Amber Archive Jan 2013: by subject

[AMBER] 27th Molecular Modelling Workshop 2013 Feb., 25th-27th in Erlangen, Germany
- Harald Lanig (Tue Jan 22 2013 - 02:52:51 PST)
[AMBER] [AMBER: gauche effect in OS-CT-CT-F
- Jason Swails (Mon Jan 21 2013 - 13:25:31 PST)
- Steven M. Graham (Mon Jan 21 2013 - 12:46:58 PST)
- Karl N. Kirschner (Mon Jan 21 2013 - 02:20:49 PST)
- Steven M. Graham (Sat Jan 19 2013 - 15:00:44 PST)
[AMBER] [q4md-fft] Issue with creating topology file due to atom type not being recognised in frcmod
- Giri tomp (Sat Jan 05 2013 - 11:18:18 PST)
- David A Case (Fri Jan 04 2013 - 10:50:15 PST)
- FyD (Fri Jan 04 2013 - 06:06:51 PST)
[AMBER] A link atoms between protein and sugar!
- FyD (Thu Jan 17 2013 - 01:09:35 PST)
- john Kerk (Thu Jan 17 2013 - 00:40:13 PST)
- FyD (Wed Jan 16 2013 - 23:57:27 PST)
- john Kerk (Wed Jan 16 2013 - 00:33:52 PST)
[AMBER] about iwrap=1 and ntxo=2
- Jason Swails (Sun Jan 27 2013 - 06:23:17 PST)
- Thomas Evangelidis (Sun Jan 27 2013 - 03:57:33 PST)
[AMBER] Amber 12 cuda test suite: some tests 'hang'
- Alessandro Contini (Thu Jan 31 2013 - 12:11:54 PST)
- Scott Le Grand (Thu Jan 31 2013 - 10:24:35 PST)
- Ross Walker (Thu Jan 31 2013 - 10:16:50 PST)
- Jason Swails (Thu Jan 31 2013 - 09:24:54 PST)
- Alessandro Contini (Thu Jan 31 2013 - 08:45:40 PST)
[AMBER] amber 12 patch for cuda-5.0
- Jason Swails (Mon Jan 28 2013 - 04:35:51 PST)
- Asmita Gupta (Mon Jan 28 2013 - 00:50:55 PST)
[AMBER] AMBER 4.1 Manual
- Romelia Salomon (Thu Jan 31 2013 - 10:03:41 PST)
- David A Case (Wed Jan 30 2013 - 15:02:52 PST)
- Romelia Salomon (Wed Jan 30 2013 - 08:57:38 PST)
- Gerald Monard (Tue Jan 29 2013 - 13:03:50 PST)
- Romelia Salomon (Tue Jan 29 2013 - 09:49:09 PST)
[AMBER] AMBER bonded parameters
- David A Case (Fri Jan 11 2013 - 06:44:29 PST)
- Dr. Vitaly Chaban (Thu Jan 10 2013 - 14:50:34 PST)
[AMBER] Amber ff03w/tip4p2005
- David A Case (Tue Jan 22 2013 - 04:47:10 PST)
- Neha Gandhi (Tue Jan 22 2013 - 00:10:20 PST)
[AMBER] Amber LES.MPI crash
- Kirill Nuzhdin (Wed Jan 02 2013 - 14:57:47 PST)
- David A Case (Wed Jan 02 2013 - 12:52:44 PST)
- David A Case (Wed Jan 02 2013 - 12:50:44 PST)
- Kirill Nuzhdin (Wed Jan 02 2013 - 11:54:37 PST)
- Kirill Nuzhdin (Wed Jan 02 2013 - 11:54:34 PST)
- David A Case (Wed Jan 02 2013 - 09:40:29 PST)
- Carlos Simmerling (Wed Jan 02 2013 - 09:04:07 PST)
- Kirill Nuzhdin (Wed Jan 02 2013 - 08:08:16 PST)
[AMBER] amber organic box
- Bill Ross (Mon Jan 14 2013 - 10:41:32 PST)
- David A Case (Mon Jan 14 2013 - 05:10:01 PST)
- 纪晓峰 (Mon Jan 14 2013 - 02:16:59 PST)
[AMBER] AMBER parameter problem
- David A Case (Mon Jan 07 2013 - 07:52:58 PST)
- osalo.abo.fi (Mon Jan 07 2013 - 06:25:08 PST)
[AMBER] AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead
- Marko Wehle (Wed Jan 30 2013 - 12:14:46 PST)
- Jason Swails (Wed Jan 30 2013 - 07:43:34 PST)
- Marko Wehle (Wed Jan 30 2013 - 07:29:20 PST)
[AMBER] amber11 installation test files
- Mary Varughese (Wed Jan 30 2013 - 10:19:00 PST)
- Daniel Roe (Mon Jan 21 2013 - 09:25:43 PST)
- Jason Swails (Mon Jan 21 2013 - 09:14:10 PST)
- Mary Varughese (Mon Jan 21 2013 - 02:28:40 PST)
[AMBER] amber12
- Daniel Sindhikara (Thu Jan 10 2013 - 23:05:23 PST)
- Bio Learner (Thu Jan 10 2013 - 22:41:30 PST)
[AMBER] Amber12 Cuda installation issues
- Ross Walker (Wed Jan 23 2013 - 00:58:54 PST)
- Vivek Shankar Bharadwaj (Tue Jan 22 2013 - 10:05:43 PST)
[AMBER] AMBER12 Installation failed
- Tru Huynh (Thu Jan 10 2013 - 13:23:36 PST)
- Jason Swails (Tue Jan 08 2013 - 04:50:27 PST)
- Udaysankar Midya (Mon Jan 07 2013 - 22:39:31 PST)
[AMBER] AMD
- Bill Ross (Tue Jan 15 2013 - 15:08:32 PST)
- Ross Walker (Tue Jan 15 2013 - 07:46:33 PST)
- pooja chahal (Tue Jan 15 2013 - 03:32:58 PST)
- Jason Swails (Tue Jan 15 2013 - 03:27:04 PST)
- pooja chahal (Tue Jan 15 2013 - 03:18:15 PST)
- Jason Swails (Sat Jan 12 2013 - 06:52:51 PST)
- Hirdesh Kumar (Sat Jan 12 2013 - 00:31:39 PST)
- Ganesh Kamath (Fri Jan 11 2013 - 21:04:32 PST)
- Bill Ross (Fri Jan 11 2013 - 21:01:29 PST)
