Amber Archive Jun 2009: by subject

[AMBER]
- Raja Pandian (Thu Jun 18 2009 - 05:35:10 PDT)
- guntheyp.aston.ac.uk (Thu Jun 18 2009 - 04:48:21 PDT)
[AMBER] "loadoff tRNA.lib" in Leap
- Ju Zhang (Tue Jun 23 2009 - 13:55:25 PDT)
[AMBER] (no subject)
- David A. Case (Thu Jun 11 2009 - 04:54:38 PDT)
- david.lisgarten.canterbury.ac.uk (Thu Jun 11 2009 - 01:28:56 PDT)
- david.lisgarten.canterbury.ac.uk (Tue Jun 09 2009 - 06:56:32 PDT)
- David A. Case (Tue Jun 09 2009 - 04:47:59 PDT)
- david.lisgarten.canterbury.ac.uk (Tue Jun 09 2009 - 03:23:57 PDT)
- FyD (Mon Jun 08 2009 - 10:14:05 PDT)
- Karl Kirschner (Mon Jun 08 2009 - 04:38:42 PDT)
- Vishal Maingi (Mon Jun 08 2009 - 04:14:22 PDT)
[AMBER] 2 restraints with different force constants
- David A. Case (Fri Jun 19 2009 - 05:06:18 PDT)
- David A. Case (Fri Jun 19 2009 - 04:41:01 PDT)
- Aust, Susanne (Fri Jun 19 2009 - 00:14:50 PDT)
[AMBER] 2-step vs 3-step TI, and softcores question
- steinbrt.rci.rutgers.edu (Tue Jun 23 2009 - 15:27:46 PDT)
- Jodi Hadden (Tue Jun 23 2009 - 15:00:02 PDT)
[AMBER] a method or program to try to guess the net charge of a small molecule
- Alan (Fri Jun 26 2009 - 03:00:48 PDT)
[AMBER] About the "FATAL: Atom err!"
- Aurum Bai (Mon Jun 22 2009 - 03:12:23 PDT)
[AMBER] About the "FATAL: Atom err"!
- case (Mon Jun 22 2009 - 04:47:59 PDT)
- Aurum Bai (Mon Jun 22 2009 - 03:14:20 PDT)
[AMBER] About the Amber tutorial
- Aurum Bai (Mon Jun 22 2009 - 03:03:49 PDT)
[AMBER] ADD SALT
- Simon Becker (Thu Jun 25 2009 - 02:57:37 PDT)
- Rilei Yu (Thu Jun 25 2009 - 02:22:20 PDT)
[AMBER] ADD SALT additional question
- Vlad Cojocaru (Thu Jun 25 2009 - 07:55:15 PDT)
- Vlad Cojocaru (Thu Jun 25 2009 - 07:51:54 PDT)
- Simon Becker (Thu Jun 25 2009 - 05:34:36 PDT)
[AMBER] addions
- Shubhra Gupta (Tue Jun 02 2009 - 22:47:11 PDT)
[AMBER] AMBER 10: sleap diff errors?
- David A. Case (Thu Jun 04 2009 - 12:19:44 PDT)
- Catein Catherine (Wed Jun 03 2009 - 22:37:35 PDT)
[AMBER] AMBER ERROR
- Vikas Sharma (Sat Jun 13 2009 - 00:16:52 PDT)
[AMBER] AMBER question: bad atom type: MN
- Edward M (Mon Jun 22 2009 - 20:05:51 PDT)
[AMBER] Amber tools 1.2 , Bug report (PTRAJ: dumpq with strip)
- Myunggi Yi (Wed Jun 24 2009 - 11:57:25 PDT)
[AMBER] Amber10 Parallel Installation
- case (Sat Jun 20 2009 - 15:04:14 PDT)
[AMBER] Amber10 Parallel Installation 8%
- Hopkins, Robert (Mon Jun 22 2009 - 12:54:17 PDT)
[AMBER] AMBER10: error message mdfil flag.....
- David A. Case (Wed Jun 03 2009 - 07:30:08 PDT)
- Catein Catherine (Wed Jun 03 2009 - 07:14:50 PDT)
[AMBER] Analysis of the solt-bridge
- Rilei Yu (Mon Jun 29 2009 - 15:42:23 PDT)
- Alessandro Nascimento (Mon Jun 29 2009 - 05:58:49 PDT)
- Rilei Yu (Sun Jun 28 2009 - 15:24:28 PDT)
[AMBER] Antechamber am1bcc questions
- gilbert.bluemarble.net (Mon Jun 15 2009 - 06:04:19 PDT)
[AMBER] Antechamber: stuck at bondtype
- Ye MEI (Wed Jun 17 2009 - 06:48:18 PDT)
- David A. Case (Wed Jun 17 2009 - 06:28:15 PDT)
- Jack Shultz (Wed Jun 17 2009 - 05:50:11 PDT)
[AMBER] Are ntrp=1000, ntwx=1000, ntwr=500 reasonable for long MD simulations?
- Ross Walker (Mon Jun 15 2009 - 07:49:43 PDT)
- Catein Catherine (Mon Jun 15 2009 - 03:04:53 PDT)
[AMBER] ask for parm99MOD
- xiaoqin huang (Mon Jun 01 2009 - 13:25:02 PDT)
- Carlos Simmerling (Mon Jun 01 2009 - 13:12:47 PDT)
[AMBER] Atom names
- Rose Tamil (Wed Jun 03 2009 - 13:43:56 PDT)
- David A. Case (Wed Jun 03 2009 - 09:00:15 PDT)
- Rose Tamil (Wed Jun 03 2009 - 07:53:51 PDT)
- Rose Tamil (Tue Jun 02 2009 - 04:50:47 PDT)
- David A. Case (Tue Jun 02 2009 - 04:44:39 PDT)
- Carlos Simmerling (Tue Jun 02 2009 - 04:39:25 PDT)
- Rose Tamil (Tue Jun 02 2009 - 03:53:50 PDT)
[AMBER] atom number exceeds the MAXATOM when running antechamber
- Gustavo Seabra (Tue Jun 02 2009 - 08:04:33 PDT)
- xueqin pang (Mon Jun 01 2009 - 05:53:23 PDT)
[AMBER] atom type
- Taufik Al-Sarraj (Fri Jun 05 2009 - 09:07:14 PDT)
- Taufik Al-Sarraj (Fri Jun 05 2009 - 06:58:50 PDT)
- David A. Case (Fri Jun 05 2009 - 05:32:45 PDT)
- Taufik Al-Sarraj (Thu Jun 04 2009 - 18:03:14 PDT)
[AMBER] Atom Type List
- Bill Ross (Mon Jun 22 2009 - 09:43:39 PDT)
- Javier Klett (Mon Jun 22 2009 - 09:34:43 PDT)
- case (Mon Jun 22 2009 - 04:38:24 PDT)
- Javier Klett (Mon Jun 22 2009 - 02:54:43 PDT)
[AMBER] atom type no recognize - xleap version 10 but fine in v 9
- case (Sat Jun 20 2009 - 11:31:40 PDT)
- Peter Gannett (Fri Jun 19 2009 - 12:40:47 PDT)
[AMBER] atomtypes in gaff
- FyD (Thu Jun 25 2009 - 04:45:16 PDT)
- FyD (Thu Jun 25 2009 - 01:55:03 PDT)
[AMBER] average torsional energy
- Francesco Pietra (Mon Jun 08 2009 - 02:11:52 PDT)
- Karl Kirschner (Mon Jun 08 2009 - 01:29:05 PDT)
- Carlos Simmerling (Sun Jun 07 2009 - 09:14:17 PDT)
- Adrian Roitberg (Sun Jun 07 2009 - 09:09:14 PDT)
- Francesco Pietra (Sat Jun 06 2009 - 09:57:49 PDT)
[AMBER] bad atom type: MN
- Edward M (Mon Jun 22 2009 - 16:12:09 PDT)
- Edward M (Mon Jun 22 2009 - 16:10:54 PDT)
[AMBER] Binding Energy
- Vikas Sharma (Thu Jun 04 2009 - 04:25:01 PDT)
[AMBER] bond length energy
- Karl Kirschner (Fri Jun 19 2009 - 02:57:04 PDT)
- Mark Williamson (Wed Jun 17 2009 - 10:29:09 PDT)
- Thomas Lake (Wed Jun 17 2009 - 07:04:55 PDT)
[AMBER] Box Center
- Jagan Mohan (Fri Jun 26 2009 - 01:02:05 PDT)
[AMBER] calculating the hydrogen bonding energy between the two molecule
- bharat lakhani (Wed Jun 24 2009 - 02:19:01 PDT)
[AMBER] Can we define +1 or -1 charge for an organic drug using GAFF?
