Amber Archive Dec 2012: by subject

[AMBER] [apbs-users] iapbs installation
- Jason Swails (Sun Dec 09 2012 - 07:39:56 PST)
- Miguel Ortiz Lombardia (Sat Dec 08 2012 - 23:10:43 PST)
- Robert Konecny (Sat Dec 08 2012 - 17:41:45 PST)
- Jason Swails (Fri Dec 07 2012 - 10:49:32 PST)
- Miguel Ortiz Lombardía (Thu Dec 06 2012 - 08:23:30 PST)
- Miguel Ortiz Lombardia (Tue Dec 04 2012 - 23:13:41 PST)
- Robert Konecny (Tue Dec 04 2012 - 10:59:52 PST)
[AMBER] About restraint on GPU
- David A Case (Wed Dec 12 2012 - 04:59:04 PST)
- 王军 (Wed Dec 12 2012 - 00:37:35 PST)
[AMBER] Accelerated MD
- Romelia Salomon (Mon Dec 03 2012 - 12:01:37 PST)
- Shafinaz Chowdhury (Mon Dec 03 2012 - 10:43:03 PST)
[AMBER] alanine scanning
- Jonathan Gough (Mon Dec 17 2012 - 17:17:41 PST)
- Jason Swails (Mon Dec 17 2012 - 17:10:45 PST)
- Jonathan Gough (Mon Dec 17 2012 - 14:01:52 PST)
[AMBER] Amber force field formula
- case (Sat Dec 08 2012 - 05:20:23 PST)
- Shaandar Nyamtulga (Sat Dec 08 2012 - 04:41:36 PST)
[AMBER] Amber LES.MPI crash
- Kirill Nuzhdin (Wed Dec 26 2012 - 11:03:21 PST)
- Carlos Simmerling (Wed Dec 26 2012 - 10:39:32 PST)
- Kirill Nuzhdin (Wed Dec 26 2012 - 10:25:09 PST)
[AMBER] amber on intel Xeon 5680
- Jason Swails (Tue Dec 04 2012 - 16:02:37 PST)
- Marcela Madrid (Tue Dec 04 2012 - 15:48:48 PST)
[AMBER] AMBER to TINKER style trajectory
- Indrajit Deb (Mon Dec 17 2012 - 01:58:34 PST)
[AMBER] amber workshop question
- psu4.uic.edu (Tue Dec 11 2012 - 16:20:22 PST)
- Jonathan Gough (Mon Dec 10 2012 - 17:15:19 PST)
- Ross Walker (Mon Dec 10 2012 - 17:05:52 PST)
- psu4.uic.edu (Mon Dec 10 2012 - 16:57:19 PST)
[AMBER] Amber12 with Plumed
- davide branduardi (Thu Dec 13 2012 - 01:50:48 PST)
- Rajeswari A. (Thu Dec 13 2012 - 01:26:35 PST)
- Rajeswari A. (Mon Dec 10 2012 - 06:40:40 PST)
- davide branduardi (Mon Dec 10 2012 - 06:14:33 PST)
- Rajeswari A. (Mon Dec 10 2012 - 02:32:00 PST)
[AMBER] analyzing DESMOND MD trajectories in cpptraj...
- Shashidhar Rao (Thu Dec 20 2012 - 13:36:18 PST)
- Jason Swails (Thu Dec 20 2012 - 13:11:04 PST)
- Shashidhar Rao (Thu Dec 20 2012 - 11:01:44 PST)
[AMBER] Antechamber with jaguar outputs
- David A Case (Tue Dec 18 2012 - 06:22:28 PST)
- eneas.usal.es (Tue Dec 18 2012 - 02:24:41 PST)
- eneas.usal.es (Wed Dec 12 2012 - 06:35:49 PST)
- eneas.usal.es (Mon Dec 10 2012 - 14:53:26 PST)
[AMBER] Any possibility of scripting in tleap?
- Sajeewa Pemasinghe (Mon Dec 10 2012 - 06:35:57 PST)
- David A Case (Mon Dec 10 2012 - 05:49:44 PST)
- Sajeewa Pemasinghe (Sun Dec 09 2012 - 23:28:07 PST)
- Aron Broom (Sun Dec 09 2012 - 23:19:50 PST)
- Sajeewa Pemasinghe (Sun Dec 09 2012 - 23:03:08 PST)
[AMBER] Atom rename after RESP fitting by antechamber
- Ravi Tripathi (Fri Nov 30 2012 - 20:15:08 PST)
- Liu Denis (Fri Nov 30 2012 - 19:17:16 PST)
[AMBER] atom type
- David A Case (Sun Dec 23 2012 - 05:54:46 PST)
- john Kerk (Sun Dec 23 2012 - 01:47:49 PST)
[AMBER] branched disaccharide in leap
- FyD (Tue Dec 18 2012 - 22:40:50 PST)
- Lachele Foley (Lists) (Mon Dec 17 2012 - 12:14:18 PST)
- Krisztina Feher (Mon Dec 17 2012 - 03:27:17 PST)
- Lachele Foley (Lists) (Sun Dec 16 2012 - 10:19:12 PST)
- FyD (Sun Dec 16 2012 - 00:22:28 PST)
- Aron Broom (Sat Dec 15 2012 - 22:54:54 PST)
- Lachele Foley (Lists) (Sat Dec 15 2012 - 19:01:34 PST)
- Aron Broom (Sat Dec 15 2012 - 14:16:46 PST)
- Krisztina Feher (Sat Dec 15 2012 - 12:25:15 PST)
[AMBER] Brookhaven National Labs
- Jonathan Gough (Wed Dec 12 2012 - 04:53:45 PST)
[AMBER] Building peptides in a random conformation in AMBER....
