rodrigo Salazar (Tue Sep 03 2013 - 18:01:44 PDT)
[AMBER] problems with reimage cmd
- Jason Swails (Wed Sep 18 2013 - 04:00:06 PDT)
- Chiara Pallara (Wed Sep 18 2013 - 01:11:50 PDT)
[AMBER] Problems with sander.MPI
- Moacyr Comar (Wed Sep 25 2013 - 11:24:54 PDT)
- Jason Swails (Wed Sep 25 2013 - 10:18:52 PDT)
- Moacyr Comar (Wed Sep 25 2013 - 10:12:35 PDT)
[AMBER] protein in popc bilayer simulation
- David A Case (Fri Sep 27 2013 - 04:39:12 PDT)
- Wang Chern Hoe (Dr) (Thu Sep 26 2013 - 23:23:06 PDT)
- David A Case (Thu Sep 26 2013 - 04:46:01 PDT)
- Wang Chern Hoe (Dr) (Wed Sep 25 2013 - 23:58:38 PDT)
- Ross Walker (Wed Sep 25 2013 - 20:19:40 PDT)
- Wang Chern Hoe (Dr) (Wed Sep 25 2013 - 19:46:43 PDT)
[AMBER] Protonated Histidine (HIP) charges in Amber03 (AMBERFF03)
- FyD (Wed Sep 25 2013 - 01:32:01 PDT)
- case (Tue Sep 24 2013 - 18:33:54 PDT)
- Adam (Tue Sep 24 2013 - 12:07:25 PDT)
[AMBER] Query on Alanine scanning
- Jason Swails (Wed Sep 11 2013 - 05:05:00 PDT)
- Mannan (Wed Sep 11 2013 - 02:29:55 PDT)
[AMBER] query reg ptraj RMSD calculation
- Daniel Roe (Thu Sep 12 2013 - 09:12:33 PDT)
- Asmita Gupta (Thu Sep 12 2013 - 08:50:56 PDT)
- Daniel Roe (Thu Sep 12 2013 - 08:32:58 PDT)
- Asmita Gupta (Thu Sep 12 2013 - 06:45:18 PDT)
[AMBER] Question about MMPBSA.py
- rohitarora10.gmail.com (Thu Sep 05 2013 - 08:16:51 PDT)
[AMBER] Question about QM/MM?
- Jason Swails (Mon Sep 09 2013 - 05:23:01 PDT)
- X Sun (Sun Sep 08 2013 - 22:39:26 PDT)
[AMBER] question of analyze matrix command of ptraj
- Daniel Roe (Mon Sep 09 2013 - 09:41:53 PDT)
- 张明焜 (Mon Sep 09 2013 - 03:52:12 PDT)
[AMBER] Question: MM/PBSA and MM/GBSA
- Ray Luo, Ph.D. (Fri Sep 13 2013 - 11:40:35 PDT)
- Hiromasa WATANABE (Thu Sep 12 2013 - 19:06:36 PDT)
- Ray Luo, Ph.D. (Wed Sep 11 2013 - 22:06:43 PDT)
- Hiromasa WATANABE (Wed Sep 11 2013 - 18:06:42 PDT)
- Ray Luo, Ph.D. (Wed Sep 11 2013 - 06:00:46 PDT)
- Wang Baifan (Wed Sep 11 2013 - 00:12:00 PDT)
- Hiromasa WATANABE (Tue Sep 10 2013 - 22:56:06 PDT)
[AMBER] Questions about TI calculation
- steinbrt.rci.rutgers.edu (Thu Sep 05 2013 - 00:16:51 PDT)
- yuandandan05 (Wed Sep 04 2013 - 18:24:30 PDT)
[AMBER] R.E.D. double bond revisit
- FyD (Wed Sep 25 2013 - 13:40:33 PDT)
- psu4.uic.edu (Wed Sep 25 2013 - 10:51:09 PDT)
[AMBER] radial distribution function results
- Daniel Roe (Mon Sep 16 2013 - 08:41:15 PDT)
- Vijay Manickam Achari (Mon Sep 16 2013 - 02:25:15 PDT)
[AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file
- FyD (Mon Sep 30 2013 - 13:07:01 PDT)
[AMBER] RED-vIII.52 problems
- FyD (Tue Sep 03 2013 - 00:41:47 PDT)
- Julio Dominguez (Mon Sep 02 2013 - 18:58:41 PDT)
[AMBER] RED-vIII52 problems...