- David A. Case (Mon Jun 08 2009 - 09:47:54 PDT)
- Catein Catherine (Mon Jun 08 2009 - 08:16:23 PDT)
[AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy
- jacky zhao (Wed Jun 03 2009 - 06:44:12 PDT)
- Marc Baaden (Tue Jun 02 2009 - 13:56:29 PDT)
- Gustavo Seabra (Tue Jun 02 2009 - 07:53:19 PDT)
[AMBER] Choice of force feild
- Gustavo Seabra (Tue Jun 02 2009 - 07:58:11 PDT)
[AMBER] Choice of force field
- Carlos Simmerling (Mon Jun 01 2009 - 04:14:09 PDT)
[AMBER] Coarse grained MD in AMBER ?
- Lili Peng (Wed Jun 17 2009 - 11:57:58 PDT)
- Siddharth Rastogi (Wed Jun 17 2009 - 11:50:13 PDT)
[AMBER] Compiling amber 9 with openMPI
- Myunggi Yi (Tue Jun 23 2009 - 11:11:46 PDT)
- case (Tue Jun 23 2009 - 07:13:18 PDT)
- Myunggi Yi (Tue Jun 23 2009 - 06:31:58 PDT)
[AMBER] compiling amber10 with mac intel, ifort/icc and mpi
- Alan (Sat Jun 13 2009 - 11:37:54 PDT)
- David Watson (Thu Jun 11 2009 - 05:43:28 PDT)
- Alan (Thu Jun 11 2009 - 04:14:42 PDT)
- David A. Case (Wed Jun 10 2009 - 09:54:38 PDT)
- Alan (Wed Jun 10 2009 - 09:26:13 PDT)
- David A. Case (Wed Jun 10 2009 - 08:34:59 PDT)
- Alan (Wed Jun 10 2009 - 07:47:00 PDT)
[AMBER] Compiling and running NAB programs in parallel using MPI
- case (Tue Jun 30 2009 - 09:02:57 PDT)
- Kaushik Raha (Tue Jun 30 2009 - 07:48:11 PDT)
- case (Mon Jun 29 2009 - 05:19:10 PDT)
- Kaushik Raha (Fri Jun 26 2009 - 08:12:11 PDT)
- case (Fri Jun 26 2009 - 06:19:04 PDT)
- Kaushik Raha (Thu Jun 25 2009 - 14:36:35 PDT)
[AMBER] Completed installation of AmberTools, version 1.1
- David A. Case (Wed Jun 10 2009 - 07:10:22 PDT)
- Alan (Wed Jun 10 2009 - 06:13:37 PDT)
[AMBER] Computational Alanine Scanning using mm_pbsa, any tutorial for amber9 or amber 10 version?
- Haizhen Zhong (Fri Jun 05 2009 - 16:17:01 PDT)
[AMBER] connecting residues
- Bill Ross (Tue Jun 16 2009 - 09:39:02 PDT)
- Bill Ross (Tue Jun 16 2009 - 09:37:33 PDT)
- KIRTANA S (Tue Jun 16 2009 - 08:59:37 PDT)
[AMBER] Constant pH simulation
- Tom Joseph (Wed Jun 10 2009 - 18:08:36 PDT)
- Rukman Hertadi (Wed Jun 10 2009 - 17:56:59 PDT)
[AMBER] converting vibrational frequency
- aneesh cna (Mon Jun 01 2009 - 09:53:22 PDT)
- David A. Case (Mon Jun 01 2009 - 04:39:32 PDT)
- aneesh cna (Mon Jun 01 2009 - 04:22:01 PDT)
[AMBER] Copper semiempirical parameters
- Ross Walker (Thu Jun 11 2009 - 09:09:14 PDT)
- Jacopo Sgrignani (Thu Jun 11 2009 - 06:49:50 PDT)
[AMBER] correlation motion at production simulation period still changing. Is it normal?
- Catein Catherine (Mon Jun 22 2009 - 02:26:40 PDT)
[AMBER] covalent interaction
- 廖青华 (Mon Jun 15 2009 - 01:06:52 PDT)
[AMBER] create a simulation box
- Gustavo Seabra (Tue Jun 02 2009 - 08:08:46 PDT)
[AMBER] creating bond
- Bill Ross (Wed Jun 03 2009 - 14:40:09 PDT)
- Jorgen Simonsen (Wed Jun 03 2009 - 12:56:29 PDT)
- Bill Ross (Wed Jun 03 2009 - 11:40:52 PDT)
- David A. Case (Wed Jun 03 2009 - 11:32:57 PDT)
- Jorgen Simonsen (Wed Jun 03 2009 - 10:04:11 PDT)
[AMBER] different comformations to choose for RESP
- FyD (Mon Jun 01 2009 - 07:32:21 PDT)
- xueqin pang (Mon Jun 01 2009 - 06:47:30 PDT)
[AMBER] dipole printing
- Hemant Kumar (Fri Jun 12 2009 - 12:03:17 PDT)
- Ross Walker (Fri Jun 12 2009 - 09:13:30 PDT)
- Hemant Kumar (Fri Jun 12 2009 - 08:58:29 PDT)
[AMBER] Distance restraints between groups of atoms
- David A. Case (Tue Jun 09 2009 - 04:45:14 PDT)
- Germain Vallverdu (Tue Jun 09 2009 - 01:39:45 PDT)
- David A. Case (Wed Jun 03 2009 - 09:32:33 PDT)
- Germain Vallverdu (Wed Jun 03 2009 - 07:43:37 PDT)
- David A. Case (Wed Jun 03 2009 - 05:27:04 PDT)
- Germain Vallverdu (Tue Jun 02 2009 - 23:58:57 PDT)
[AMBER] Distance-covariance and PCA questions...
- Hannes Loeffler (Wed Jun 17 2009 - 00:41:42 PDT)
- Bill Ross (Tue Jun 16 2009 - 09:18:40 PDT)
- Cihan Aydin (Mon Jun 15 2009 - 21:18:58 PDT)
[AMBER] DNA as well as protein distorted during MD run in sander
- Jayalakshmi Sridhar (Tue Jun 09 2009 - 09:02:56 PDT)
- Carlos Simmerling (Tue Jun 09 2009 - 08:48:30 PDT)
- Jesse Dylan Ziebarth (jziebrth) (Tue Jun 09 2009 - 08:47:34 PDT)
- Carlos Simmerling (Tue Jun 09 2009 - 08:36:50 PDT)
- Jayalakshmi Sridhar (Tue Jun 09 2009 - 08:33:51 PDT)
- Carlos Simmerling (Tue Jun 09 2009 - 07:38:14 PDT)
- Jayalakshmi Sridhar (Tue Jun 09 2009 - 07:30:39 PDT)
[AMBER] Dyndom
- Chunliyan (Thu Jun 18 2009 - 08:12:44 PDT)
[AMBER] entangle-less building
- Bill Ross (Wed Jun 10 2009 - 15:38:31 PDT)
- Vishal Maingi (Wed Jun 10 2009 - 10:52:51 PDT)
[AMBER] Error in AMBER ( Vertex atom mismatch in Amber)
- Vikas Sharma (Wed Jun 10 2009 - 06:14:28 PDT)
[AMBER] Error in MM PBSA
- Ray Luo (Mon Jun 08 2009 - 11:12:22 PDT)
- Vikas Sharma (Mon Jun 08 2009 - 10:44:06 PDT)
- Ray Luo (Sun Jun 07 2009 - 12:17:30 PDT)
- Vikas Sharma (Sun Jun 07 2009 - 10:02:03 PDT)
- Ray Luo (Sat Jun 06 2009 - 07:37:43 PDT)
- Vikas Sharma (Sat Jun 06 2009 - 02:03:22 PDT)
- Ray Luo (Thu Jun 04 2009 - 14:00:51 PDT)
- Vikas Sharma (Thu Jun 04 2009 - 07:58:43 PDT)
- Vikas Sharma (Wed Jun 03 2009 - 07:24:14 PDT)
- David A. Case (Wed Jun 03 2009 - 04:43:54 PDT)
- Vikas Sharma (Tue Jun 02 2009 - 23:46:06 PDT)
- Vikas Sharma (Tue Jun 02 2009 - 23:46:03 PDT)
- Vikas Sharma (Tue Jun 02 2009 - 23:45:35 PDT)
- David A. Case (Tue Jun 02 2009 - 07:05:09 PDT)
- Vikas Sharma (Tue Jun 02 2009 - 06:42:16 PDT)
[AMBER] Error in MM PBSA (vertex atom mismatch)
- Vikas Sharma (Mon Jun 08 2009 - 23:33:38 PDT)
[AMBER] error in tleap of AMBER 10
- case (Fri Jun 26 2009 - 05:09:58 PDT)
- kureeckal ramesh (Fri Jun 26 2009 - 00:10:56 PDT)
- case (Thu Jun 25 2009 - 04:54:47 PDT)
- kureeckal ramesh (Tue Jun 23 2009 - 22:03:55 PDT)
[AMBER] Error message? INFO: Old style inpcrd file read
- Catein Catherine (Sun Jun 07 2009 - 20:55:28 PDT)
- Robert Duke (Sun Jun 07 2009 - 20:19:38 PDT)
- Catein Catherine (Sun Jun 07 2009 - 20:11:27 PDT)
[AMBER] Error on equilibriation of Amber10
- Masakazu SEKIJIMA (Mon Jun 22 2009 - 03:59:55 PDT)
[AMBER] Error when installing amber11 on OpenSuse
- steinbrt.rci.rutgers.edu (Thu Jun 25 2009 - 05:19:59 PDT)
[AMBER] explicit solvent NMR refinement
- case (Sun Jun 28 2009 - 06:19:11 PDT)
- Carlos Simmerling (Sun Jun 28 2009 - 05:36:42 PDT)
- Sally Pias (Sun Jun 28 2009 - 01:46:56 PDT)
[AMBER] Fe and Mn simulations
- Alessandro Nascimento (Tue Jun 30 2009 - 13:22:14 PDT)
[AMBER] Fe-S topology
- case (Tue Jun 30 2009 - 10:45:27 PDT)
- Markus Kaukonen (Tue Jun 30 2009 - 00:28:51 PDT)
- subarna thakur (Mon Jun 29 2009 - 23:29:16 PDT)
[AMBER] Fix Residue continued...