- Bill Ross (Sat Dec 15 2012 - 10:29:19 PST)
- Baldoni Hector Armando (Fri Dec 14 2012 - 15:41:53 PST)
- Shashidhar Rao (Fri Dec 14 2012 - 13:26:34 PST)
- Ilyas Yildirim (Fri Dec 14 2012 - 12:10:03 PST)
- Carlos Simmerling (Fri Dec 14 2012 - 12:06:14 PST)
- Shashidhar Rao (Fri Dec 14 2012 - 12:02:58 PST)
- Jason Swails (Fri Dec 14 2012 - 11:58:07 PST)
- Shashidhar Rao (Fri Dec 14 2012 - 11:20:56 PST)
[AMBER] calcium ion in AMBER
- deeptinayar.gmail.com (Tue Dec 25 2012 - 10:25:47 PST)
- HM (Tue Dec 25 2012 - 12:04:32 PST)
[AMBER] calculating single side-chain RMSF with ptraj / cpptraj
- Daniel Roe (Thu Dec 13 2012 - 08:00:11 PST)
- Marc van der Kamp (Thu Dec 13 2012 - 02:09:45 PST)
- Daniel Roe (Wed Dec 12 2012 - 10:38:05 PST)
- Marc van der Kamp (Tue Dec 11 2012 - 07:00:57 PST)
[AMBER] calculating velocity auto-correlation function
- Jason Swails (Mon Dec 17 2012 - 06:45:29 PST)
- Jason Swails (Mon Dec 17 2012 - 06:08:24 PST)
- Vijay Manickam Achari (Mon Dec 17 2012 - 04:27:25 PST)
[AMBER] Call for paper
- Siavoush Dastmalchi (Thu Dec 06 2012 - 12:53:21 PST)
[AMBER] cannot use more than one node
- Jiri Wiesner (Sun Dec 16 2012 - 05:24:38 PST)
- Fabian Glaser (Sun Dec 16 2012 - 00:26:13 PST)
[AMBER] cluster analysis groups conformers without doing alignment
- Sun (Thu Dec 20 2012 - 20:07:44 PST)
- Daniel Roe (Thu Dec 20 2012 - 19:54:26 PST)
- Sun (Thu Dec 20 2012 - 19:39:22 PST)
- Daniel Roe (Thu Dec 20 2012 - 07:22:27 PST)
- Sun (Thu Dec 20 2012 - 00:38:33 PST)
[AMBER] compare Delphi result using MMPBSA.py.MPI
- Ray Luo, Ph.D. (Sat Dec 08 2012 - 15:45:45 PST)
- psu4.uic.edu (Sat Dec 08 2012 - 11:02:22 PST)
[AMBER] conditional restraints
- Carlos Simmerling (Tue Dec 11 2012 - 03:11:27 PST)
- Thomas Evangelidis (Tue Dec 11 2012 - 00:31:18 PST)
[AMBER] cpptraj rmsd, 'perrescenter' clarification
- Daniel Roe (Thu Dec 13 2012 - 07:54:35 PST)
- Marcus Arieno (Wed Dec 12 2012 - 12:22:09 PST)
[AMBER] Density in QM/MM
- case (Mon Dec 03 2012 - 04:40:42 PST)
- marawan hussain (Mon Dec 03 2012 - 04:19:43 PST)
- Marc van der Kamp (Mon Dec 03 2012 - 01:14:22 PST)
- Marc van der Kamp (Mon Dec 03 2012 - 01:10:38 PST)
- marawan hussain (Mon Dec 03 2012 - 01:02:48 PST)
[AMBER] deprotonation with SHAKE
- Antonija Tomić (Wed Dec 19 2012 - 05:48:50 PST)
- Brian Radak (Wed Dec 19 2012 - 05:42:34 PST)
- Antonija Tomić (Wed Dec 19 2012 - 05:32:11 PST)
[AMBER] developing parameters for HID-CU
- FyD (Wed Dec 12 2012 - 21:59:32 PST)
- Tomasz Borowski (Sat Dec 08 2012 - 22:07:53 PST)
- francesco oteri (Fri Dec 07 2012 - 03:53:05 PST)
- osalo.abo.fi (Fri Dec 07 2012 - 00:05:03 PST)
[AMBER] DNA planarity constraints in AMBER
- case (Thu Dec 20 2012 - 06:37:12 PST)
- 丁鹏飞 (Sat Dec 08 2012 - 19:14:10 PST)
[AMBER] EGB discrepancy between sander and pmemd
- Jason Swails (Tue Dec 04 2012 - 15:40:36 PST)
- Jason Swails (Tue Dec 04 2012 - 15:29:22 PST)
- case (Tue Dec 04 2012 - 15:02:47 PST)
- Eng H Yap (Tue Dec 04 2012 - 13:59:47 PST)
- Jason Swails (Tue Dec 04 2012 - 12:35:42 PST)
- David A Case (Tue Dec 04 2012 - 10:15:30 PST)
- Eng H Yap (Tue Dec 04 2012 - 08:02:18 PST)
[AMBER] enthalpy and sum of per residue energy decomposition not euqal
- Sangita Kachhap (Mon Dec 10 2012 - 10:34:08 PST)
- Jason Swails (Mon Dec 10 2012 - 07:44:19 PST)
- Sangita Kachhap (Mon Dec 10 2012 - 01:09:21 PST)
[AMBER] Error in MM-PBSA execution
- Ray Luo, Ph.D. (Fri Dec 07 2012 - 10:58:21 PST)
- Anogna (Thu Dec 06 2012 - 22:32:14 PST)
[AMBER] Error of restraint of atom using "pmemd" program in Amber 11
- case (Sat Dec 08 2012 - 05:12:45 PST)
- dbaogen (Fri Dec 07 2012 - 17:53:03 PST)
- Jason Swails (Fri Dec 07 2012 - 04:30:23 PST)
- dbaogen (Fri Dec 07 2012 - 02:42:35 PST)
[AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius!