- Daniel Sindhikara (Fri Jan 11 2013 - 20:58:40 PST)
- pooja chahal (Fri Jan 11 2013 - 20:30:44 PST)
- Jason Swails (Fri Jan 11 2013 - 05:27:14 PST)
- pooja chahal (Fri Jan 11 2013 - 02:28:31 PST)
[AMBER] Amoeba water model parameters
- Kirill Nuzhdin (Thu Jan 17 2013 - 08:25:01 PST)
[AMBER] Analyzing AMBER10 trajectories using AmberTools1.4
- Kamali Sripathi (Sat Jan 26 2013 - 06:55:14 PST)
- Jason Swails (Wed Jan 23 2013 - 15:18:03 PST)
- Daniel Roe (Wed Jan 23 2013 - 15:03:06 PST)
- Kamali Sripathi (Wed Jan 23 2013 - 14:53:44 PST)
- Daniel Roe (Wed Jan 23 2013 - 07:31:12 PST)
- Jason Swails (Wed Jan 23 2013 - 05:19:06 PST)
- Kamali Sripathi (Wed Jan 23 2013 - 04:52:18 PST)
[AMBER] Announcement: Release of DOCK 6.6
- Scott Brozell (Fri Jan 04 2013 - 20:02:33 PST)
[AMBER] antechamber problem
- Changqing Yan (Fri Jan 11 2013 - 21:31:47 PST)
- M. L. Dodson (Fri Jan 11 2013 - 05:30:50 PST)
- Jason Swails (Fri Jan 11 2013 - 05:01:33 PST)
- Ravi Tripathi (Thu Jan 10 2013 - 20:58:09 PST)
- Changqing Yan (Thu Jan 10 2013 - 19:15:45 PST)
[AMBER] Atom reordering for TI
- Thomas Exner (Tue Jan 15 2013 - 07:43:36 PST)
- David A Case (Tue Jan 15 2013 - 05:07:32 PST)
- Thomas Exner (Tue Jan 15 2013 - 04:25:01 PST)
[AMBER] atom type definition mm_pbsa
- Jason Swails (Tue Jan 15 2013 - 08:38:57 PST)
- Andrew Anighoro (Tue Jan 15 2013 - 08:01:13 PST)
[AMBER] bad atom type: f
- Jason Swails (Fri Jan 11 2013 - 05:03:58 PST)
- Vaibhav Dixit (Thu Jan 10 2013 - 21:08:39 PST)
- Date, Mihir (Thu Jan 10 2013 - 13:06:03 PST)
- Vaibhav Dixit (Fri Jan 04 2013 - 20:16:58 PST)
- Date, Mihir (Fri Jan 04 2013 - 10:42:21 PST)
[AMBER] Bug in amber12, pmemd ch2int function
- Jason Swails (Mon Jan 21 2013 - 05:53:13 PST)
- Ake Sandgren (Mon Jan 21 2013 - 03:50:35 PST)
[AMBER] bug in sander nmr.F90, amber12?
- David A Case (Fri Jan 11 2013 - 07:17:00 PST)
- Fabian Zeller (Thu Jan 10 2013 - 06:27:09 PST)
[AMBER] bugfix.31
- Jason Swails (Mon Jan 07 2013 - 13:24:16 PST)
- Norah Schlacter (Mon Jan 07 2013 - 12:50:11 PST)
[AMBER] Building a new structure!
- FyD (Wed Jan 23 2013 - 23:51:33 PST)
- David A Case (Wed Jan 23 2013 - 10:58:13 PST)
- Ibrahim Said (Wed Jan 23 2013 - 09:25:18 PST)
- David A Case (Wed Jan 23 2013 - 05:21:56 PST)
- Ibrahim Said (Tue Jan 22 2013 - 08:39:33 PST)
[AMBER] Charge relocation
- CHAMI F. (Wed Jan 23 2013 - 05:56:33 PST)
- CHAMI F. (Mon Jan 21 2013 - 08:52:48 PST)
[AMBER] Citrate ion (-3) parameters
- FyD (Mon Jan 21 2013 - 23:58:41 PST)
- moitrayee.mbu.iisc.ernet.in (Mon Jan 21 2013 - 09:39:00 PST)
- FyD (Mon Jan 21 2013 - 00:46:32 PST)
- moitrayee.mbu.iisc.ernet.in (Sat Jan 19 2013 - 05:27:17 PST)
- FyD (Thu Jan 17 2013 - 00:05:38 PST)
- moitrayee.mbu.iisc.ernet.in (Wed Jan 16 2013 - 01:28:08 PST)
- FyD (Tue Jan 15 2013 - 22:31:29 PST)
- moitrayee.mbu.iisc.ernet.in (Mon Jan 14 2013 - 03:34:13 PST)
[AMBER] coexisting nab and nab openmp
- Scott Brozell (Tue Jan 29 2013 - 22:58:51 PST)
- David A Case (Tue Jan 29 2013 - 18:09:51 PST)
- Jason Swails (Tue Jan 29 2013 - 15:24:36 PST)
- Scott Brozell (Tue Jan 29 2013 - 15:19:14 PST)
[AMBER] command used to upload pdb
- Prajwal Nandekar (Mon Jan 14 2013 - 01:42:37 PST)
- Bio Learner (Mon Jan 14 2013 - 00:51:40 PST)
[AMBER] CPPTRAJ Parmstrip error
- HM (Wed Jan 30 2013 - 06:09:20 PST)
- Jason Swails (Tue Jan 29 2013 - 08:59:58 PST)
- HM (Tue Jan 29 2013 - 08:20:00 PST)
[AMBER] Cpptraj: distance does not work with center of mass
- Daniel Roe (Thu Jan 24 2013 - 07:52:19 PST)
- Vlastimil Zíma (Thu Jan 24 2013 - 00:47:05 PST)
[AMBER] cudaMemcpyToSymbol
- Lars Skjærven (Mon Jan 28 2013 - 03:09:09 PST)
- Ross Walker (Sun Jan 27 2013 - 17:12:12 PST)
- Lars Skjærven (Sun Jan 27 2013 - 13:01:02 PST)
[AMBER] cudaMemcpyToSymbol: SetSim copy to Sim failed for K20x using JAC and Cellulose benchmarks
- Ross Walker (Wed Jan 09 2013 - 14:23:00 PST)
- Mohammad Ashraf Bhuiyan (Wed Jan 09 2013 - 14:02:41 PST)
[AMBER] Defining a dihedral torsional energy for non-serial atoms.