- Carlos Simmerling (Thu Jun 18 2009 - 11:56:54 PDT)
- Vishal Maingi (Thu Jun 18 2009 - 11:48:03 PDT)
[AMBER] Fix the local structure as a rigid body
- David A. Case (Tue Jun 16 2009 - 08:41:04 PDT)
- Carlos Simmerling (Tue Jun 16 2009 - 07:13:45 PDT)
- Yunjie Zhao (Tue Jun 16 2009 - 06:57:10 PDT)
- Carlos Simmerling (Tue Jun 16 2009 - 06:15:12 PDT)
- Yunjie Zhao (Tue Jun 16 2009 - 06:11:43 PDT)
[AMBER] force field choice
- ahmed said (Fri Jun 26 2009 - 01:21:16 PDT)
[AMBER] Force field parameter for Unionized Phenylalanine HOOC-CH(NH2)-CH2-C6H5
- FyD (Fri Jun 19 2009 - 01:47:39 PDT)
- Madhurima Jana (Thu Jun 18 2009 - 23:40:43 PDT)
[AMBER] force units
- Brad Dickson (Thu Jun 18 2009 - 00:14:31 PDT)
[AMBER] force.f routine
- David A. Case (Wed Jun 10 2009 - 07:09:47 PDT)
- Brad Dickson (Wed Jun 10 2009 - 05:56:39 PDT)
[AMBER] From DLG to Antechamber
- FyD (Fri Jun 19 2009 - 08:54:05 PDT)
- Jack Shultz (Fri Jun 19 2009 - 07:34:33 PDT)
- Jack Shultz (Fri Jun 19 2009 - 07:21:37 PDT)
- gilbert.bluemarble.net (Fri Jun 19 2009 - 07:17:09 PDT)
- Jack Shultz (Fri Jun 19 2009 - 06:09:06 PDT)
- gilbert.bluemarble.net (Fri Jun 19 2009 - 05:57:04 PDT)
- Jack Shultz (Fri Jun 19 2009 - 05:27:20 PDT)
- FyD (Fri Jun 19 2009 - 02:26:46 PDT)
- Jack Shultz (Thu Jun 18 2009 - 17:04:15 PDT)
[AMBER] Fwd: average torsional energy
- Francesco Pietra (Sun Jun 07 2009 - 09:09:37 PDT)
[AMBER] GAFF and solvents.lib error
- David A. Case (Wed Jun 10 2009 - 08:54:05 PDT)
- Vishal Maingi (Wed Jun 10 2009 - 03:25:38 PDT)
[AMBER] GAFF atom type question
- Cen Gao (Sun Jun 14 2009 - 21:12:19 PDT)
- Cen Gao (Thu Jun 11 2009 - 17:31:25 PDT)
- Ross Walker (Thu Jun 11 2009 - 08:43:50 PDT)
- Cen Gao (Thu Jun 11 2009 - 06:36:52 PDT)
- Cen Gao (Wed Jun 10 2009 - 08:49:00 PDT)
[AMBER] Generating LeAP file for helix containing non-standard amino acid
- Brothers, Michael Charles (Fri Jun 19 2009 - 10:46:25 PDT)
- FyD (Thu Jun 18 2009 - 22:41:54 PDT)
- Brothers, Michael Charles (Thu Jun 18 2009 - 14:01:52 PDT)
- FyD (Thu Jun 18 2009 - 12:55:34 PDT)
- Brothers, Michael Charles (Thu Jun 18 2009 - 10:38:53 PDT)
- FyD (Wed Jun 10 2009 - 23:48:27 PDT)
- Brothers, Michael Charles (Wed Jun 10 2009 - 12:40:21 PDT)
- David A. Case (Wed Jun 10 2009 - 12:23:36 PDT)
- David A. Case (Wed Jun 10 2009 - 12:14:49 PDT)
- Brothers, Michael Charles (Wed Jun 10 2009 - 11:26:32 PDT)
[AMBER] GLYCAM: warnings by writing topology
- Sergey Samsonov (Thu Jun 18 2009 - 05:49:31 PDT)
- Bill Ross (Wed Jun 17 2009 - 10:32:43 PDT)
- FyD (Wed Jun 17 2009 - 08:40:06 PDT)
- Shubhra Gupta (Wed Jun 17 2009 - 03:33:50 PDT)
- Sergey Samsonov (Wed Jun 17 2009 - 02:09:23 PDT)
- Karl Kirschner (Wed Jun 17 2009 - 01:33:55 PDT)
- Sergey Samsonov (Wed Jun 17 2009 - 01:18:33 PDT)
- Sergey Samsonov (Wed Jun 17 2009 - 01:10:33 PDT)
- Bill Ross (Wed Jun 17 2009 - 01:01:28 PDT)
- Sergey Samsonov (Wed Jun 17 2009 - 00:50:46 PDT)
- FyD (Wed Jun 17 2009 - 00:30:26 PDT)
- Sergey Samsonov (Tue Jun 16 2009 - 23:38:56 PDT)
[AMBER] glycopeptide Parametrization
- FyD (Sat Jun 13 2009 - 00:40:00 PDT)
- Ross Walker (Fri Jun 12 2009 - 09:09:37 PDT)
- Karl Kirschner (Fri Jun 12 2009 - 08:06:17 PDT)
- guardiani.fi.infn.it (Fri Jun 12 2009 - 07:06:24 PDT)
- FyD (Fri Jun 12 2009 - 00:05:51 PDT)
- Ahammadunny Pathiaseril (Wed Jun 10 2009 - 13:25:21 PDT)
- guardiani.fi.infn.it (Wed Jun 10 2009 - 08:41:14 PDT)
[AMBER] guessing the charge of a small molecule
- Alan (Tue Jun 23 2009 - 01:06:51 PDT)
[AMBER] Half charge reported during NN ?
- Marek Maly (Wed Jun 24 2009 - 10:43:26 PDT)
- case (Wed Jun 24 2009 - 10:31:45 PDT)
- Marek Maly (Wed Jun 24 2009 - 09:33:54 PDT)
[AMBER] Hard limit in Amber10?