- David A Case (Wed Dec 26 2012 - 18:15:29 PST)
- Vijay Manickam Achari (Tue Dec 25 2012 - 19:10:44 PST)
- David A Case (Mon Dec 24 2012 - 06:21:54 PST)
- Vijay Manickam Achari (Sun Dec 23 2012 - 22:23:42 PST)
[AMBER] ERROR: Regenerate prmtop file with bondi radii
- Jason Swails (Thu Dec 06 2012 - 15:00:39 PST)
- Jason Swails (Thu Dec 06 2012 - 14:59:14 PST)
- Thomas Evangelidis (Thu Dec 06 2012 - 13:51:46 PST)
- Jason Swails (Thu Dec 06 2012 - 09:05:16 PST)
- Thomas Evangelidis (Thu Dec 06 2012 - 07:55:31 PST)
[AMBER] Ethanol as solvent
- FyD (Tue Dec 18 2012 - 22:32:42 PST)
- David A Case (Tue Dec 18 2012 - 05:15:22 PST)
- Bill Ross (Mon Dec 17 2012 - 16:57:05 PST)
- Chinthaka Ratnaweera (Mon Dec 17 2012 - 15:12:10 PST)
- Jason Swails (Mon Dec 17 2012 - 05:53:17 PST)
- amin.imtech.res.in (Mon Dec 17 2012 - 03:16:25 PST)
- Chinthaka Ratnaweera (Sun Dec 16 2012 - 22:33:51 PST)
- Aron Broom (Sun Dec 16 2012 - 22:14:44 PST)
- Chinthaka Ratnaweera (Sun Dec 16 2012 - 22:07:41 PST)
- Aron Broom (Sun Dec 16 2012 - 21:58:25 PST)
- Chinthaka Ratnaweera (Sun Dec 16 2012 - 21:14:01 PST)
[AMBER] extract velocity from traj files
- Vijay Manickam Achari (Fri Dec 14 2012 - 06:27:50 PST)
- Jason Swails (Fri Dec 14 2012 - 05:24:19 PST)
- Vijay Manickam Achari (Fri Dec 14 2012 - 03:46:03 PST)
- Vijay Manickam Achari (Thu Dec 13 2012 - 21:03:06 PST)
- Jason Swails (Thu Dec 13 2012 - 04:54:43 PST)
- Vijay Manickam Achari (Thu Dec 13 2012 - 01:08:20 PST)
[AMBER] Extraction of Box dimensions from MD Trajectories
- Jagur Lambix (Fri Dec 14 2012 - 15:20:10 PST)
[AMBER] Fatal Error: File 'netcdf.mod' opened at (1) is not a GFORTRAN module file
- Ismail, Mohd F. (Thu Dec 06 2012 - 10:14:22 PST)
- Jason Swails (Thu Dec 06 2012 - 08:53:12 PST)
- Thomas Evangelidis (Thu Dec 06 2012 - 07:37:55 PST)
- Jason Swails (Wed Dec 05 2012 - 16:30:57 PST)
- Thomas Evangelidis (Wed Dec 05 2012 - 15:18:20 PST)
- Jason Swails (Wed Dec 05 2012 - 14:54:30 PST)
- Thomas Evangelidis (Wed Dec 05 2012 - 13:57:16 PST)
- Jason Swails (Wed Dec 05 2012 - 11:00:07 PST)
- Mark Williamson (Wed Dec 05 2012 - 10:36:33 PST)
- Thomas Evangelidis (Wed Dec 05 2012 - 07:42:21 PST)
- case (Wed Dec 05 2012 - 05:41:10 PST)
- Thomas Evangelidis (Wed Dec 05 2012 - 03:52:03 PST)
[AMBER] FATAL: Atom does not have a type.
- Jonathan Gough (Fri Dec 07 2012 - 13:39:28 PST)
- David A Case (Fri Dec 07 2012 - 13:18:51 PST)
- Jonathan Gough (Fri Dec 07 2012 - 12:47:36 PST)
[AMBER] FF99CHI and Modified nucleoside parameter combination
- Ilyas Yildirim (Mon Dec 17 2012 - 03:52:52 PST)
- Indrajit Deb (Mon Dec 17 2012 - 02:25:41 PST)
- Ilyas Yildirim (Fri Dec 14 2012 - 11:54:27 PST)
- Indrajit Deb (Fri Dec 14 2012 - 11:16:41 PST)
- Jason Swails (Fri Dec 14 2012 - 04:55:25 PST)
- Indrajit Deb (Thu Dec 13 2012 - 23:38:11 PST)
[AMBER] For TI do corresponding same atoms in ligand pairs need to have the same charge
- Yulin Huang (Mon Dec 10 2012 - 11:56:58 PST)
- David A Case (Mon Dec 10 2012 - 11:45:30 PST)
- Yulin Huang (Mon Dec 10 2012 - 11:28:37 PST)
- steinbrt.rci.rutgers.edu (Mon Dec 10 2012 - 11:26:08 PST)
- Yulin Huang (Mon Dec 10 2012 - 09:51:48 PST)
- Yulin Huang (Sat Dec 08 2012 - 19:13:04 PST)
- case (Sat Dec 08 2012 - 19:03:10 PST)
- Yulin Huang (Sat Dec 08 2012 - 12:15:34 PST)
[AMBER] Force calculation during SMD (jar=1): I'm looking for insights
- Jan-Philip Gehrcke (Tue Dec 11 2012 - 05:34:20 PST)
- Jason Swails (Tue Dec 11 2012 - 05:21:27 PST)
- Jan-Philip Gehrcke (Tue Dec 11 2012 - 03:01:28 PST)
- Jason Swails (Mon Dec 10 2012 - 08:29:57 PST)
- Jan-Philip Gehrcke (Mon Dec 10 2012 - 02:31:13 PST)
[AMBER] forcefield for PLP
- Bala Subramani (Sat Dec 01 2012 - 01:07:49 PST)
[AMBER] Fwd: difference between GLYCAM_06 and GLYCAM_06h
- Subrata Paul (Wed Dec 26 2012 - 05:01:15 PST)
[AMBER] Fwd: FF99CHI and Modified nucleoside parameter combination
- Indrajit Deb (Mon Dec 17 2012 - 23:48:53 PST)
- Ilyas Yildirim (Mon Dec 17 2012 - 15:18:33 PST)
- Indrajit Deb (Mon Dec 17 2012 - 14:57:36 PST)
- Indrajit Deb (Mon Dec 17 2012 - 13:40:12 PST)
- Indrajit Deb (Mon Dec 17 2012 - 13:27:12 PST)
- Ilyas Yildirim (Mon Dec 17 2012 - 13:04:21 PST)
- Ilyas Yildirim (Mon Dec 17 2012 - 13:00:31 PST)
- Indrajit Deb (Mon Dec 17 2012 - 12:58:52 PST)
- Ilyas Yildirim (Mon Dec 17 2012 - 12:57:59 PST)
- Indrajit Deb (Mon Dec 17 2012 - 12:45:45 PST)
- Indrajit Deb (Mon Dec 17 2012 - 12:32:21 PST)
[AMBER] Fwd: Fwd: FF99CHI and Modified nucleoside parameter combination
- Indrajit Deb (Thu Dec 20 2012 - 12:04:24 PST)
- Ilyas Yildirim (Tue Dec 18 2012 - 05:37:41 PST)
- Indrajit Deb (Tue Dec 18 2012 - 04:49:27 PST)
[AMBER] Fwd: pbsa forces printout from sander (amber12)
- Ray Luo, Ph.D. (Mon Dec 03 2012 - 09:53:31 PST)
[AMBER] GAFF atom types for the headgroup of the LDAO surfactant
- FyD (Wed Dec 12 2012 - 21:35:57 PST)
- ABEL Stephane 175950 (Mon Dec 10 2012 - 08:43:17 PST)
[AMBER] Getting error messages during testing the installation.