- Carlos Simmerling (Mon Jan 21 2013 - 06:30:29 PST)
- Negar Ashari Astani (Mon Jan 21 2013 - 06:27:12 PST)
[AMBER] density for PBC system; addles error
- David A Case (Thu Jan 17 2013 - 06:01:17 PST)
- Kirill Nuzhdin (Wed Jan 16 2013 - 15:33:52 PST)
- Kirill Nuzhdin (Wed Jan 16 2013 - 15:24:11 PST)
- David A Case (Wed Jan 16 2013 - 13:35:10 PST)
- Kirill Nuzhdin (Wed Jan 16 2013 - 11:41:47 PST)
- Kirill Nuzhdin (Wed Jan 16 2013 - 08:41:42 PST)
- case (Tue Jan 15 2013 - 17:00:25 PST)
- Kirill Nuzhdin (Tue Jan 15 2013 - 15:03:56 PST)
- David A Case (Tue Jan 15 2013 - 04:58:57 PST)
- Kirill Nuzhdin (Mon Jan 14 2013 - 14:17:53 PST)
[AMBER] difficulty with basic tutorial 1
- mhclewett.msn.com (Fri Jan 18 2013 - 07:20:25 PST)
- Brian Radak (Thu Jan 17 2013 - 12:32:33 PST)
- Daniel Roe (Thu Jan 17 2013 - 11:15:51 PST)
- mhclewett.msn.com (Thu Jan 17 2013 - 10:50:22 PST)
[AMBER] Dihedral angle PCA
- Jian Yin (Thu Jan 24 2013 - 09:40:58 PST)
- Daniel Roe (Thu Jan 24 2013 - 08:31:09 PST)
- Sergey Samsonov (Thu Jan 24 2013 - 08:27:48 PST)
[AMBER] Dihedral energy for non-serial atoms
- Negar Ashari Astani (Mon Jan 21 2013 - 10:13:21 PST)
- Jason Swails (Mon Jan 21 2013 - 09:09:24 PST)
- Negar Ashari Astani (Mon Jan 21 2013 - 07:32:25 PST)
[AMBER] distance restraints between the primary molecule and its periodic image
- Jason Swails (Wed Jan 30 2013 - 09:37:22 PST)
- Thomas Evangelidis (Wed Jan 30 2013 - 08:40:51 PST)
- Thomas Evangelidis (Mon Jan 28 2013 - 02:56:54 PST)
- Ross Walker (Sun Jan 27 2013 - 17:07:50 PST)
- Daniel Roe (Sun Jan 27 2013 - 14:34:19 PST)
- Thomas Evangelidis (Sun Jan 27 2013 - 10:22:50 PST)
[AMBER] dnaiontracker command in cpptraj
- Daniel Roe (Fri Jan 11 2013 - 12:19:24 PST)
- Le,Huy Tuan (Fri Jan 11 2013 - 11:50:41 PST)
[AMBER] does iwrap=1 work with dodecahedra ?
- Thomas Evangelidis (Thu Jan 31 2013 - 13:49:57 PST)
- Daniel Roe (Thu Jan 31 2013 - 13:26:38 PST)
- Jason Swails (Thu Jan 31 2013 - 13:25:28 PST)
- Thomas Evangelidis (Thu Jan 31 2013 - 13:16:52 PST)
- Brian Radak (Thu Jan 31 2013 - 12:58:51 PST)
- Thomas Evangelidis (Thu Jan 31 2013 - 12:21:22 PST)
- David A Case (Thu Jan 31 2013 - 04:54:12 PST)
- Thomas Evangelidis (Thu Jan 31 2013 - 04:24:13 PST)
[AMBER] error in running a minimization job....
- Shashidhar Rao (Thu Jan 24 2013 - 08:12:37 PST)
- case (Wed Jan 23 2013 - 14:43:41 PST)
- Shashidhar Rao (Wed Jan 23 2013 - 12:16:32 PST)
[AMBER] Error running sander.MPI "rfree: End of file on unit 5 "
- Jason Swails (Thu Jan 24 2013 - 09:11:59 PST)
- Daniel Roe (Thu Jan 24 2013 - 08:29:42 PST)
- Urszula Uciechowska (Thu Jan 24 2013 - 08:25:03 PST)
[AMBER] error while running mmpbsa.py in amber12
- Jason Swails (Wed Jan 30 2013 - 07:34:37 PST)
- Alessandro Contini (Wed Jan 30 2013 - 07:27:02 PST)
- Jason Swails (Wed Jan 30 2013 - 07:23:28 PST)
- Alessandro Contini (Wed Jan 30 2013 - 07:18:12 PST)
- Alessandro Contini (Wed Jan 30 2013 - 06:51:43 PST)
- Jason Swails (Wed Jan 30 2013 - 05:35:38 PST)
- Alessandro Contini (Wed Jan 30 2013 - 04:54:55 PST)
- Jason Swails (Wed Jan 30 2013 - 04:29:43 PST)
- Alessandro Contini (Wed Jan 30 2013 - 03:47:41 PST)
[AMBER] Error with TIP4P
- George M Giambasu (Thu Jan 10 2013 - 08:57:44 PST)
- case (Wed Jan 09 2013 - 06:07:57 PST)
- Chandrasekaran, Suryanarayanan (Tue Jan 08 2013 - 06:18:25 PST)
[AMBER] Errors while reading a MOL2 file with "parm" in cpptraj...