- Ross Walker (Wed Jun 24 2009 - 09:02:17 PDT)
- Yang, Ping (Mon Jun 22 2009 - 18:52:39 PDT)
- Yang, Ping (Sat Jun 20 2009 - 16:44:11 PDT)
- Ross Walker (Sat Jun 20 2009 - 10:40:46 PDT)
- Yang, Ping (Fri Jun 19 2009 - 17:21:14 PDT)
[AMBER] hbond_DNAtraj
- Jianyin Shao (Wed Jun 03 2009 - 09:52:41 PDT)
[AMBER] help
- Ross Walker (Fri Jun 12 2009 - 09:02:06 PDT)
- KIRTANA S (Fri Jun 12 2009 - 06:42:04 PDT)
[AMBER] help with parameters for ions
- rebeca (Tue Jun 02 2009 - 11:33:41 PDT)
- InSuk Joung (Tue Jun 02 2009 - 11:14:46 PDT)
- rebeca (Tue Jun 02 2009 - 10:38:00 PDT)
- InSuk Joung (Tue Jun 02 2009 - 08:28:55 PDT)
- rebeca (Tue Jun 02 2009 - 08:10:17 PDT)
- David A. Case (Tue Jun 02 2009 - 06:46:40 PDT)
- rebeca (Tue Jun 02 2009 - 05:46:14 PDT)
[AMBER] Histidine, which form?
- M. L. Dodson (Mon Jun 15 2009 - 09:45:25 PDT)
- Ross Walker (Mon Jun 15 2009 - 09:39:04 PDT)
- s. Bill (Mon Jun 15 2009 - 09:28:27 PDT)
- Ross Walker (Mon Jun 15 2009 - 08:06:49 PDT)
- Carlos Simmerling (Mon Jun 15 2009 - 07:57:40 PDT)
- s_bill36.yahoo.co.uk (Mon Jun 15 2009 - 07:54:05 PDT)
[AMBER] how to add ions
- bharat lakhani (Tue Jun 02 2009 - 00:25:46 PDT)
[AMBER] how to add water for membrane, in Z direction only or xyz
- xueqin pang (Thu Jun 04 2009 - 01:13:07 PDT)
[AMBER] How to build amide bond etween two protein chains
- FyD (Tue Jun 23 2009 - 23:18:25 PDT)
- journal.update (Tue Jun 23 2009 - 21:36:07 PDT)
[AMBER] How to calculate SASA in vmd
- Mannan (Tue Jun 16 2009 - 23:40:05 PDT)
[AMBER] How to calculate the distance of CA of all residues in the trajectory
- Thomas Leonard (Sun Jun 07 2009 - 18:45:54 PDT)
[AMBER] how to choose different comformations for RESP
- cgji (Mon Jun 01 2009 - 22:14:02 PDT)
- xueqin pang (Mon Jun 01 2009 - 17:32:51 PDT)
[AMBER] how to creat an mixture sovlent of hexane and water
- TaoPaul (Sun Jun 28 2009 - 08:58:19 PDT)
[AMBER] how to create prmtop and inpcrd files for covalent neutral phenylalanine
- Madhurima Jana (Thu Jun 18 2009 - 05:39:03 PDT)
[AMBER] how to know that adequate equilibration from rmsd curve of equilibration
- Cihan Aydin (Sun Jun 28 2009 - 09:19:07 PDT)
- Naser Alijabbari (Sat Jun 27 2009 - 11:19:23 PDT)
- Cihan Aydin (Sat Jun 27 2009 - 07:29:21 PDT)
[AMBER] IGB=7 vs IGB=5
- guardiani.fi.infn.it (Thu Jun 25 2009 - 04:20:15 PDT)
[AMBER] Improper dihedrals between residues?
- Bill Ross (Tue Jun 09 2009 - 14:17:03 PDT)
- Ben Roberts (Tue Jun 09 2009 - 12:12:07 PDT)
- Bill Ross (Tue Jun 09 2009 - 12:04:02 PDT)
- Carlos Simmerling (Tue Jun 09 2009 - 10:51:40 PDT)
- David A. Case (Tue Jun 09 2009 - 10:14:57 PDT)
- Carlos Simmerling (Tue Jun 09 2009 - 09:28:04 PDT)
- Ben Roberts (Tue Jun 09 2009 - 09:11:15 PDT)
[AMBER] Improper dihedrals from .off and .lib files
- David A. Case (Thu Jun 18 2009 - 04:28:40 PDT)
- Johan Sund (Thu Jun 18 2009 - 03:15:37 PDT)
[AMBER] improper torsion problem
- Bill Ross (Wed Jun 17 2009 - 00:47:12 PDT)
- Youn Kyeung Lee (Tue Jun 16 2009 - 19:36:14 PDT)
[AMBER] input coordinates for vdW transition step in Amber 10 TI
- steinbrt.rci.rutgers.edu (Thu Jun 11 2009 - 03:42:51 PDT)
- Ye MEI (Thu Jun 11 2009 - 01:22:34 PDT)
- Tom Joseph (Wed Jun 10 2009 - 18:02:51 PDT)
- Jodi Hadden (Wed Jun 10 2009 - 13:27:16 PDT)
[AMBER] installation of RESP programm
- FyD (Fri Jun 26 2009 - 02:15:39 PDT)
- subarna thakur (Fri Jun 26 2009 - 01:52:57 PDT)
[AMBER] Is the result of sander same as that of pmemd?
- Ross Walker (Sat Jun 13 2009 - 09:12:51 PDT)
- Catein Catherine (Fri Jun 12 2009 - 19:55:10 PDT)
- Robert Duke (Fri Jun 12 2009 - 07:09:45 PDT)
- Catein Catherine (Fri Jun 12 2009 - 07:04:38 PDT)
[AMBER] J coupling constant calculation
- Gustavo Seabra (Tue Jun 02 2009 - 07:18:08 PDT)
[AMBER] ligand QM/semi-empirical coords optmisation
- Francesco Pietra (Fri Jun 05 2009 - 11:17:45 PDT)
- Junmei Wang (Fri Jun 05 2009 - 08:01:32 PDT)
- Alan (Thu Jun 04 2009 - 11:05:27 PDT)
- David A. Case (Thu Jun 04 2009 - 08:06:28 PDT)
- Alan (Thu Jun 04 2009 - 07:19:28 PDT)
[AMBER] Lost mail
- Robert Duke (Mon Jun 08 2009 - 04:58:02 PDT)
[AMBER] makeDIST_RST: no map function for ambiguous restraint
- Peter Varnai (Mon Jun 01 2009 - 12:49:36 PDT)
[AMBER] making leap to recognize 5' phosphate
- FyD (Tue Jun 23 2009 - 23:02:42 PDT)
- FyD (Tue Jun 23 2009 - 02:48:34 PDT)
- Bala subramanian (Tue Jun 23 2009 - 01:49:05 PDT)
- FyD (Tue Jun 23 2009 - 00:45:31 PDT)
- Bala subramanian (Mon Jun 22 2009 - 06:45:43 PDT)
[AMBER] max atoms for antechamber
- Alan (Mon Jun 22 2009 - 06:00:48 PDT)
- case (Mon Jun 22 2009 - 05:48:43 PDT)
- Alan (Mon Jun 22 2009 - 05:37:39 PDT)
[AMBER] Max filename length in Sander?
- Robert Duke (Tue Jun 09 2009 - 08:01:39 PDT)
- Paul Mortenson (Tue Jun 09 2009 - 07:47:57 PDT)
- Robert Duke (Mon Jun 08 2009 - 10:30:47 PDT)
- David A. Case (Mon Jun 08 2009 - 05:36:32 PDT)
- David A. Case (Mon Jun 08 2009 - 05:28:41 PDT)
- Paul Mortenson (Mon Jun 08 2009 - 03:59:52 PDT)
[AMBER] MaxRad ?
- Marek Maly (Sat Jun 06 2009 - 13:56:44 PDT)
[AMBER] methyl group at the N-terminal
- FyD (Fri Jun 19 2009 - 05:12:36 PDT)
- Francesca Poletti (Fri Jun 19 2009 - 05:03:56 PDT)
[AMBER] minimization to reduce covalent deviation
- David A. Case (Tue Jun 02 2009 - 06:38:58 PDT)
- Peter Varnai (Mon Jun 01 2009 - 13:25:07 PDT)
[AMBER] MM decomp energy - zero values for Eele, Evdw
- Thomas Lake (Tue Jun 16 2009 - 08:36:50 PDT)
[AMBER] MM PBSA ( Vertex atom mismatch in Amber)
- Vikas Sharma (Tue Jun 09 2009 - 20:28:22 PDT)
[AMBER] MM PBSA ERROR
- Vikas Sharma (Fri Jun 12 2009 - 07:04:25 PDT)
[AMBER] MM-PBSA nmode statistics
- Ray Luo (Mon Jun 01 2009 - 12:05:48 PDT)
- Dmitry Osolodkin (Mon Jun 01 2009 - 06:12:15 PDT)
[AMBER] mm_pbsa_statistics-CALC DELTA parameter ?