- FyD (Wed Sep 04 2013 - 07:47:46 PDT)
- Julio Dominguez (Wed Sep 04 2013 - 07:06:22 PDT)
[AMBER] REGARDING UMBRELLA SAMPLING TUTORIAL
- Sourav Purohit (Tue Sep 24 2013 - 08:24:54 PDT)
- Ross Walker (Mon Sep 23 2013 - 21:23:56 PDT)
- Sourav Purohit (Mon Sep 23 2013 - 20:49:56 PDT)
- Ross Walker (Mon Sep 23 2013 - 20:36:31 PDT)
- Sourav Purohit (Mon Sep 23 2013 - 20:03:26 PDT)
[AMBER] rem.log file generated in REMD simulation
- Jason Swails (Mon Sep 16 2013 - 07:02:26 PDT)
- Gargi Borgohai (Mon Sep 16 2013 - 06:00:46 PDT)
[AMBER] REMD exchange
- Francesco Pietra (Wed Sep 11 2013 - 07:09:22 PDT)
- Ross Walker (Wed Sep 11 2013 - 06:42:59 PDT)
- Francesco Pietra (Wed Sep 11 2013 - 06:40:53 PDT)
- Jason Swails (Wed Sep 11 2013 - 04:58:01 PDT)
- Carlos Simmerling (Wed Sep 11 2013 - 03:55:39 PDT)
- Hai Nguyen (Wed Sep 11 2013 - 01:34:27 PDT)
- Francesco Pietra (Tue Sep 10 2013 - 23:03:16 PDT)
- Hai Nguyen (Tue Sep 10 2013 - 14:59:58 PDT)
- Francesco Pietra (Tue Sep 10 2013 - 08:22:53 PDT)
- Carlos Simmerling (Tue Sep 10 2013 - 07:13:58 PDT)
- Niel Henriksen (Tue Sep 10 2013 - 07:01:10 PDT)
- Francesco Pietra (Tue Sep 10 2013 - 06:45:20 PDT)
- Jason Swails (Tue Sep 10 2013 - 04:12:36 PDT)
- Francesco Pietra (Tue Sep 10 2013 - 00:38:25 PDT)
[AMBER] REMD jobs crashing repeatedly on GPUs
- Scott Le Grand (Fri Sep 06 2013 - 11:13:27 PDT)
- Christina Bergonzo (Fri Sep 06 2013 - 11:07:59 PDT)
- Joe Passman (Fri Sep 06 2013 - 10:57:42 PDT)
[AMBER] RESP_ A1-charge failed
- Shomesankar Bhunia (Thu Sep 19 2013 - 08:34:34 PDT)
- Shomesankar Bhunia (Thu Sep 19 2013 - 05:47:06 PDT)
- Shomesankar Bhunia (Thu Sep 19 2013 - 05:43:37 PDT)
- Shomesankar Bhunia (Thu Sep 19 2013 - 05:36:47 PDT)
- FyD (Thu Sep 19 2013 - 05:36:06 PDT)
- Shomesankar Bhunia (Thu Sep 19 2013 - 05:24:10 PDT)
- FyD (Thu Sep 19 2013 - 05:12:34 PDT)
- FyD (Thu Sep 19 2013 - 02:42:40 PDT)
- Shomesankar Bhunia (Wed Sep 18 2013 - 23:16:30 PDT)
[AMBER] rmsd
- Sajeewa Pemasinghe (Tue Sep 17 2013 - 08:52:10 PDT)
- Daniel Roe (Tue Sep 17 2013 - 08:51:06 PDT)
- 김준기 (Tue Sep 17 2013 - 08:41:54 PDT)
- Sajeewa Pemasinghe (Tue Sep 17 2013 - 04:34:30 PDT)
- 김준기 (Mon Sep 16 2013 - 23:43:10 PDT)
- Daniel Roe (Fri Sep 06 2013 - 20:37:30 PDT)
- 김준기 (Fri Sep 06 2013 - 19:57:20 PDT)
[AMBER] rmsd and hbond
- Mary Varughese (Mon Sep 09 2013 - 17:48:00 PDT)
- Daniel Roe (Mon Sep 09 2013 - 09:54:21 PDT)
- Mary Varughese (Mon Sep 09 2013 - 02:20:39 PDT)
[AMBER] rotational diffusion error
- Daniel Roe (Mon Sep 30 2013 - 14:49:58 PDT)
- David A Case (Mon Sep 30 2013 - 05:08:28 PDT)
- Vijay Manickam Achari (Mon Sep 30 2013 - 00:15:46 PDT)
[AMBER] Running Amber on a SGI cluster
- George Tzotzos (Wed Sep 25 2013 - 11:35:43 PDT)
- Ross Walker (Wed Sep 25 2013 - 09:30:38 PDT)
- George Tzotzos (Wed Sep 25 2013 - 09:20:25 PDT)
- Jason Swails (Wed Sep 25 2013 - 08:54:52 PDT)
- Ross Walker (Wed Sep 25 2013 - 08:53:24 PDT)
- George Tzotzos (Wed Sep 25 2013 - 08:26:20 PDT)
- Jason Swails (Wed Sep 25 2013 - 04:52:42 PDT)
- George Tzotzos (Tue Sep 24 2013 - 12:32:25 PDT)
[AMBER] running simulation using increased number of cores
- onetwo (Sat Sep 14 2013 - 22:21:18 PDT)
- Jason Swails (Sat Sep 14 2013 - 06:53:47 PDT)
- onetwo (Fri Sep 13 2013 - 21:13:50 PDT)
[AMBER] Sander aborted during the minimization of the whole system.