- Daniel Roe (Wed Jan 16 2013 - 16:04:47 PST)
- Shashidhar Rao (Wed Jan 16 2013 - 15:04:58 PST)
[AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters
- Sanjib Paul (Wed Jan 30 2013 - 20:38:40 PST)
- David A Case (Tue Jan 29 2013 - 07:12:50 PST)
- Sanjib Paul (Tue Jan 29 2013 - 04:22:28 PST)
[AMBER] Explicit ions in GB solvent
- Bill Ross (Tue Jan 29 2013 - 15:34:19 PST)
- manikanthan bhavaraju (Mon Jan 28 2013 - 07:46:29 PST)
- Jason Swails (Mon Jan 28 2013 - 07:38:31 PST)
- Aron Broom (Mon Jan 28 2013 - 07:09:27 PST)
- Debayan Chakraborty (Mon Jan 28 2013 - 06:04:31 PST)
[AMBER] frcmod file dihedrals -phase shift question
- Carlos Simmerling (Tue Jan 08 2013 - 04:37:08 PST)
- osalo.abo.fi (Tue Jan 08 2013 - 04:28:18 PST)
[AMBER] Fwd: Query regarding umbrella sampling
- Brian Radak (Sun Jan 13 2013 - 09:31:23 PST)
- minhazul arfeen (Sat Jan 12 2013 - 08:07:30 PST)
[AMBER] Fwd: Regarding the problem with ligand conformation
- Karl N. Kirschner (Thu Jan 31 2013 - 08:42:42 PST)
- aneesh cna (Thu Jan 31 2013 - 03:35:56 PST)
- Karl N. Kirschner (Thu Jan 31 2013 - 01:10:05 PST)
- Bill Ross (Wed Jan 30 2013 - 07:53:52 PST)
- aneesh cna (Tue Jan 29 2013 - 23:22:33 PST)
- Bill Ross (Tue Jan 29 2013 - 22:01:33 PST)
- aneesh cna (Tue Jan 29 2013 - 21:38:55 PST)
- Karl N. Kirschner (Tue Jan 29 2013 - 07:59:56 PST)
- aneesh cna (Tue Jan 29 2013 - 05:12:38 PST)
[AMBER] Fwd: Sampling of a point by a molecule while keeping the relative position of the molecule unchanged in TMD
- Sajeewa Pemasinghe (Thu Jan 31 2013 - 13:02:05 PST)
[AMBER] GAFFlipid FF concern
- Ganesh Kamath (Wed Jan 09 2013 - 10:46:11 PST)
- David A Case (Wed Jan 09 2013 - 10:38:54 PST)
- Dickson, Callum (Wed Jan 09 2013 - 06:08:24 PST)
- jfloresc.andrew.cmu.edu (Tue Jan 08 2013 - 13:54:28 PST)
[AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file
- FyD (Mon Jan 28 2013 - 02:59:32 PST)
- case (Sun Jan 27 2013 - 14:38:24 PST)
- Jonathan Saboury (Sun Jan 27 2013 - 12:42:45 PST)
- Jonathan Saboury (Sun Jan 27 2013 - 12:33:34 PST)
- Jason Swails (Sun Jan 27 2013 - 12:08:08 PST)
- Jonathan Saboury (Sun Jan 27 2013 - 11:53:29 PST)
- Jason Swails (Sun Jan 27 2013 - 06:16:14 PST)
- Jonathan Saboury (Sun Jan 27 2013 - 00:42:59 PST)
[AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file (2)
- Jonathan Saboury (Sun Jan 27 2013 - 13:49:17 PST)
[AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file(case)
- David A Case (Tue Jan 29 2013 - 07:03:10 PST)
- Jonathan Saboury (Mon Jan 28 2013 - 18:38:13 PST)
[AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file(jason)
- Jonathan Saboury (Mon Jan 28 2013 - 18:43:47 PST)
[AMBER] Generating Electrostatic Potential Maps
- Ray Luo, Ph.D. (Sat Jan 26 2013 - 08:14:56 PST)
- Kamali Sripathi (Sat Jan 26 2013 - 07:00:50 PST)
[AMBER] generating restart file with velocity information
- Jason Swails (Thu Jan 17 2013 - 06:30:11 PST)
- Vijay Manickam Achari (Wed Jan 16 2013 - 22:53:31 PST)
[AMBER] Getting AmberTools12 to work in Ubuntu 12.04?
- Jason Swails (Mon Jan 14 2013 - 16:26:39 PST)
- David Dubins (Mon Jan 14 2013 - 14:39:21 PST)
[AMBER] Getting total dipole moment of molecules in periodic box.
- Jason Swails (Tue Jan 15 2013 - 07:00:02 PST)
- 강현아 (Tue Jan 15 2013 - 06:47:00 PST)
[AMBER] glibc detected in ptraj
- Jason Swails (Wed Jan 23 2013 - 10:20:02 PST)
- Jagur Lambix (Wed Jan 23 2013 - 07:56:47 PST)
- Daniel Roe (Tue Jan 22 2013 - 16:53:31 PST)
- Jagur Lambix (Tue Jan 22 2013 - 15:55:50 PST)
[AMBER] Glycam_06 in amber12
- Lachele Foley (Lists) (Mon Jan 14 2013 - 08:23:10 PST)
- Subrata Paul (Sun Jan 13 2013 - 23:54:14 PST)
- Lachele Foley (Lists) (Sat Jan 12 2013 - 10:48:58 PST)
- Subrata Paul (Fri Jan 11 2013 - 20:32:00 PST)
- Lachele Foley (Lists) (Fri Jan 11 2013 - 07:08:44 PST)
- Urszula Uciechowska (Fri Jan 11 2013 - 02:27:35 PST)
- Subrata Paul (Fri Jan 11 2013 - 02:03:53 PST)
[AMBER] GPUs and PBSPro
- Ross Walker (Sun Jan 06 2013 - 20:50:47 PST)
- Vijay Manickam Achari (Sun Jan 06 2013 - 20:05:45 PST)
[AMBER] Group specification for energy decomposition in thermodynamic integration
- Joel Dockray (Mon Jan 07 2013 - 10:24:57 PST)
[AMBER] Group specification for energy decomposition in thermodynamic integration (Corrected spacing)
- Joel Dockray (Mon Jan 07 2013 - 10:35:00 PST)
[AMBER] H-bond analysis of backbone atoms
- HM (Thu Jan 17 2013 - 02:30:53 PST)
[AMBER] how to assign atom types.
- FyD (Tue Jan 08 2013 - 00:03:34 PST)
- Jason Swails (Mon Jan 07 2013 - 03:27:28 PST)
- Salma Zahir (Mon Jan 07 2013 - 02:43:12 PST)
[AMBER] How to calculate PMF using Jarzynski’s equality?