- David A Case (Mon Dec 10 2012 - 05:39:55 PST)
- Sanjib Paul (Sun Dec 09 2012 - 21:13:29 PST)
- case (Sat Dec 08 2012 - 05:17:35 PST)
- Sanjib Paul (Sat Dec 08 2012 - 03:14:43 PST)
- Jason Swails (Fri Dec 07 2012 - 05:58:49 PST)
- Sanjib Paul (Fri Dec 07 2012 - 05:00:08 PST)
[AMBER] getting warning when loading PDB created in amber9 in amber12 ..
- Vijay Manickam Achari (Tue Dec 18 2012 - 08:47:23 PST)
[AMBER] GLYCAM_06 & GLYCAM_06h
- Lachele Foley (Lists) (Thu Dec 27 2012 - 08:48:37 PST)
- Subrata Paul (Thu Dec 27 2012 - 03:03:22 PST)
- Lachele Foley (Lists) (Wed Dec 26 2012 - 23:23:33 PST)
- Subrata Paul (Wed Dec 26 2012 - 22:10:41 PST)
[AMBER] glycam_06h atom types
- Lachele Foley (Lists) (Fri Dec 14 2012 - 12:58:53 PST)
- Urszula Uciechowska (Fri Dec 14 2012 - 12:18:23 PST)
- Lachele Foley (Lists) (Fri Dec 14 2012 - 11:09:49 PST)
- Urszula Uciechowska (Fri Dec 14 2012 - 09:54:11 PST)
- Lachele Foley (Lists) (Fri Dec 14 2012 - 09:35:59 PST)
- Urszula Uciechowska (Fri Dec 14 2012 - 09:03:58 PST)
- Urszula Uciechowska (Fri Dec 14 2012 - 08:14:54 PST)
[AMBER] H-REMD, pmemd fails to calculate potential energy of neighbor coordinates
- Jiri Wiesner (Sun Dec 16 2012 - 15:06:27 PST)
- Jason Swails (Sun Dec 16 2012 - 07:20:39 PST)
- Jiri Wiesner (Sat Dec 15 2012 - 20:26:41 PST)
[AMBER] Higher values for polar contribution
- Jason Swails (Sat Dec 15 2012 - 05:12:58 PST)
- RANAJIT SHINDE (Sat Dec 15 2012 - 04:23:01 PST)
[AMBER] how to define head and tail for several residues?
- FyD (Thu Dec 20 2012 - 02:31:34 PST)
- osalo.abo.fi (Thu Dec 20 2012 - 01:58:36 PST)
[AMBER] how to define solvated box dimensions
- Thomas Evangelidis (Mon Dec 17 2012 - 06:54:26 PST)
- David A Case (Mon Dec 17 2012 - 05:33:14 PST)
- Thomas Evangelidis (Mon Dec 17 2012 - 02:46:34 PST)
- Thomas Evangelidis (Fri Dec 14 2012 - 15:02:00 PST)
[AMBER] How to disable Coulomb interactions between two group of atoms
- Shenglong Wang (Wed Dec 19 2012 - 06:13:59 PST)
- David A Case (Wed Dec 19 2012 - 04:56:05 PST)
- Shenglong Wang (Tue Dec 18 2012 - 11:24:46 PST)
- David A Case (Tue Dec 18 2012 - 11:13:41 PST)
- Shenglong Wang (Tue Dec 18 2012 - 06:43:04 PST)
[AMBER] How to Run MD of Glycol Nucleic Acid (GNA)
- FyD (Wed Dec 12 2012 - 22:19:23 PST)
- FyD (Wed Dec 12 2012 - 21:47:54 PST)
- ros (Fri Dec 07 2012 - 08:37:36 PST)
- Mu Xia (Thu Dec 06 2012 - 17:01:04 PST)
- FyD (Thu Dec 06 2012 - 09:37:16 PST)
- Mu Xia (Thu Dec 06 2012 - 01:02:07 PST)
[AMBER] how to speed up implicit solvent simulation with infinite cutoff
- Hai Nguyen (Mon Dec 10 2012 - 14:01:59 PST)
- case (Sat Dec 08 2012 - 18:59:45 PST)
- Jason Swails (Sat Dec 08 2012 - 14:50:57 PST)
- Thomas Evangelidis (Sat Dec 08 2012 - 08:17:40 PST)
[AMBER] how to use cpptraj in AMBER10 or 11 to generate new topology file
- HM (Mon Dec 24 2012 - 13:52:53 PST)
- Daniel Roe (Fri Dec 21 2012 - 05:24:28 PST)
- HM (Fri Dec 21 2012 - 02:06:09 PST)
- Daniel Roe (Thu Dec 20 2012 - 06:49:11 PST)
- HM (Thu Dec 20 2012 - 06:36:07 PST)
[AMBER] iapbs installation
- Miguel Ortiz Lombardía (Fri Dec 07 2012 - 01:39:12 PST)
- Miguel Ortiz Lombardía (Tue Dec 04 2012 - 01:52:17 PST)
[AMBER] If scee is no longer in Amber11, can I simply remove it?