- Marek Maly (Mon Jun 08 2009 - 12:16:19 PDT)
[AMBER] MMPBSA and mm_pbsa_statistics.pl error
- Ray Luo (Tue Jun 02 2009 - 21:49:34 PDT)
- john smith (Mon Jun 01 2009 - 22:38:54 PDT)
[AMBER] mol2 file to amber pdb file format
- David A. Case (Thu Jun 04 2009 - 09:55:39 PDT)
- balaji nagarajan (Thu Jun 04 2009 - 09:32:06 PDT)
[AMBER] NAB memory
- case (Fri Jun 26 2009 - 11:42:03 PDT)
- E.M. (Fri Jun 26 2009 - 11:06:41 PDT)
[AMBER] NAB memory increase
- Bill Ross (Thu Jun 25 2009 - 09:34:58 PDT)
- case (Thu Jun 25 2009 - 04:33:03 PDT)
- E.M. (Wed Jun 24 2009 - 13:12:09 PDT)
[AMBER] Need help with nab code to access the m_prm struct in a molecule
- M. L. Dodson (Mon Jun 15 2009 - 12:49:02 PDT)
[AMBER] net charge
- case (Tue Jun 23 2009 - 07:34:07 PDT)
- Vishal Maingi (Tue Jun 23 2009 - 07:19:51 PDT)
[AMBER] no output when running Antechamber(espgen)
- xueqin pang (Wed Jun 03 2009 - 23:02:32 PDT)
[AMBER] NO output when running espgen?
- xueqin pang (Wed Jun 03 2009 - 06:13:06 PDT)
[AMBER] NOE
- David A. Case (Thu Jun 11 2009 - 10:29:06 PDT)
- Beale, John (Thu Jun 11 2009 - 05:30:36 PDT)
[AMBER] Nonstandard molecules simulated with parm99EP ?
- case (Tue Jun 30 2009 - 09:19:00 PDT)
- FyD (Tue Jun 30 2009 - 00:31:53 PDT)
- Marek Maly (Mon Jun 29 2009 - 13:48:52 PDT)
- FyD (Mon Jun 29 2009 - 11:28:19 PDT)
- Marek Maly (Mon Jun 29 2009 - 10:06:27 PDT)
[AMBER] only ff94 and ff99 for GBSA?
- David A. Case (Wed Jun 03 2009 - 05:24:56 PDT)
- Andrew Voronkov (Wed Jun 03 2009 - 04:52:13 PDT)
- Carlos Simmerling (Wed Jun 03 2009 - 03:51:09 PDT)
- Andrew Voronkov (Wed Jun 03 2009 - 03:28:15 PDT)
[AMBER] parallel error
- Tom Joseph (Mon Jun 15 2009 - 04:54:19 PDT)
- 廖青华 (Mon Jun 15 2009 - 00:31:27 PDT)
[AMBER] parameter for dihedral angle
- Catein Catherine (Sun Jun 07 2009 - 20:08:17 PDT)
- David A. Case (Sat Jun 06 2009 - 05:47:35 PDT)
- raja pandian (Fri Jun 05 2009 - 22:13:52 PDT)
- David A. Case (Fri Jun 05 2009 - 12:50:03 PDT)
- Jorgen Simonsen (Fri Jun 05 2009 - 08:16:56 PDT)
[AMBER] parameters Fe4S4 cluster
- KIRTANA S (Sun Jun 21 2009 - 19:30:08 PDT)
[AMBER] PARMSCAN
- alegil.fq.uh.cu (Tue Jun 02 2009 - 15:41:54 PDT)
- alegil.fq.uh.cu (Tue Jun 02 2009 - 15:26:42 PDT)
[AMBER] partial charges from AM1-BCC and RESP differ a lot
- FyD (Tue Jun 16 2009 - 23:32:11 PDT)
- xueqin pang (Tue Jun 16 2009 - 00:57:25 PDT)
- FyD (Thu Jun 11 2009 - 11:59:27 PDT)
- xueqin pang (Wed Jun 10 2009 - 05:39:31 PDT)
[AMBER] Partial charges of heme
- Justine Shaw Condo (Tue Jun 30 2009 - 11:28:11 PDT)
[AMBER] PCA for CA of specific resiudes
- case (Thu Jun 25 2009 - 05:27:01 PDT)
- Patrick Gedeon (Thu Jun 25 2009 - 04:43:20 PDT)
[AMBER] PDMED
- Ross Walker (Mon Jun 08 2009 - 23:35:25 PDT)
- Catein Catherine (Mon Jun 08 2009 - 23:18:59 PDT)
- Ross Walker (Mon Jun 08 2009 - 22:19:36 PDT)
- Catein Catherine (Mon Jun 08 2009 - 21:28:58 PDT)
[AMBER] Pentavalent Phosphorous and Antechamber
- FyD (Wed Jun 03 2009 - 23:29:59 PDT)
- Shubhra Gupta (Wed Jun 03 2009 - 21:37:08 PDT)
- David A. Case (Wed Jun 03 2009 - 09:35:26 PDT)
- Peterson, Matthew W. (Wed Jun 03 2009 - 07:12:44 PDT)
[AMBER] pKa data base....
- s. Bill (Mon Jun 15 2009 - 09:01:14 PDT)
[AMBER] PLEASE HELP - PDB Modification
- Tom Joseph (Sun Jun 14 2009 - 16:36:16 PDT)
- s_bill36.yahoo.co.uk (Sun Jun 14 2009 - 10:29:31 PDT)
[AMBER] PMEMD compilation
- Ross Walker (Sat Jun 20 2009 - 21:32:18 PDT)
- manoj singh (Sat Jun 20 2009 - 21:30:17 PDT)
- manoj singh (Sat Jun 20 2009 - 21:22:01 PDT)
- Ross Walker (Sat Jun 20 2009 - 21:15:23 PDT)
- manoj singh (Sat Jun 20 2009 - 21:05:44 PDT)
- Ross Walker (Sat Jun 20 2009 - 10:36:14 PDT)
- manoj singh (Fri Jun 19 2009 - 15:49:31 PDT)
[AMBER] POL3
- Hemant Kumar (Sun Jun 07 2009 - 11:27:29 PDT)
[AMBER] POL3 & SHAKE
- David A. Case (Wed Jun 10 2009 - 12:11:40 PDT)
- Hemant Gangwar (Tue Jun 09 2009 - 13:53:27 PDT)
[AMBER] Postdoc position in biomolecular simulation
- Ivaylo, Ivanov (Thu Jun 18 2009 - 16:26:05 PDT)
[AMBER] preparation of two solutes of organic molecules in a simulation box
- Workalemhu Berhanu (Tue Jun 02 2009 - 16:09:04 PDT)
[AMBER] PRINCIPAL QUESTION
- Marek Maly (Thu Jun 11 2009 - 08:41:42 PDT)
[AMBER] problem in pressure equillibration
- David A. Case (Tue Jun 16 2009 - 04:56:34 PDT)
- wong105.llnl.gov (Mon Jun 15 2009 - 23:18:22 PDT)
[AMBER] problem with creation of prmtop and prmcrd files
- Tom Joseph (Wed Jun 10 2009 - 18:30:19 PDT)
- moitrayee.mbu.iisc.ernet.in (Mon Jun 08 2009 - 06:00:18 PDT)
[AMBER] Problem with modified trna[Fwd: problem with creation of prmtop and prmcrd files]
- moitrayee.mbu.iisc.ernet.in (Mon Jun 08 2009 - 07:28:14 PDT)
[AMBER] Problem with modified trna[Fwd: problem with creation of prmtop and prmcrd files]]
- moitrayee.mbu.iisc.ernet.in (Mon Jun 08 2009 - 07:30:21 PDT)
[AMBER] problem with parametrization
- janzso.brc.hu (Mon Jun 29 2009 - 02:30:50 PDT)
- FyD (Thu Jun 25 2009 - 06:47:31 PDT)
- janzso.brc.hu (Thu Jun 25 2009 - 05:04:27 PDT)
- FyD (Thu Jun 25 2009 - 04:52:45 PDT)
- janzso.brc.hu (Thu Jun 25 2009 - 04:40:35 PDT)
- FyD (Thu Jun 25 2009 - 03:04:27 PDT)
- janzso.brc.hu (Thu Jun 25 2009 - 02:49:50 PDT)
- FyD (Wed Jun 24 2009 - 22:15:23 PDT)
- Brothers, Michael Charles (Wed Jun 24 2009 - 11:34:16 PDT)
- janzso.brc.hu (Wed Jun 24 2009 - 11:24:45 PDT)
[AMBER] Problem with radial distribution function
- aneesh cna (Fri Jun 26 2009 - 01:56:09 PDT)
[AMBER] Problems using nmode in NAB
- Andreas Svrcek-Seiler (Thu Jun 25 2009 - 06:03:15 PDT)
- E.M. (Wed Jun 24 2009 - 21:15:38 PDT)
- E.M. (Wed Jun 24 2009 - 02:09:44 PDT)
- Andreas Svrcek-Seiler (Wed Jun 24 2009 - 01:52:30 PDT)
- E.M. (Tue Jun 23 2009 - 23:05:50 PDT)
[AMBER] problems with EP of TIP4PEW
- rebeca (Wed Jun 03 2009 - 11:40:12 PDT)
- David A. Case (Wed Jun 03 2009 - 09:29:43 PDT)
- rebeca (Wed Jun 03 2009 - 08:43:58 PDT)
[AMBER] problems with ptraj option IMAGE
- Antonija Tomić (Mon Jun 29 2009 - 08:27:54 PDT)
- Carlos Simmerling (Mon Jun 29 2009 - 08:00:59 PDT)
- Antonija Tomić (Mon Jun 29 2009 - 07:48:54 PDT)
[AMBER] Proper ISTRNG value ?