- David A Case (Tue Sep 03 2013 - 04:38:40 PDT)
- X Sun (Mon Sep 02 2013 - 21:42:17 PDT)
[AMBER] Setting forcefield parameters
- Jason Swails (Fri Sep 13 2013 - 07:03:21 PDT)
- Tanmoy Paul (Fri Sep 13 2013 - 06:44:28 PDT)
[AMBER] shortest distance
- Jason Swails (Thu Sep 26 2013 - 17:01:29 PDT)
- Norah Schlacter (Thu Sep 26 2013 - 16:39:32 PDT)
- Daniel Roe (Thu Sep 26 2013 - 15:58:09 PDT)
- Norah Schlacter (Thu Sep 26 2013 - 14:19:20 PDT)
[AMBER] significance of 3-10 helixes in Secstruct
- Daniel Roe (Sun Sep 15 2013 - 10:28:11 PDT)
- Chinthaka Ratnaweera (Sat Sep 14 2013 - 14:51:30 PDT)
[AMBER] Sodium Ion Citation
- Brian Radak (Wed Sep 25 2013 - 12:28:42 PDT)
- Lars Holte (Wed Sep 25 2013 - 10:26:04 PDT)
- Brian Radak (Wed Sep 25 2013 - 06:08:34 PDT)
- Lars Holte (Tue Sep 24 2013 - 21:27:07 PDT)
[AMBER] some questions about PCA
- Daniel Roe (Thu Sep 05 2013 - 09:25:46 PDT)
- qiao xue (Mon Sep 02 2013 - 19:55:35 PDT)
[AMBER] Superposition of 3D structures for wid type and mutants with VMD
- Daniel Roe (Fri Sep 27 2013 - 07:40:57 PDT)
- Nhai (Fri Sep 27 2013 - 01:57:33 PDT)
- Yanyan ZHU (Thu Sep 26 2013 - 19:16:36 PDT)
- Daniel Roe (Wed Sep 25 2013 - 07:32:20 PDT)
- Yanyan ZHU (Tue Sep 24 2013 - 18:46:57 PDT)
[AMBER] Temperature based trajectory in REMD
- Carlos Simmerling (Tue Sep 24 2013 - 08:11:44 PDT)
- Daniel Roe (Tue Sep 24 2013 - 07:56:54 PDT)
- Gargi Borgohai (Tue Sep 24 2013 - 05:44:43 PDT)
[AMBER] the difference between proper torsion and improper torsion
- James Maier (Wed Sep 25 2013 - 08:58:36 PDT)
- Ming Huang (Wed Sep 25 2013 - 08:43:02 PDT)
[AMBER] Three body potential
- Jason Swails (Fri Sep 13 2013 - 12:15:39 PDT)
- David A Case (Fri Sep 13 2013 - 12:15:21 PDT)
- MOHD HOMAIDUR RAHMAN (Fri Sep 13 2013 - 11:47:50 PDT)
[AMBER] TI input files in A9 tutorial and Amber12 manual
- Hamed S. Hayatshahi (Tue Sep 10 2013 - 16:52:56 PDT)
- Hamed S. Hayatshahi (Tue Sep 10 2013 - 12:35:54 PDT)
- steinbrt.rci.rutgers.edu (Sun Sep 08 2013 - 09:56:16 PDT)
- Hamed S. Hayatshahi (Fri Sep 06 2013 - 10:52:32 PDT)
- steinbrt.rci.rutgers.edu (Thu Sep 05 2013 - 00:27:48 PDT)
- case (Wed Sep 04 2013 - 18:05:53 PDT)
- Hamed S. Hayatshahi (Wed Sep 04 2013 - 15:02:32 PDT)
[AMBER] Ti problem - system must be very inhomogeneous
- Fabrício Bracht (Wed Sep 18 2013 - 13:39:28 PDT)
- David A Case (Wed Sep 18 2013 - 13:24:18 PDT)
- Fabrício Bracht (Wed Sep 18 2013 - 13:02:25 PDT)
[AMBER] to generate a Glycine(NH2-CH2-COOH) complete prmtop file?