- Amparo Garcia Lopez (Wed Dec 12 2012 - 05:12:20 PST)
- David A Case (Wed Dec 12 2012 - 05:00:54 PST)
- Jason Swails (Wed Dec 12 2012 - 04:52:26 PST)
- Amparo Garcia Lopez (Wed Dec 12 2012 - 03:19:38 PST)
[AMBER] imaging issues during RMSF
- Daniel Roe (Wed Dec 12 2012 - 10:56:49 PST)
- Sangeetha B (Thu Dec 06 2012 - 04:05:03 PST)
- Daniel Roe (Wed Dec 05 2012 - 13:48:58 PST)
[AMBER] Is GTX580/GTX680 compatible with the sever motherboards?
- Ross Walker (Sat Dec 29 2012 - 11:39:36 PST)
- Mu Xia (Sat Dec 29 2012 - 05:04:05 PST)
- Scott Le Grand (Fri Dec 28 2012 - 12:21:01 PST)
- Jason Swails (Fri Dec 28 2012 - 09:03:28 PST)
- Mu Xia (Thu Dec 27 2012 - 22:54:11 PST)
[AMBER] Ligand parameterization in AMOEBA to use in AMBER
- Jagur Lambix (Fri Dec 14 2012 - 08:32:24 PST)
- case (Thu Dec 13 2012 - 18:35:32 PST)
- Jagur Lambix (Thu Dec 13 2012 - 14:29:04 PST)
[AMBER] lmod error with large number of degrees of freedom
- David A Case (Tue Dec 18 2012 - 05:19:50 PST)
- Wong, Sergio E. (Mon Dec 17 2012 - 16:04:17 PST)
[AMBER] Lys-bound retinal parameters?
- FyD (Wed Dec 12 2012 - 22:08:19 PST)
- Scarlett Dong (Mon Dec 10 2012 - 03:59:25 PST)
- FyD (Mon Dec 03 2012 - 21:17:54 PST)
- Scarlett Dong (Mon Dec 03 2012 - 15:31:07 PST)
[AMBER] MD Average pdb
- Jonathan Gough (Fri Dec 21 2012 - 11:46:24 PST)
- Jason Swails (Fri Dec 21 2012 - 10:24:32 PST)
- Aron Broom (Fri Dec 21 2012 - 07:48:23 PST)
- edu troche (Fri Dec 21 2012 - 04:26:11 PST)
[AMBER] MD simulation
- Kshatresh Dutta Dubey (Fri Dec 28 2012 - 11:25:11 PST)
- Jeremy AHHH (Fri Dec 28 2012 - 10:28:10 PST)
[AMBER] MMGBSA result difference from whether use &decomp or not
- Liu Denis (Tue Dec 11 2012 - 16:54:36 PST)
- Jason Swails (Tue Dec 11 2012 - 05:03:08 PST)
- Liu Denis (Tue Dec 11 2012 - 00:49:06 PST)
[AMBER] MMPBSA - GB is negative, but PB is positive? what am I missing?
- Jonathan Gough (Thu Dec 20 2012 - 12:18:25 PST)
- Ray Luo, Ph.D. (Thu Dec 20 2012 - 12:10:05 PST)
- Jonathan Gough (Thu Dec 20 2012 - 11:54:12 PST)
- Ray Luo, Ph.D. (Thu Dec 20 2012 - 11:05:52 PST)
- Jonathan Gough (Thu Dec 20 2012 - 10:58:42 PST)
- Jason Swails (Wed Dec 19 2012 - 09:40:28 PST)
- Jonathan Gough (Wed Dec 19 2012 - 08:20:32 PST)
[AMBER] MMPBSA Alanine Scanning AttrubuteError
- Jason Swails (Sat Dec 29 2012 - 11:56:54 PST)
- BERGY (Sat Dec 29 2012 - 00:18:26 PST)
- Jason Swails (Fri Dec 28 2012 - 08:51:41 PST)
- BERGY (Thu Dec 27 2012 - 21:26:42 PST)
- Jason Swails (Thu Dec 27 2012 - 16:24:17 PST)
- BERGY (Thu Dec 27 2012 - 04:12:31 PST)
[AMBER] MMPBSA.py fails with sander.APBS
- Miguel Ortiz Lombardía (Fri Dec 07 2012 - 05:24:52 PST)
[AMBER] MMPBSA.py.MPI import error
- Jason Swails (Thu Dec 13 2012 - 05:02:25 PST)
- marawan hussain (Wed Dec 12 2012 - 18:08:42 PST)
- Jason Swails (Wed Dec 12 2012 - 04:49:36 PST)
- marawan hussain (Wed Dec 12 2012 - 00:14:23 PST)
[AMBER] MMPBSA.py.MPI: multiple trajectory mmPBSA question
- Aron Broom (Wed Dec 12 2012 - 11:24:02 PST)
- psu4.uic.edu (Wed Dec 12 2012 - 10:00:14 PST)
[AMBER] movement of PBC
- Jason Swails (Wed Dec 26 2012 - 04:58:31 PST)
- Vijay Manickam Achari (Tue Dec 25 2012 - 22:12:02 PST)
[AMBER] N-Methylacetamide-molecule-force field
- FyD (Wed Dec 26 2012 - 07:40:37 PST)
- David A Case (Wed Dec 26 2012 - 05:42:59 PST)
- Subrata Paul (Wed Dec 26 2012 - 04:51:01 PST)
[AMBER] NAB nmode memory requirements
- Jason Swails (Mon Dec 10 2012 - 11:51:13 PST)
- David A Case (Mon Dec 10 2012 - 11:14:15 PST)