- Marek Maly (Fri Jun 05 2009 - 09:24:58 PDT)
[AMBER] ptraj "image" "center" commands
- Ross Walker (Thu Jun 11 2009 - 08:30:08 PDT)
- Catein Catherine (Thu Jun 11 2009 - 02:13:38 PDT)
[AMBER] ptraj amber 10 file.
- Catein Catherine (Wed Jun 10 2009 - 09:02:32 PDT)
[AMBER] ptraj clustering with sieve- unexpected Bus Error
- Rachel Rice (Tue Jun 30 2009 - 08:06:03 PDT)
- David Watson (Fri Jun 26 2009 - 04:31:26 PDT)
- Rachel Rice (Thu Jun 25 2009 - 20:24:18 PDT)
- David Watson (Thu Jun 25 2009 - 19:51:11 PDT)
- Rachel Rice (Thu Jun 25 2009 - 19:36:06 PDT)
- David Watson (Thu Jun 25 2009 - 19:28:22 PDT)
- Rachel Rice (Thu Jun 25 2009 - 17:54:31 PDT)
- David Watson (Thu Jun 25 2009 - 11:53:16 PDT)
- Rachel Rice (Thu Jun 25 2009 - 08:24:25 PDT)
[AMBER] ptraj correlation
- Catein Catherine (Thu Jun 18 2009 - 06:47:01 PDT)
[AMBER] ptraj image in non-orthorhombic cell
- Joanna Panecka (Wed Jun 03 2009 - 13:19:52 PDT)
[AMBER] ptraj quasiharmonic analysis
- Hannes Loeffler (Tue Jun 09 2009 - 00:19:23 PDT)
- Neha Gandhi (Mon Jun 08 2009 - 23:38:01 PDT)
[AMBER] PTRAJ, rms for separated residues.
- Germain Vallverdu (Mon Jun 22 2009 - 02:27:43 PDT)
- Catein Catherine (Mon Jun 22 2009 - 02:20:36 PDT)
[AMBER] ptraj_hbond_problem
- Thomas Cheatham (Thu Jun 04 2009 - 22:28:11 PDT)
- balaji nagarajan (Thu Jun 04 2009 - 15:08:24 PDT)
[AMBER] QQD psuedoatom restraints
- David A. Case (Mon Jun 15 2009 - 05:00:23 PDT)
- Titus, Jamie (bairdje) (Fri Jun 12 2009 - 11:51:25 PDT)
- Titus, Jamie (bairdje) (Mon Jun 01 2009 - 04:21:19 PDT)
[AMBER] query about the charge fitting procedure about C- and N-terminal residues
- FyD (Fri Jun 26 2009 - 02:41:52 PDT)
- Ye MEI (Fri Jun 26 2009 - 02:19:47 PDT)
[AMBER] question
- Ross Walker (Wed Jun 10 2009 - 20:19:01 PDT)
- lev kantorovich (Wed Jun 10 2009 - 07:20:08 PDT)
[AMBER] Question of about MM-PBSA and mm_pbsa_createinput.pm script
- David A. Case (Tue Jun 09 2009 - 06:20:22 PDT)
- Samuel Genheden (Tue Jun 09 2009 - 05:43:19 PDT)
[AMBER] radial distribution without normalization
- Thomas Cheatham (Wed Jun 10 2009 - 15:11:40 PDT)
- CHAMI F. (Wed Jun 10 2009 - 08:48:12 PDT)
[AMBER] reclaiming space from amber10 installation
- Ross Walker (Mon Jun 22 2009 - 18:26:36 PDT)
- Alan (Sun Jun 21 2009 - 15:04:53 PDT)
[AMBER] RED Geometry Calculation Error
- FyD (Fri Jun 19 2009 - 23:41:46 PDT)
- Brothers, Michael Charles (Fri Jun 19 2009 - 14:10:12 PDT)
- FyD (Fri Jun 19 2009 - 12:19:00 PDT)
- Brothers, Michael Charles (Fri Jun 19 2009 - 11:52:37 PDT)
[AMBER] Reference Correction
- Mahmoud A. A. Ibrahim (Sun Jun 21 2009 - 13:11:34 PDT)
[AMBER] Regd: parameter Fe4S4
- FyD (Mon Jun 29 2009 - 12:03:22 PDT)
- KIRTANA S (Mon Jun 29 2009 - 09:11:49 PDT)
[AMBER] REMD
- Carlos Simmerling (Tue Jun 23 2009 - 03:07:39 PDT)
- Shaikh Abdul R S Ramaju (Mon Jun 22 2009 - 22:32:34 PDT)
[AMBER] rescaling velocities
- abi ghanem (Thu Jun 04 2009 - 09:39:02 PDT)
- Carlos Simmerling (Thu Jun 04 2009 - 09:43:20 PDT)
[AMBER] residue
- KIRTANA S (Thu Jun 18 2009 - 12:59:50 PDT)
[AMBER] Residues
- Roman Osman (Thu Jun 18 2009 - 14:58:53 PDT)
- Bill Ross (Thu Jun 18 2009 - 14:13:53 PDT)
- FyD (Thu Jun 18 2009 - 13:24:16 PDT)
- KIRTANA S (Thu Jun 18 2009 - 12:57:11 PDT)
- FyD (Sun Jun 14 2009 - 23:51:56 PDT)
- FyD (Sun Jun 14 2009 - 00:02:02 PDT)
- KIRTANA S (Sat Jun 13 2009 - 17:14:31 PDT)
- Bill Ross (Fri Jun 12 2009 - 12:49:09 PDT)
- KIRTANA S (Fri Jun 12 2009 - 12:41:02 PDT)
- FyD (Fri Jun 12 2009 - 08:36:10 PDT)
- KIRTANA S (Fri Jun 12 2009 - 08:07:50 PDT)
- FyD (Fri Jun 12 2009 - 07:24:35 PDT)
- KIRTANA S (Fri Jun 12 2009 - 07:10:39 PDT)
[AMBER] RESP
- case (Mon Jun 29 2009 - 04:52:19 PDT)
- Syed Tarique Moin (Mon Jun 29 2009 - 00:42:51 PDT)
[AMBER] RNA and polarizable force field
- Abhishek Singh (Wed Jun 10 2009 - 08:30:29 PDT)
[AMBER] Saccharides chains termini
- FyD (Tue Jun 30 2009 - 08:47:04 PDT)
- Karl Kirschner (Tue Jun 30 2009 - 07:57:46 PDT)
- Lachele Foley (Lists) (Tue Jun 30 2009 - 07:46:09 PDT)
- Sergey Samsonov (Tue Jun 30 2009 - 07:32:53 PDT)
[AMBER] SANDER BOMB in subroutine nonbond_list
- Bill Ross (Tue Jun 23 2009 - 09:54:30 PDT)
- Siddharth Rastogi (Tue Jun 23 2009 - 09:39:58 PDT)
[AMBER] sander error
- Robert Duke (Mon Jun 08 2009 - 20:27:52 PDT)
- Ross Walker (Mon Jun 08 2009 - 18:41:06 PDT)
- Beale, John (Mon Jun 08 2009 - 07:43:24 PDT)
[AMBER] Sander imin=5 option
- Paul Mortenson (Tue Jun 16 2009 - 08:09:54 PDT)
- Carlos Simmerling (Tue Jun 16 2009 - 07:50:43 PDT)
- Paul Mortenson (Tue Jun 16 2009 - 07:46:37 PDT)
[AMBER] Seg-fault when creating residue
- Bill Ross (Wed Jun 17 2009 - 00:51:02 PDT)
- Valla Fatemi (Tue Jun 16 2009 - 18:28:43 PDT)
[AMBER] setBox truncated octahedron
- Myunggi Yi (Thu Jun 11 2009 - 10:27:26 PDT)
[AMBER] setting atomic radii for GB version 7
- case (Thu Jun 25 2009 - 05:20:36 PDT)
- Workalemhu Berhanu (Wed Jun 24 2009 - 20:12:55 PDT)
[AMBER] Simulations including RNA-protein complexes...