- Adrian Roitberg (Tue Jan 29 2013 - 08:39:03 PST)
- Brian Radak (Tue Jan 29 2013 - 08:36:33 PST)
- Cuiyl (Tue Jan 29 2013 - 00:34:27 PST)
[AMBER] How to choose the boost for aMD when using restraints
- Thomas Evangelidis (Tue Jan 15 2013 - 12:32:35 PST)
[AMBER] how to construct new molecule
- Maxier Acosta Santiago (Fri Jan 11 2013 - 00:09:18 PST)
- Bio Learner (Fri Jan 11 2013 - 00:00:50 PST)
[AMBER] how to keep the previous restart file when saving the current one
- Jason Swails (Thu Jan 24 2013 - 06:45:34 PST)
- Thomas Evangelidis (Thu Jan 24 2013 - 05:11:23 PST)
- case (Wed Jan 23 2013 - 16:36:08 PST)
- Jason Swails (Wed Jan 23 2013 - 15:26:19 PST)
- Aron Broom (Wed Jan 23 2013 - 14:33:14 PST)
- Thomas Evangelidis (Wed Jan 23 2013 - 14:17:35 PST)
[AMBER] How to save secondary structure gnuplot as image
- ros (Thu Jan 31 2013 - 09:56:37 PST)
- HM (Thu Jan 31 2013 - 09:36:48 PST)
- HM (Thu Jan 31 2013 - 09:32:17 PST)
- Daniel Roe (Wed Jan 30 2013 - 10:03:25 PST)
- steinbrt.rci.rutgers.edu (Wed Jan 30 2013 - 06:40:43 PST)
- HM (Wed Jan 30 2013 - 06:13:27 PST)
[AMBER] hybrid imlicit/explicit system
- case (Wed Jan 09 2013 - 05:57:25 PST)
- Алексей Раевский (Wed Jan 09 2013 - 02:44:16 PST)
[AMBER] installation error
- Jason Swails (Tue Jan 15 2013 - 03:20:42 PST)
- Bio Learner (Mon Jan 14 2013 - 22:19:48 PST)
- Jason Swails (Mon Jan 14 2013 - 07:56:46 PST)
- Daniel Roe (Mon Jan 14 2013 - 07:30:01 PST)
- Bio Learner (Mon Jan 14 2013 - 01:58:27 PST)
[AMBER] installation of amber10 in cluster fails
- Jason Swails (Mon Jan 28 2013 - 04:34:21 PST)
- Jorgen Simonsen (Sun Jan 27 2013 - 23:16:44 PST)
[AMBER] installation problem
- JD John (Fri Jan 11 2013 - 09:38:37 PST)
- Jason Swails (Fri Jan 11 2013 - 05:30:43 PST)
- Tanmoy Paul (Fri Jan 11 2013 - 03:09:30 PST)
[AMBER] Is AM1-BCC charges ok for ligands with idodine atoms
- FyD (Wed Jan 09 2013 - 04:15:38 PST)
- FyD (Wed Jan 09 2013 - 00:56:50 PST)
- Shulin Zhuang (Tue Jan 08 2013 - 17:54:10 PST)
[AMBER] Is it possible to do TI calculations with pmemd?
- Anna Bauß (Wed Jan 16 2013 - 00:23:47 PST)
- Ross Walker (Tue Jan 15 2013 - 07:41:48 PST)
- steinbrt.rci.rutgers.edu (Tue Jan 15 2013 - 07:40:44 PST)
- Anna Bauß (Tue Jan 15 2013 - 07:10:07 PST)
[AMBER] Issue with creating topology file due to atom type not being recognised in frcmod
- Giri tomp (Thu Jan 03 2013 - 16:34:52 PST)
[AMBER] KCl crystals with Dang parameters ?
- Vlad Cojocaru (Fri Jan 25 2013 - 06:10:13 PST)
- Jason Swails (Fri Jan 25 2013 - 05:53:32 PST)
- Vlad Cojocaru (Fri Jan 25 2013 - 05:08:49 PST)
- Jason Swails (Fri Jan 25 2013 - 05:00:23 PST)
- Vlad Cojocaru (Fri Jan 25 2013 - 04:49:18 PST)
- Vlad Cojocaru (Thu Jan 24 2013 - 00:43:59 PST)
- Thomas Cheatham (Wed Jan 23 2013 - 16:41:00 PST)
- InSuk Joung (Wed Jan 23 2013 - 15:25:29 PST)
- Vlad Cojocaru (Wed Jan 23 2013 - 12:24:39 PST)
- Daniel Roe (Wed Jan 23 2013 - 12:03:42 PST)
- Vlad Cojocaru (Wed Jan 23 2013 - 11:23:34 PST)
[AMBER] LJ parameters for Ho in GLYCAM06 changes
- Jason Swails (Wed Jan 16 2013 - 09:06:11 PST)
- ABEL Stephane 175950 (Wed Jan 16 2013 - 05:05:26 PST)
[AMBER] Membrane-Peptide Simulation ( peptide going away from membrane)
- Ross Walker (Sun Jan 27 2013 - 16:53:21 PST)
- HM (Tue Jan 22 2013 - 00:35:47 PST)
- Ross Walker (Mon Jan 21 2013 - 15:47:58 PST)
- HM (Mon Jan 21 2013 - 05:25:30 PST)
- Benjamin D Madej (Fri Jan 18 2013 - 12:21:36 PST)
- Thomas Evangelidis (Fri Jan 18 2013 - 07:09:10 PST)
- Aldo Segura (Fri Jan 18 2013 - 05:21:00 PST)
- HM (Fri Jan 18 2013 - 01:07:11 PST)
- Ross Walker (Fri Jan 18 2013 - 00:38:48 PST)
- HM (Fri Jan 18 2013 - 00:28:41 PST)
- Thomas Evangelidis (Fri Jan 18 2013 - 00:22:34 PST)
- HM (Fri Jan 18 2013 - 00:10:49 PST)
- Thomas Evangelidis (Thu Jan 17 2013 - 23:52:46 PST)
- HM (Thu Jan 17 2013 - 23:29:11 PST)
- Benjamin D Madej (Thu Jan 17 2013 - 15:07:18 PST)
- HM (Thu Jan 17 2013 - 02:28:17 PST)
- Benjamin D Madej (Tue Jan 15 2013 - 10:38:41 PST)
- manikanthan bhavaraju (Tue Jan 15 2013 - 10:10:35 PST)