- Ryan Pavlovicz (Mon Dec 10 2012 - 09:43:19 PST)
[AMBER] need assistance to generate forcefield for Pyridoxal phosphate
- case (Mon Dec 03 2012 - 04:44:07 PST)
- BALA SUBRAMANI G L (Mon Dec 03 2012 - 04:03:31 PST)
[AMBER] NMR Order Parameter Restraints
- Brown, Kyle (Thu Dec 20 2012 - 13:38:50 PST)
- case (Thu Dec 20 2012 - 06:39:58 PST)
- Brown, Kyle (Wed Dec 05 2012 - 08:52:22 PST)
[AMBER] NPT and NVE Energy
- Jason Swails (Sun Dec 30 2012 - 08:34:08 PST)
- David A Case (Sun Dec 30 2012 - 06:19:24 PST)
- Ismail, Mohd F. (Sun Dec 30 2012 - 01:28:00 PST)
- Ismail, Mohd F. (Sun Dec 30 2012 - 01:19:40 PST)
- Andreas Goetz (Fri Dec 28 2012 - 16:28:33 PST)
- Dr. Vitaly Chaban (Fri Dec 28 2012 - 13:50:37 PST)
- Ismail, Mohd F. (Fri Dec 28 2012 - 13:06:43 PST)
[AMBER] nvidia driver installation problem
- Fenley, Andrew (Fri Dec 07 2012 - 15:30:28 PST)
- Andreas Goetz (Fri Dec 07 2012 - 12:14:15 PST)
- Jason Swails (Fri Dec 07 2012 - 04:26:48 PST)
- Sanjib Paul (Thu Dec 06 2012 - 22:30:54 PST)
[AMBER] Pairwise interaction energy between resiudes using MMPBSA.py in Amber 11
- Aron Broom (Sat Dec 08 2012 - 23:51:14 PST)
- dbaogen (Sat Dec 08 2012 - 22:08:39 PST)
[AMBER] Patching Error occurred while Bugfixing
- Anogna (Wed Dec 05 2012 - 07:50:32 PST)
- Jason Swails (Wed Dec 05 2012 - 06:49:19 PST)
- Anogna (Tue Dec 04 2012 - 23:23:14 PST)
[AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 14 CB 2C
- BERGY (Thu Dec 27 2012 - 03:55:00 PST)
- Jason Swails (Mon Dec 03 2012 - 11:55:06 PST)
- Rahul Banerjee (Mon Dec 03 2012 - 11:40:52 PST)
[AMBER] PBC value become small at Z direction
- Vijay Manickam Achari (Sun Dec 23 2012 - 21:29:02 PST)
[AMBER] pbsa forces printout from sander (amber12)
- Dr. Holger Kruse (Fri Dec 07 2012 - 01:07:27 PST)
- Qin Cai (Mon Dec 03 2012 - 15:01:13 PST)
- Dr. Holger Kruse (Mon Dec 03 2012 - 07:08:34 PST)
[AMBER] Porcupine_Plots_Script
- monica.imtech.res.in (Sun Dec 02 2012 - 20:30:13 PST)
[AMBER] PostDoc molecular modeling of enzymes
- Jan Brezovsky (Mon Dec 03 2012 - 05:17:17 PST)
[AMBER] prmtop file
- Jason Swails (Tue Dec 11 2012 - 05:13:26 PST)
- Chandrasekaran, Suryanarayanan (Tue Dec 11 2012 - 02:01:51 PST)
- Chandrasekaran, Suryanarayanan (Mon Dec 10 2012 - 16:35:56 PST)
- Bill Miller III (Mon Dec 10 2012 - 04:26:46 PST)
- Chandrasekaran, Suryanarayanan (Mon Dec 10 2012 - 04:04:46 PST)
[AMBER] problem in applying patches in AMBER12 and AMBERTools12
- Prabu Manoharan (Sun Dec 23 2012 - 23:56:12 PST)
- case (Thu Dec 20 2012 - 06:24:43 PST)
- Prabu Manoharan (Thu Dec 20 2012 - 03:02:06 PST)
[AMBER] problem in loading pdb in xleap
- Jason Swails (Sat Dec 01 2012 - 06:35:14 PST)
[AMBER] Problem in Nmode entropy calculation
- Jason Swails (Mon Dec 10 2012 - 08:33:41 PST)
- Mu Xia (Mon Dec 10 2012 - 08:02:52 PST)
[AMBER] problem in solvation of binding pocket
- Daniel Sindhikara (Tue Dec 04 2012 - 14:25:49 PST)
- Chris Chris (Tue Dec 04 2012 - 09:00:34 PST)
- Zhenquan Hu (Tue Dec 04 2012 - 08:42:31 PST)
[AMBER] problem related to the amber9 installation
- Sindrila Dutta banik (Mon Dec 17 2012 - 21:21:48 PST)
- David A Case (Mon Dec 17 2012 - 05:37:57 PST)
- Sindrila Dutta banik (Mon Dec 17 2012 - 05:23:37 PST)
- Vijay Manickam Achari (Mon Dec 17 2012 - 05:04:14 PST)
- Sindrila Dutta banik (Mon Dec 17 2012 - 04:11:11 PST)
- Sindrila Dutta banik (Mon Dec 17 2012 - 04:06:57 PST)
[AMBER] problem to install amber9 in a cluster.