- Cihan Aydin (Sun Jun 28 2009 - 15:29:10 PDT)
[AMBER] sleap and delete
- FyD (Mon Jun 01 2009 - 00:35:32 PDT)
[AMBER] SOS - too high binding energy
- Marek Maly (Wed Jun 10 2009 - 12:47:58 PDT)
- Marek Maly (Tue Jun 09 2009 - 03:49:43 PDT)
[AMBER] spc.itp for the Amber force field
- Alan (Wed Jun 03 2009 - 08:38:56 PDT)
- rebeca (Wed Jun 03 2009 - 07:46:46 PDT)
[AMBER] Specifying improper dihedrals
- Bill Ross (Wed Jun 17 2009 - 12:25:55 PDT)
- Ben Roberts (Wed Jun 17 2009 - 12:18:41 PDT)
- Ben Roberts (Wed Jun 17 2009 - 12:17:12 PDT)
- David A. Case (Wed Jun 17 2009 - 10:56:20 PDT)
- Bill Ross (Wed Jun 17 2009 - 10:56:26 PDT)
- Mark Williamson (Wed Jun 17 2009 - 10:12:08 PDT)
- Ben Roberts (Wed Jun 17 2009 - 08:24:14 PDT)
[AMBER] Steps for NMR structure minimization
- Prem Prakash Pathak (Mon Jun 29 2009 - 07:09:34 PDT)
[AMBER] steps for NMR structure minimization of protein
- Prem Prakash Pathak (Mon Jun 29 2009 - 07:13:33 PDT)
- Prem Prakash Pathak (Mon Jun 29 2009 - 07:12:40 PDT)
[AMBER] Strange contacts with water molecules
- Jordan MONNET (Wed Jun 17 2009 - 10:00:46 PDT)
- Jordan MONNET (Tue Jun 09 2009 - 09:01:53 PDT)
- Ross Walker (Mon Jun 08 2009 - 20:16:41 PDT)
- Jordan MONNET (Mon Jun 08 2009 - 14:39:26 PDT)
[AMBER] Sulfates parameterization for GAGs in GLYCAM_06
- Sergey Samsonov (Thu Jun 18 2009 - 06:07:17 PDT)
[AMBER] Targeted MD and QM/MM
- Gabriel Urquiza (Tue Jun 02 2009 - 15:08:11 PDT)
- Gustavo Seabra (Tue Jun 02 2009 - 07:43:35 PDT)
[AMBER] Thanks Simon and Vlad!
- Rilei Yu (Thu Jun 25 2009 - 16:32:35 PDT)
[AMBER] Thermodynamic parameters in mm_PBSA - NAB ?
- Marek Maly (Wed Jun 10 2009 - 12:47:41 PDT)
- David A. Case (Wed Jun 10 2009 - 09:01:26 PDT)
- Marek Maly (Wed Jun 10 2009 - 03:33:59 PDT)
[AMBER] to check basepair in ptraj
- balaji nagarajan (Mon Jun 15 2009 - 07:23:28 PDT)
[AMBER] to unsubscribe email
- backy (Wed Jun 17 2009 - 01:22:19 PDT)
- Ross Walker (Wed Jun 17 2009 - 01:09:39 PDT)
- backy (Wed Jun 17 2009 - 00:13:02 PDT)
- Ross Walker (Mon Jun 15 2009 - 09:59:06 PDT)
- Urszula Uciechowska (Mon Jun 15 2009 - 05:59:46 PDT)
[AMBER] too high in binding energy (MM-PBSA)
- Maryam Hamzehee (Sat Jun 13 2009 - 02:53:43 PDT)
[AMBER] total charge for NPRO in ff03ua
- Edyta Malolepsza (Tue Jun 16 2009 - 02:42:55 PDT)
- Jun Wang (Mon Jun 15 2009 - 16:35:39 PDT)
- Edyta Malolepsza (Mon Jun 15 2009 - 03:09:35 PDT)
[AMBER] Trying to patch amber 9
- Jack Shultz (Wed Jun 24 2009 - 08:25:41 PDT)
- Jack Shultz (Wed Jun 24 2009 - 08:18:23 PDT)
- case (Wed Jun 24 2009 - 07:58:48 PDT)
- Jack Shultz (Wed Jun 24 2009 - 06:24:40 PDT)
[AMBER] unit of charge in prep files
- moitrayee.mbu.iisc.ernet.in (Tue Jun 09 2009 - 18:18:58 PDT)
- David A. Case (Tue Jun 09 2009 - 06:07:08 PDT)
- moitrayee.mbu.iisc.ernet.in (Tue Jun 09 2009 - 04:35:51 PDT)
[AMBER] unit of force constant
- aneesh cna (Tue Jun 09 2009 - 22:06:50 PDT)
[AMBER] Unknown residue: MOL number: 30 type: Terminal/last
- David A. Case (Tue Jun 09 2009 - 04:51:42 PDT)
- Workalemhu Berhanu (Mon Jun 08 2009 - 11:30:43 PDT)
[AMBER] use of random seed in multiple runs
- Marek Maly (Fri Jun 05 2009 - 12:40:13 PDT)
- Gustavo Seabra (Fri Jun 05 2009 - 12:18:35 PDT)
- Robert Duke (Fri Jun 05 2009 - 08:45:09 PDT)
- Naser Alijabbari (Fri Jun 05 2009 - 08:30:55 PDT)
- Gustavo Seabra (Fri Jun 05 2009 - 08:16:00 PDT)
- Robert Duke (Fri Jun 05 2009 - 07:45:32 PDT)
- Robert Duke (Fri Jun 05 2009 - 07:37:14 PDT)
- Marek Maly (Fri Jun 05 2009 - 06:49:14 PDT)
- Gustavo Seabra (Fri Jun 05 2009 - 06:37:42 PDT)
- Gustavo Seabra (Fri Jun 05 2009 - 06:28:03 PDT)
- Marek Maly (Thu Jun 04 2009 - 13:01:54 PDT)
- Carlos Simmerling (Thu Jun 04 2009 - 12:20:59 PDT)
- Marek Maly (Thu Jun 04 2009 - 12:16:50 PDT)
- Robert Duke (Thu Jun 04 2009 - 10:02:58 PDT)
- Marek Maly (Thu Jun 04 2009 - 09:35:57 PDT)
- Jifeng Wang (Thu Jun 04 2009 - 07:43:25 PDT)
- Robert Duke (Thu Jun 04 2009 - 07:31:32 PDT)
- Jifeng Wang (Thu Jun 04 2009 - 07:10:50 PDT)
- Robert Duke (Wed Jun 03 2009 - 20:59:48 PDT)
- Gustavo Seabra (Wed Jun 03 2009 - 19:00:51 PDT)
- Andrew Voronkov (Wed Jun 03 2009 - 12:26:48 PDT)
- Andrew Voronkov (Wed Jun 03 2009 - 10:00:32 PDT)
- Gustavo Seabra (Wed Jun 03 2009 - 06:55:24 PDT)
- Carlos Simmerling (Wed Jun 03 2009 - 03:13:23 PDT)
- Andrew Voronkov (Wed Jun 03 2009 - 02:28:52 PDT)
[AMBER] Velocity rescaling and ig...