- Benjamin D Madej (Tue Jan 15 2013 - 09:49:00 PST)
- HM (Tue Jan 15 2013 - 09:18:16 PST)
[AMBER] Membrane-protein simulation using amber12
- manikanthan bhavaraju (Tue Jan 15 2013 - 10:36:44 PST)
- Benjamin D Madej (Tue Jan 15 2013 - 10:25:07 PST)
- manikanthan bhavaraju (Tue Jan 15 2013 - 09:36:27 PST)
- Benjamin D Madej (Tue Jan 15 2013 - 09:08:05 PST)
- Manikanthan Bhavaraju (Mon Jan 14 2013 - 20:38:11 PST)
[AMBER] Minimization failure of a ligand
- Bill Ross (Tue Jan 22 2013 - 10:57:01 PST)
- David A Case (Tue Jan 22 2013 - 05:01:07 PST)
- Sun (Tue Jan 22 2013 - 01:25:43 PST)
- Hirdesh Kumar (Tue Jan 22 2013 - 01:04:07 PST)
- Sun (Tue Jan 22 2013 - 00:58:27 PST)
[AMBER] minimization problem
- Daniel Roe (Thu Jan 24 2013 - 08:17:56 PST)
- Sanjib Paul (Thu Jan 24 2013 - 03:52:39 PST)
- Sanjib Paul (Wed Jan 23 2013 - 22:27:04 PST)
[AMBER] Minimum distance between the protein and membrane
- Manikanthan Bhavaraju (Sun Jan 20 2013 - 20:21:26 PST)
- Aron Broom (Sun Jan 20 2013 - 18:54:30 PST)
- Manikanthan Bhavaraju (Sun Jan 20 2013 - 16:59:32 PST)
[AMBER] Mixing Small Organic + Water
- Ismail, Mohd F. (Sat Jan 26 2013 - 20:17:08 PST)
- case (Sat Jan 26 2013 - 11:31:40 PST)
- Ismail, Mohd F. (Sat Jan 26 2013 - 01:27:41 PST)
[AMBER] mmPBSA and restraint energy decreasing
- psu4.uic.edu (Thu Jan 31 2013 - 15:37:29 PST)
[AMBER] MMPBSA error
- marawan hussain (Mon Jan 07 2013 - 18:48:19 PST)
- Jason Swails (Mon Jan 07 2013 - 03:35:19 PST)
- marawan hussain (Mon Jan 07 2013 - 02:44:19 PST)
- Jason Swails (Sun Jan 06 2013 - 16:11:40 PST)
- marawan hussain (Sun Jan 06 2013 - 15:28:32 PST)
- Jason Swails (Fri Jan 04 2013 - 08:19:55 PST)
- marawan hussain (Thu Jan 03 2013 - 18:04:21 PST)
- Jason Swails (Thu Jan 03 2013 - 16:47:04 PST)
- marawan hussain (Thu Jan 03 2013 - 15:10:48 PST)
- Jason Swails (Thu Jan 03 2013 - 04:43:58 PST)
- marawan hussain (Wed Jan 02 2013 - 21:11:59 PST)
[AMBER] mmpbsa-with and without entropy
- David A Case (Tue Jan 22 2013 - 04:56:15 PST)
- Kshatresh Dutta Dubey (Tue Jan 22 2013 - 02:02:03 PST)
- colvin (Tue Jan 22 2013 - 00:20:18 PST)
[AMBER] mmPBSA.py: mmGBSA and solute dielectric constant
- Jason Swails (Wed Jan 30 2013 - 19:00:06 PST)
- psu4.uic.edu (Wed Jan 30 2013 - 18:01:26 PST)
[AMBER] MMPBSA/Disulfide bond error
- Jason Swails (Tue Jan 15 2013 - 14:37:19 PST)
- Jason Swails (Tue Jan 15 2013 - 13:28:08 PST)
- Divi (Tue Jan 15 2013 - 11:22:34 PST)
[AMBER] multi pmemd and REMD
- David A Case (Tue Jan 22 2013 - 05:03:18 PST)
- Jason Swails (Tue Jan 22 2013 - 04:49:05 PST)
- Neha Gandhi (Tue Jan 22 2013 - 02:21:06 PST)
- Neha Gandhi (Tue Jan 22 2013 - 01:20:58 PST)
[AMBER] Need assistance to generate forcefield for PYRIDOXAL-5'-PHOSPHATE
- BALA SUBRAMANI G L (Wed Jan 02 2013 - 05:27:21 PST)
[AMBER] not getting dipole moment values in pmemd.cuda
- Sanjib Paul (Tue Jan 01 2013 - 03:36:05 PST)
[AMBER] NPT and NVE Energy
- Ismail, Mohd F. (Tue Jan 01 2013 - 20:58:16 PST)
[AMBER] parameters for deoxyADP
- FyD (Tue Jan 15 2013 - 22:22:28 PST)
- Jorgen Simonsen (Tue Jan 15 2013 - 11:30:04 PST)
[AMBER] patching problem amber12
- Vaibhav Dixit (Wed Jan 30 2013 - 22:11:42 PST)
- Vaibhav Dixit (Wed Jan 30 2013 - 22:05:07 PST)
- Daniel Sindhikara (Wed Jan 30 2013 - 22:01:29 PST)
- Vaibhav Dixit (Wed Jan 30 2013 - 21:53:55 PST)
- Jason Swails (Wed Jan 30 2013 - 05:28:41 PST)
- Vaibhav Dixit (Wed Jan 30 2013 - 05:28:31 PST)
- Jason Swails (Wed Jan 30 2013 - 05:24:01 PST)
- Vaibhav Dixit (Wed Jan 30 2013 - 05:11:11 PST)
- Daniel Sindhikara (Wed Jan 30 2013 - 04:54:11 PST)
- Jason Swails (Wed Jan 30 2013 - 04:27:21 PST)
- Vaibhav Dixit (Tue Jan 29 2013 - 21:27:54 PST)
- Daniel Sindhikara (Tue Jan 29 2013 - 21:17:06 PST)
- Vaibhav Dixit (Tue Jan 29 2013 - 20:55:21 PST)
- Daniel Sindhikara (Tue Jan 29 2013 - 20:31:10 PST)
- Vaibhav Dixit (Tue Jan 29 2013 - 20:03:56 PST)
- Vaibhav Dixit (Mon Jan 28 2013 - 20:19:26 PST)
[AMBER] PMEMD and cutoff
- Ross Walker (Fri Jan 18 2013 - 06:34:25 PST)