- Jason Swails (Mon Dec 17 2012 - 06:01:29 PST)
- Sindrila Dutta banik (Mon Dec 17 2012 - 03:39:35 PST)
[AMBER] Problem while running MMPBSA - stuck
- Ray Luo, Ph.D. (Mon Dec 03 2012 - 15:18:28 PST)
- Jonathan Gough (Mon Dec 03 2012 - 15:13:08 PST)
[AMBER] problem with closest in cpptraj: trajout still writes all solvent molecules
- Marc van der Kamp (Wed Dec 05 2012 - 13:48:41 PST)
- Daniel Roe (Wed Dec 05 2012 - 12:52:52 PST)
- Marc van der Kamp (Wed Dec 05 2012 - 12:22:16 PST)
[AMBER] problem with cpptraj hbond action
- Marek Maly (Sun Dec 02 2012 - 04:05:04 PST)
- Daniel Roe (Sat Dec 01 2012 - 21:12:02 PST)
- Marek Maly (Sat Dec 01 2012 - 17:12:22 PST)
[AMBER] problem with imposing planarity to a N3P3 ring
- Giovanni Pavan (Fri Dec 07 2012 - 10:36:08 PST)
[AMBER] Problem with molecule containing sulfonic acid substitution
- David A Case (Mon Dec 10 2012 - 05:56:02 PST)
- Bernhard Poll (Mon Dec 10 2012 - 02:32:27 PST)
[AMBER] problem with parallel installation of amber12 - MPI_COMM_WORLD
- Jason Swails (Tue Dec 25 2012 - 17:58:04 PST)
- Amparo Garcia Lopez (Tue Dec 25 2012 - 14:41:55 PST)
- David A Case (Mon Dec 24 2012 - 21:37:47 PST)
- Amparo Garcia Lopez (Mon Dec 24 2012 - 08:58:01 PST)
- David A Case (Mon Dec 24 2012 - 06:28:12 PST)
- Amparo Garcia Lopez (Mon Dec 24 2012 - 05:50:32 PST)
[AMBER] Problems with restart file - coordinates values are too high
- Jason Swails (Sun Dec 16 2012 - 06:53:39 PST)
- tommaso.casalini.mail.polimi.it (Sun Dec 16 2012 - 04:53:51 PST)
[AMBER] ptraj centering problem
- Daniel Roe (Wed Dec 05 2012 - 07:01:57 PST)
- Jason Swails (Wed Dec 05 2012 - 06:49:59 PST)
- Hirdesh Kumar (Wed Dec 05 2012 - 05:53:45 PST)
- Fabian Glaser (Tue Dec 04 2012 - 23:27:48 PST)
- Daniel Roe (Tue Dec 04 2012 - 09:00:05 PST)
- Fabian Glaser (Tue Dec 04 2012 - 07:56:59 PST)
[AMBER] ptraj vs cpptraj: optimal clusters number choice
- adarm.nencki.gov.pl (Mon Dec 10 2012 - 16:03:48 PST)
[AMBER] QM/MM AMBER-ORCA repulsion
- marawan hussain (Tue Dec 18 2012 - 14:39:11 PST)
- Andreas Goetz (Tue Dec 18 2012 - 12:11:04 PST)
- marawan hussain (Sat Dec 15 2012 - 21:16:14 PST)
- Andreas Goetz (Fri Dec 14 2012 - 01:29:39 PST)
- marawan hussain (Thu Dec 13 2012 - 19:47:45 PST)
- Andreas Goetz (Thu Dec 13 2012 - 11:28:47 PST)
- marawan hussain (Wed Dec 12 2012 - 22:07:31 PST)
[AMBER] query regarding two different restrain on protein residues
- HM (Mon Dec 24 2012 - 13:57:14 PST)
[AMBER] question about adaptive QM/MM
- Andreas Goetz (Sat Dec 29 2012 - 22:26:33 PST)
- yeqing2.ustc.edu.cn (Sat Dec 29 2012 - 00:29:47 PST)
[AMBER] Question in umbrella sampling
- Aron Broom (Mon Dec 31 2012 - 14:54:46 PST)
- Aron Broom (Mon Dec 31 2012 - 14:53:30 PST)
- Sajeewa Pemasinghe (Sat Dec 29 2012 - 17:53:51 PST)
- Aron Broom (Sat Dec 29 2012 - 14:36:35 PST)
- Sajeewa Pemasinghe (Fri Dec 28 2012 - 07:16:14 PST)
- Daniel Sindhikara (Fri Dec 28 2012 - 06:37:37 PST)
- Sajeewa Pemasinghe (Fri Dec 28 2012 - 06:08:39 PST)
[AMBER] Questions regarding mmpbsa...
- Jonathan Gough (Mon Dec 03 2012 - 13:45:17 PST)
- Jason Swails (Mon Dec 03 2012 - 13:08:25 PST)
- Jonathan Gough (Mon Dec 03 2012 - 12:29:15 PST)
[AMBER] restart file ERROR: I could not understand line 71821
- Thomas Evangelidis (Tue Dec 25 2012 - 03:00:04 PST)
[AMBER] rmsd of trajectories with different no. of residues in same protein?
- Vaibhav Dixit (Tue Dec 04 2012 - 19:15:46 PST)
- Daniel Roe (Tue Dec 04 2012 - 14:08:47 PST)
- Vaibhav Dixit (Tue Dec 04 2012 - 09:30:52 PST)
- Vaibhav Dixit (Tue Dec 04 2012 - 09:17:23 PST)
- Daniel Roe (Tue Dec 04 2012 - 09:12:11 PST)
- Vaibhav Dixit (Mon Dec 03 2012 - 08:56:14 PST)
- Jason Swails (Mon Dec 03 2012 - 06:53:05 PST)
- Vaibhav Dixit (Mon Dec 03 2012 - 06:25:35 PST)
- monica.imtech.res.in (Mon Dec 03 2012 - 04:32:17 PST)
- Vaibhav Dixit (Mon Dec 03 2012 - 03:16:28 PST)
[AMBER] RMSD reported in lmod output
- Daniel Roe (Wed Dec 12 2012 - 10:30:08 PST)
- Wong, Sergio E. (Tue Dec 11 2012 - 11:37:43 PST)
[AMBER] sander.MPI
- Jason Swails (Wed Dec 19 2012 - 09:11:13 PST)
- Fabian Glaser (Wed Dec 19 2012 - 05:10:54 PST)
- Fabian Glaser (Wed Dec 19 2012 - 04:53:33 PST)
- David A Case (Tue Dec 18 2012 - 06:18:21 PST)
- Jason Swails (Tue Dec 18 2012 - 03:53:18 PST)
- Fabian Glaser (Tue Dec 18 2012 - 03:21:05 PST)
- Fabian Glaser (Tue Dec 18 2012 - 01:20:57 PST)
- Jason Swails (Mon Dec 17 2012 - 05:44:39 PST)
- Fabian Glaser (Sun Dec 16 2012 - 22:38:52 PST)
- Jason Swails (Sun Dec 16 2012 - 06:48:36 PST)
- Fabian Glaser (Sat Dec 15 2012 - 23:21:35 PST)
- Fabian Glaser (Sun Dec 02 2012 - 04:59:58 PST)
[AMBER] Should I optimize the structure before obtaining the RESP charges?