- Cihan Aydin (Sun Jun 28 2009 - 09:22:29 PDT)
- Ross Walker (Sun Jun 28 2009 - 09:18:08 PDT)
- Cihan Aydin (Sun Jun 28 2009 - 09:08:32 PDT)
- Carlos Simmerling (Sun Jun 28 2009 - 08:35:37 PDT)
- Cihan Aydin (Sun Jun 28 2009 - 07:52:30 PDT)
[AMBER] Vertex atom mismatch in Amber
- Vikas Sharma (Wed Jun 10 2009 - 20:29:57 PDT)
- Vikas Sharma (Tue Jun 09 2009 - 06:41:33 PDT)
[AMBER] vlimit in TI with soft core potential
- Ye MEI (Wed Jun 17 2009 - 02:13:40 PDT)
- steinbrt.rci.rutgers.edu (Wed Jun 17 2009 - 01:47:38 PDT)
- Ye MEI (Wed Jun 17 2009 - 01:20:31 PDT)
[AMBER] vs_vikassharma.yahoo.co.in has sent you a private message
- Vikas S (Sun Jun 07 2009 - 12:28:03 PDT)
[AMBER] Warning: No sp2 improper torsion term for
- Alan (Mon Jun 08 2009 - 07:54:50 PDT)
- Ross Walker (Fri Jun 05 2009 - 07:13:53 PDT)
- Alan (Fri Jun 05 2009 - 05:26:55 PDT)
[AMBER] What is the parallel efficiency of amber10
- Gustavo Seabra (Mon Jun 08 2009 - 06:44:26 PDT)
- David A. Case (Mon Jun 08 2009 - 05:23:11 PDT)
- Tom Joseph (Sun Jun 07 2009 - 23:07:29 PDT)
- Catein Catherine (Sun Jun 07 2009 - 20:19:37 PDT)
[AMBER] where to I get the parameters for Mg divalent ion
- Tom Joseph (Thu Jun 18 2009 - 20:53:01 PDT)
- Mannan (Wed Jun 17 2009 - 21:11:19 PDT)
[AMBER] Your private message from Vikas is about to expire
- Vikas S (Sat Jun 20 2009 - 23:41:57 PDT)
[AMBER] zinc coordination of benzimidazole
- Urszula Uciechowska (Thu Jun 11 2009 - 01:49:45 PDT)
- Aust, Susanne (Thu Jun 11 2009 - 00:09:59 PDT)
[Contact q4md] qurey reagarding RED Server
- FyD (Sat Jun 13 2009 - 01:08:26 PDT)
addions
- Shubhra Gupta (Thu Jun 04 2009 - 21:38:20 PDT)
- Peter Gannett (Wed Jun 03 2009 - 07:17:57 PDT)
- nicholus bhattacharjee (Wed Jun 03 2009 - 06:44:51 PDT)
- Shubhra Gupta (Wed Jun 03 2009 - 04:12:32 PDT)
AW: [AMBER] 2 restraints with different force constants
- Aust, Susanne (Fri Jun 19 2009 - 05:39:34 PDT)
- Aust, Susanne (Fri Jun 19 2009 - 04:51:21 PDT)
AW: [AMBER] atomtypes in gaff
- FyD (Thu Jun 25 2009 - 23:56:35 PDT)
- Bill Ross (Thu Jun 25 2009 - 09:42:01 PDT)
- Aust, Susanne (Thu Jun 25 2009 - 05:05:10 PDT)
- FyD (Thu Jun 25 2009 - 03:32:33 PDT)
- Aust, Susanne (Thu Jun 25 2009 - 02:24:07 PDT)
AW: [AMBER] zinc coordination of benzimidazole
- Aust, Susanne (Thu Jun 11 2009 - 23:13:19 PDT)
AW: AW: [AMBER] atomtypes in gaff
- FyD (Thu Jun 25 2009 - 04:36:20 PDT)
- Aust, Susanne (Thu Jun 25 2009 - 04:27:19 PDT)
AW: AW: AW: [AMBER] atomtypes in gaff
- Aust, Susanne (Thu Jun 25 2009 - 04:44:58 PDT)
connect
- Ross Walker (Mon Jun 15 2009 - 18:43:46 PDT)
- Bill Ross (Mon Jun 15 2009 - 13:39:32 PDT)
- KIRTANA S (Mon Jun 15 2009 - 13:18:54 PDT)
Error on equilibriation of Amber10
- case (Fri Jun 26 2009 - 05:17:42 PDT)
- Masakazu SEKIJIMA (Thu Jun 25 2009 - 10:41:39 PDT)
- case (Thu Jun 25 2009 - 05:07:20 PDT)
- Masakazu SEKIJIMA (Thu Jun 25 2009 - 03:45:31 PDT)
force units
- Brad Dickson (Fri Jun 19 2009 - 06:22:40 PDT)
- Catein Catherine (Thu Jun 18 2009 - 07:01:40 PDT)
- David A. Case (Thu Jun 18 2009 - 04:32:18 PDT)
- Brad Dickson (Thu Jun 18 2009 - 02:31:16 PDT)
net charge
- Junmei Wang (Tue Jun 23 2009 - 13:41:24 PDT)
- case (Tue Jun 23 2009 - 12:22:28 PDT)
- Vishal Maingi (Tue Jun 23 2009 - 11:56:52 PDT)
question about ff
- FyD (Thu Jun 25 2009 - 02:12:40 PDT)
R.E.D. error message
- FyD (Thu Jun 18 2009 - 13:13:41 PDT)
R: [AMBER] Amber10 Parallel Installation
- sgrignani.cerm.unifi.it (Sat Jun 20 2009 - 13:14:38 PDT)
Regd: Fe4S4
- case (Mon Jun 22 2009 - 11:39:57 PDT)
residue
- KIRTANA S (Fri Jun 19 2009 - 08:03:31 PDT)
Residues
- KIRTANA S (Fri Jun 12 2009 - 18:15:20 PDT)
Seg-fault when creating residue
- Valla Fatemi (Wed Jun 17 2009 - 10:41:47 PDT)
回复： [AMBER] Error in MM PBSA
- David A. Case (Tue Jun 02 2009 - 07:36:39 PDT)
- 廖青华 (Tue Jun 02 2009 - 07:30:47 PDT)
回复： [AMBER] parallel error
- Tom Joseph (Mon Jun 15 2009 - 05:51:49 PDT)
- 廖青华 (Mon Jun 15 2009 - 05:08:27 PDT)
回复： [AMBER] too high in binding energy (MM-PBSA)
- Maryam Hamzehee (Sat Jun 13 2009 - 06:56:16 PDT)
- 廖青华 (Sat Jun 13 2009 - 05:44:31 PDT)
回复：回复： [AMBER] parallel error
- Tom Joseph (Mon Jun 15 2009 - 06:25:30 PDT)
- 廖青华 (Mon Jun 15 2009 - 06:13:56 PDT)
回复：回复： [AMBER] too high in binding energy (MM-PBSA)
- Ilyas Yildirim (Sat Jun 13 2009 - 11:19:09 PDT)
- Maryam Hamzehee (Sat Jun 13 2009 - 11:02:57 PDT)
- Maryam Hamzehee (Sat Jun 13 2009 - 11:02:06 PDT)
- Maryam Hamzehee (Sat Jun 13 2009 - 11:02:16 PDT)
- 廖青华 (Sat Jun 13 2009 - 08:23:38 PDT)
回复：回复：回复： [AMBER] parallel error
- Tom Joseph (Mon Jun 15 2009 - 07:06:05 PDT)
- 廖青华 (Mon Jun 15 2009 - 06:35:58 PDT)
回复：回复：回复： [AMBER] too high in binding energy (MM-PBSA)
- Maryam Hamzehee (Mon Jun 15 2009 - 03:00:50 PDT)
- 廖青华 (Sat Jun 13 2009 - 17:48:59 PDT)
回复：回复：回复：回复： [AMBER] parallel error
- 廖青华 (Mon Jun 15 2009 - 07:20:59 PDT)
回复：回复：回复：回复： [AMBER] too high in binding energy (MM-PBSA)
- 廖青华 (Mon Jun 15 2009 - 03:45:09 PDT)

Amber Archive Jun 2009 by subject