- Urszula Uciechowska (Fri Jan 18 2013 - 06:02:35 PST)
[AMBER] pmemd.amoeba.MPI run error
- 旭东肖 (Thu Jan 17 2013 - 18:12:13 PST)
[AMBER] pmemd.cuda compilation with amber12
- Vivek Shankar Bharadwaj (Thu Jan 31 2013 - 14:41:34 PST)
[AMBER] Pocket Volume Calculation
- Soumya Lipsa Rath (Tue Jan 29 2013 - 20:21:47 PST)
- João Ribeiro (Tue Jan 29 2013 - 07:29:12 PST)
- Soumya Lipsa Rath (Tue Jan 29 2013 - 06:29:40 PST)
[AMBER] positive DeltaEel and negative DeltaGsolv in MMPBSA
- Emilio Angelina (Sat Jan 05 2013 - 20:00:00 PST)
- Ray Luo, Ph.D. (Sat Jan 05 2013 - 16:57:09 PST)
- Emilio Angelina (Sat Jan 05 2013 - 11:44:23 PST)
[AMBER] Problem compatibility pdb in tleap
- Stefan Knippenberg (Thu Jan 24 2013 - 10:09:33 PST)
- David A Case (Thu Jan 24 2013 - 06:41:46 PST)
- Stefan Knippenberg (Thu Jan 24 2013 - 02:33:51 PST)
- Daniel Roe (Wed Jan 23 2013 - 13:41:30 PST)
- Stefan Knippenberg (Wed Jan 23 2013 - 13:32:43 PST)
- David A Case (Wed Jan 23 2013 - 10:55:49 PST)
- Daniel Roe (Wed Jan 23 2013 - 10:29:19 PST)
- Stefan Knippenberg (Wed Jan 23 2013 - 10:22:35 PST)
[AMBER] problem starting amber
- Ayesha Fatima (Fri Jan 18 2013 - 06:53:54 PST)
- Ross Walker (Fri Jan 18 2013 - 06:40:12 PST)
- Ayesha Fatima (Fri Jan 18 2013 - 06:34:51 PST)
[AMBER] Problem using solvatebox for large, linear peptide
- David A Case (Thu Jan 31 2013 - 18:44:38 PST)
[AMBER] Problem with Identification of bonds
- Volker Lesch (Mon Jan 14 2013 - 06:33:07 PST)
[AMBER] problem with identifying Zn ion in Amber11
- Jason Swails (Thu Jan 10 2013 - 06:01:46 PST)
- Agnieszka Dybala-Defratyka (Wed Jan 09 2013 - 13:55:21 PST)
[AMBER] Problems creating topology file for Dfrom
- Giri tomp (Thu Jan 03 2013 - 16:31:41 PST)
[AMBER] Problems using NAB and GCC
- David A Case (Thu Jan 10 2013 - 11:22:06 PST)
- Roberto Vera (Thu Jan 10 2013 - 08:13:58 PST)
[AMBER] Query regarding Amber atom type
- FyD (Fri Jan 18 2013 - 00:43:11 PST)
- Shubhadip Das (Thu Jan 17 2013 - 23:13:21 PST)
[AMBER] Query regarding GB calculation on a protein with FE using MMPBSA.py
- Prajwal Nandekar (Wed Jan 09 2013 - 06:04:25 PST)
- Jason Swails (Tue Jan 08 2013 - 07:24:51 PST)
- Prajwal Nandekar (Tue Jan 08 2013 - 06:22:48 PST)
[AMBER] Query regarding rms2d with cpptraj
- HM (Mon Jan 21 2013 - 09:04:10 PST)
- Daniel Roe (Mon Jan 21 2013 - 08:51:19 PST)
- HM (Mon Jan 21 2013 - 08:41:17 PST)
[AMBER] question about force fields and external QM program
- Jason Swails (Fri Jan 11 2013 - 13:27:27 PST)
- Kirill Nuzhdin (Fri Jan 11 2013 - 11:59:53 PST)
[AMBER] question on the latest manifestation of AMBER force field...
- Shashidhar Rao (Mon Jan 21 2013 - 20:48:21 PST)
[AMBER] RE : LJ parameters for Ho in GLYCAM06 changes
- Lachele Foley (Lists) (Wed Jan 16 2013 - 14:56:41 PST)
- ABEL Stephane 175950 (Wed Jan 16 2013 - 11:03:10 PST)
[AMBER] REMD restart
- gargi borgohai (Fri Jan 04 2013 - 22:46:50 PST)
[AMBER] rfree parsing error in group specification
- Joel Dockray (Sat Jan 05 2013 - 16:51:47 PST)
[AMBER] RMS2D
- Syed Tarique Moin (Mon Jan 14 2013 - 02:05:12 PST)
- Daniel Roe (Sat Jan 12 2013 - 10:26:17 PST)
- Syed Tarique Moin (Sat Jan 12 2013 - 03:49:22 PST)
[AMBER] RMSD of globular proteins
- Anselm Horn (Wed Jan 30 2013 - 00:50:33 PST)
- Julio Dominguez (Fri Jan 25 2013 - 12:55:38 PST)
- Aron Broom (Thu Jan 24 2013 - 16:02:32 PST)
- Anselm Horn (Thu Jan 24 2013 - 15:05:13 PST)
[AMBER] RRES and LRES card not recognized when using idecomp with sander
- WenJuan Huang (Fri Jan 18 2013 - 12:48:48 PST)
[AMBER] Sampling of a point by a molecule while keeping the relative position of the molecule unchanged in TMD
- Sajeewa Pemasinghe (Thu Jan 31 2013 - 10:03:37 PST)
[AMBER] saving PDB with chain ID in leap
- Jason Swails (Wed Jan 30 2013 - 04:32:37 PST)
- aneesh cna (Wed Jan 30 2013 - 02:59:59 PST)
[AMBER] scaling problem in RADIAL of CPPTRAJ
- Daniel Roe (Thu Jan 31 2013 - 20:37:30 PST)
[AMBER] SHAKE error with dt=0.002
- Jason Swails (Thu Jan 17 2013 - 11:52:02 PST)