- FyD (Wed Dec 12 2012 - 22:01:15 PST)
- Mu Xia (Mon Dec 10 2012 - 01:13:43 PST)
[AMBER] solvent accessible volume vs
- Nihal Korkmaz (Tue Dec 25 2012 - 01:56:54 PST)
- Daniel Roe (Wed Dec 12 2012 - 10:50:44 PST)
- Nihal Korkmaz (Sun Dec 09 2012 - 20:08:14 PST)
[AMBER] some problems in getting the parameters of GLYCAM in Leap
- Lachele Foley (Lists) (Wed Dec 19 2012 - 11:00:51 PST)
- FyD (Wed Dec 19 2012 - 08:10:16 PST)
- 曾晓骏 (Wed Dec 19 2012 - 02:20:33 PST)
- Lachele Foley (Lists) (Mon Dec 17 2012 - 09:54:44 PST)
- David A Case (Mon Dec 17 2012 - 05:16:35 PST)
- deathsnake1991 (Sun Dec 16 2012 - 22:48:21 PST)
[AMBER] Starting Coordinates Switched?
- Aron Broom (Tue Dec 11 2012 - 19:38:50 PST)
- Ismail, Mohd F. (Tue Dec 11 2012 - 14:42:05 PST)
[AMBER] Steered Molecular Dynamics: Question
- George Tzotzos (Fri Dec 14 2012 - 11:11:15 PST)
- Jan-Philip Gehrcke (Fri Dec 14 2012 - 09:16:37 PST)
- George Tzotzos (Thu Dec 13 2012 - 07:17:46 PST)
- Adrian Roitberg (Thu Dec 13 2012 - 06:45:37 PST)
- Jason Swails (Thu Dec 13 2012 - 06:41:37 PST)
- Dr. Vitaly Chaban (Thu Dec 13 2012 - 05:59:22 PST)
- George Tzotzos (Thu Dec 13 2012 - 05:54:59 PST)
- Jason Swails (Thu Dec 13 2012 - 05:01:08 PST)
- George Tzotzos (Thu Dec 13 2012 - 04:49:56 PST)
- Dr. Vitaly Chaban (Thu Dec 13 2012 - 04:20:27 PST)
- George Tzotzos (Thu Dec 13 2012 - 03:35:31 PST)
[AMBER] stripping water molecules except few ones (384-408)
- HM (Mon Dec 24 2012 - 13:51:04 PST)
- Daniel Roe (Fri Dec 21 2012 - 05:27:21 PST)
- HM (Fri Dec 21 2012 - 02:19:37 PST)
[AMBER] The differences of MMPBSA calculations between AT1.5and AT12, especially in PBSA solvation model.
- Ray Luo, Ph.D. (Mon Dec 03 2012 - 12:34:43 PST)
[AMBER] Theoretical question about mmpbsa/docking energy values
- Aron Broom (Sat Dec 15 2012 - 14:22:23 PST)
- Chris Chris (Sat Dec 15 2012 - 13:21:44 PST)
[AMBER] TI-charge removal step
- steinbrt.rci.rutgers.edu (Sun Dec 30 2012 - 05:34:05 PST)
- Nihal Korkmaz (Sat Dec 29 2012 - 21:18:14 PST)
- steinbrt.rci.rutgers.edu (Sat Dec 29 2012 - 04:59:19 PST)
- Nihal Korkmaz (Fri Dec 28 2012 - 15:46:46 PST)
[AMBER] using D-amino acids
- Thomas Evangelidis (Fri Dec 07 2012 - 08:01:29 PST)
- case (Sun Dec 02 2012 - 18:16:06 PST)
- Thomas Evangelidis (Sun Dec 02 2012 - 14:59:25 PST)
[AMBER] voltage for membrane?
- Albert (Sun Dec 23 2012 - 01:30:46 PST)
[AMBER] water box of specific dimensions
- Manikanthan Bhavaraju (Wed Dec 19 2012 - 18:58:01 PST)
[AMBER] What are Inner Sp2 carbons and non-pure aromatic systems?
- Yun Shi (Mon Dec 03 2012 - 10:53:17 PST)
[AMBER] where is .in file for AMBER GAFF lipids?
- Albert (Sun Dec 09 2012 - 06:18:06 PST)
[AMBER] why removal of terminal phosphate group is required?
- FyD (Tue Dec 18 2012 - 22:43:59 PST)
- David A Case (Mon Dec 17 2012 - 05:13:42 PST)
- Asmita Gupta (Sun Dec 16 2012 - 22:22:39 PST)
EGB discrepancy between sander and pmemd
- Eng H Yap (Wed Dec 05 2012 - 12:41:24 PST)
- Duke, Robert E Jr (Wed Dec 05 2012 - 12:22:58 PST)
- Jason Swails (Wed Dec 05 2012 - 10:12:33 PST)
- Eng H Yap (Wed Dec 05 2012 - 08:56:30 PST)
problem in solvation of binding pocket
- zhenquan hu (Tue Dec 04 2012 - 15:58:35 PST)

Amber Archive Dec 2012 by subject