- FyD (Mon Sep 09 2013 - 03:05:19 PDT)
- Sangita Kachhap (Mon Sep 09 2013 - 00:17:34 PDT)
- 张明焜 (Sun Sep 08 2013 - 23:54:38 PDT)
- FyD (Fri Sep 06 2013 - 02:51:20 PDT)
- 张明焜 (Fri Sep 06 2013 - 02:23:27 PDT)
[AMBER] Trajectory determination and directionality in TI with softcore potentials
- David A Case (Tue Sep 17 2013 - 13:05:52 PDT)
- Ryan Muraglia (Tue Sep 17 2013 - 12:39:22 PDT)
[AMBER] Unable to run decomposition analysis using mmpbsa.py of amber12
- Jason Swails (Mon Sep 09 2013 - 12:49:42 PDT)
- Manikanthan Bhavaraju (Mon Sep 09 2013 - 12:27:12 PDT)
- Jason Swails (Sat Sep 07 2013 - 20:32:40 PDT)
- Manikanthan Bhavaraju (Sat Sep 07 2013 - 16:21:48 PDT)
[AMBER] update_amber script confuses Amber versions
- Robyn Ayscue (Fri Sep 06 2013 - 14:12:09 PDT)
- David A Case (Thu Sep 05 2013 - 13:25:15 PDT)
- Jason Swails (Thu Sep 05 2013 - 12:58:07 PDT)
- Robyn Ayscue (Thu Sep 05 2013 - 12:30:40 PDT)
[AMBER] updates for amber12 bugfix18 & 19 fail
- Jason Swails (Tue Sep 03 2013 - 06:04:32 PDT)
- peter.stauffert.boehringer-ingelheim.com (Tue Sep 03 2013 - 05:48:18 PDT)
- Jason Swails (Tue Sep 03 2013 - 05:18:57 PDT)
- Vijay Manickam Achari (Tue Sep 03 2013 - 01:08:15 PDT)
[AMBER] Use of Langevin Thermostat with Amoeba force field
- Karl Debiec (Mon Sep 30 2013 - 19:40:13 PDT)
[AMBER] Using NMODE with NAMD trajectories
- Valeria Marquez (Thu Sep 26 2013 - 11:50:38 PDT)
[AMBER] water cluster analysis
- Subrata Paul (Tue Sep 24 2013 - 01:41:58 PDT)
- Karl N. Kirschner (Tue Sep 24 2013 - 01:23:33 PDT)
- Subrata Paul (Mon Sep 23 2013 - 21:30:44 PDT)
- George Green (Mon Sep 23 2013 - 16:57:41 PDT)
- Jason Swails (Mon Sep 23 2013 - 14:51:04 PDT)
- George Green (Mon Sep 23 2013 - 13:48:05 PDT)
- Jason Swails (Mon Sep 23 2013 - 04:38:44 PDT)
- Subrata Paul (Sun Sep 22 2013 - 06:46:45 PDT)
[AMBER] Word of caution for Xcode 5, Mac OS X
- Jason Swails (Tue Sep 24 2013 - 05:24:29 PDT)
- M. L. Dodson (Mon Sep 23 2013 - 11:33:41 PDT)
- Jason Swails (Mon Sep 23 2013 - 11:06:07 PDT)
- M. L. Dodson (Mon Sep 23 2013 - 07:00:19 PDT)
- Julio Dominguez (Mon Sep 23 2013 - 06:13:51 PDT)
- M. L. Dodson (Mon Sep 23 2013 - 06:27:22 PDT)
- Jason Swails (Mon Sep 23 2013 - 06:26:09 PDT)
- M. L. Dodson (Sat Sep 21 2013 - 06:14:30 PDT)
- case (Sat Sep 21 2013 - 06:01:26 PDT)
- M. L. Dodson (Fri Sep 20 2013 - 20:05:24 PDT)
- Julio Dominguez (Fri Sep 20 2013 - 18:58:27 PDT)
[AMBER] Xleap
- arundhati dutta (Fri Sep 06 2013 - 12:09:33 PDT)
- sribone.fcq.unc.edu.ar (Fri Sep 06 2013 - 12:07:58 PDT)
- Lindsay Morrison (Fri Sep 06 2013 - 11:37:05 PDT)
R.E.D. double bond revisit
- FyD (Thu Sep 26 2013 - 00:10:02 PDT)

Amber Archive Sep 2013 by subject