- David A Case (Thu Jan 17 2013 - 10:36:51 PST)
- DEBOSTUTI GHOSHDASTIDAR (Thu Jan 17 2013 - 09:01:13 PST)
- David A Case (Thu Jan 17 2013 - 06:09:10 PST)
- DEBOSTUTI GHOSHDASTIDAR (Thu Jan 17 2013 - 02:52:22 PST)
[AMBER] Sigmoidal dielectric functions in AMBER
- case (Mon Jan 28 2013 - 18:12:47 PST)
- Debayan Chakraborty (Mon Jan 28 2013 - 15:50:15 PST)
[AMBER] Simulating Folic Acid
- M. L. Dodson (Fri Jan 11 2013 - 05:43:01 PST)
- JD John (Thu Jan 10 2013 - 22:53:10 PST)
[AMBER] Simulating one molecule in the gas phase
- Volker Lesch (Wed Jan 16 2013 - 23:09:12 PST)
[AMBER] Software announcement: Release of PUPIL 2.0
- Joan Torras (Sun Jan 13 2013 - 15:44:03 PST)
[AMBER] solvent accessible volume vs
- Daniel Roe (Mon Jan 21 2013 - 09:41:36 PST)
[AMBER] Steered MD in Specific Direction
- Jason Swails (Tue Jan 22 2013 - 08:36:28 PST)
- Kyle Roberts (Tue Jan 22 2013 - 07:55:34 PST)
[AMBER] Structure refinement protocol on the AMPS-NMR portal
- Baptiste Legrand (Wed Jan 16 2013 - 05:40:38 PST)
[AMBER] Theoretical explanation of adding ions to make the system neutral
- Brian Radak (Wed Jan 23 2013 - 05:58:57 PST)
- Aron Broom (Tue Jan 22 2013 - 15:41:24 PST)
- Mahendra B Thapa (Tue Jan 22 2013 - 14:41:57 PST)
[AMBER] Thermodynamic integration with iwrap=1 in SANDER
- Miroslav Krepl (Thu Jan 03 2013 - 04:39:30 PST)
[AMBER] TI alpha-beta glucose Glycam06h
- Kepa K. Burusco (Mon Jan 28 2013 - 10:03:56 PST)
- steinbrt.rci.rutgers.edu (Mon Jan 28 2013 - 05:10:51 PST)
- Kepa K. Burusco (Mon Jan 28 2013 - 03:32:35 PST)
- steinbrt.rci.rutgers.edu (Fri Jan 25 2013 - 08:30:40 PST)
- Kepa K. Burusco (Fri Jan 25 2013 - 05:42:45 PST)
[AMBER] two fold difference between MMPBSA.py and NAMDenergy plugin in vmd 1.9.1
- Jason Swails (Thu Jan 31 2013 - 04:23:10 PST)
- dbaogen (Wed Jan 30 2013 - 22:10:55 PST)
[AMBER] umbrella sampling
- Elisa Frezza (Wed Jan 16 2013 - 01:57:06 PST)
- Aron Broom (Tue Jan 15 2013 - 13:21:03 PST)
- Elisa Frezza (Tue Jan 15 2013 - 13:00:04 PST)
- Adrian Roitberg (Tue Jan 15 2013 - 12:52:40 PST)
- Elisa Frezza (Tue Jan 15 2013 - 12:50:04 PST)
- Adrian Roitberg (Tue Jan 15 2013 - 11:09:03 PST)
- Elisa Frezza (Tue Jan 15 2013 - 08:56:02 PST)
- ros (Tue Jan 15 2013 - 08:36:29 PST)
- Elisa Frezza (Tue Jan 15 2013 - 08:05:21 PST)
- Ross Walker (Tue Jan 15 2013 - 07:40:21 PST)
- Elisa Frezza (Tue Jan 15 2013 - 07:32:07 PST)
- Aron Broom (Tue Jan 15 2013 - 07:26:57 PST)
- Elisa Frezza (Tue Jan 15 2013 - 07:23:24 PST)
- Aron Broom (Tue Jan 15 2013 - 07:16:48 PST)
- Elisa Frezza (Tue Jan 15 2013 - 07:11:36 PST)
- Elisa Frezza (Tue Jan 15 2013 - 06:25:33 PST)
- Adrian Roitberg (Tue Jan 15 2013 - 06:19:14 PST)
- Elisa Frezza (Tue Jan 15 2013 - 06:12:16 PST)
[AMBER] using image command in cpptraj...
- Shashidhar Rao (Tue Jan 15 2013 - 11:04:04 PST)
- Daniel Roe (Tue Jan 15 2013 - 10:52:50 PST)
- Shashidhar Rao (Tue Jan 15 2013 - 10:34:52 PST)
[AMBER] Using multiple CPU cores with pmemd.cuda
- Ross Walker (Fri Jan 18 2013 - 09:19:45 PST)
- Filippo Pullara (Fri Jan 18 2013 - 09:02:15 PST)
[AMBER] velocity information lost in traj files when select frames
- Jason Swails (Thu Jan 17 2013 - 06:31:13 PST)
- Vijay Manickam Achari (Thu Jan 17 2013 - 05:43:19 PST)
[AMBER] vlimit exceeded and distorted bonds
- Chris Chris (Mon Jan 14 2013 - 15:02:33 PST)
[AMBER] xlead
- Antonio Entrena Guadix (Wed Jan 16 2013 - 23:09:17 PST)
- Daniel Roe (Wed Jan 16 2013 - 07:50:02 PST)
- Jason Swails (Wed Jan 16 2013 - 03:57:03 PST)
- Jan-Philip Gehrcke (Wed Jan 16 2013 - 03:24:34 PST)
- Antonio Entrena Guadix (Wed Jan 16 2013 - 02:40:02 PST)
- David A Case (Tue Jan 15 2013 - 05:05:35 PST)
- aentrena (Tue Jan 15 2013 - 04:03:43 PST)
[AMBER] xtc to mdcrd box coords
- Bill Ross (Wed Jan 16 2013 - 15:16:31 PST)
- Daniel Roe (Wed Jan 16 2013 - 10:11:11 PST)
- Federica Chiappori (Wed Jan 16 2013 - 09:52:43 PST)
- Daniel Roe (Wed Jan 16 2013 - 07:45:38 PST)
- Federica Chiappori (Wed Jan 16 2013 - 06:04:02 PST)

Amber Archive Jan 2013 by subject