Amber Archive Jun 2013: by subject

[AMBER] "vlimit exceeded for step" for constant surface tension simulation
- Wei Lin (Thu Jun 20 2013 - 18:09:32 PDT)
[AMBER] A and Z-DNA
- Collins Nganou (Thu Jun 20 2013 - 05:10:46 PDT)
- Vlad Cojocaru (Wed Jun 19 2013 - 15:49:54 PDT)
- Collins Nganou (Wed Jun 19 2013 - 06:10:04 PDT)
- arnab bhattacharya (Wed Jun 19 2013 - 05:55:40 PDT)
- Collins Nganou (Wed Jun 19 2013 - 05:51:48 PDT)
- David A Case (Tue Jun 18 2013 - 08:08:21 PDT)
- arnab bhattacharya (Tue Jun 18 2013 - 06:34:31 PDT)
[AMBER] Access to Quanta or CHARMM software
- Manikanthan Bhavaraju (Wed Jun 19 2013 - 12:33:13 PDT)
[AMBER] Actual Intel Compiler Version Used
- Ismail, Mohd F. (Fri Jun 28 2013 - 00:37:23 PDT)
- Ismail, Mohd F. (Fri Jun 28 2013 - 00:34:23 PDT)
- David A Case (Tue Jun 25 2013 - 04:39:17 PDT)
- Daniel Roe (Mon Jun 24 2013 - 20:35:23 PDT)
- Ismail, Mohd F. (Mon Jun 24 2013 - 20:32:10 PDT)
- Ismail, Mohd F. (Mon Jun 24 2013 - 20:30:40 PDT)
- ET (Mon Jun 24 2013 - 20:18:07 PDT)
- Ismail, Mohd F. (Mon Jun 24 2013 - 17:28:35 PDT)
- Jan-Philip Gehrcke (Mon Jun 24 2013 - 02:43:03 PDT)
- Daniel Roe (Sun Jun 23 2013 - 20:10:56 PDT)
- Ismail, Mohd F. (Sun Jun 23 2013 - 18:47:33 PDT)
[AMBER] adding Mg2+ as Counter ion for MD simulations
- FyD (Fri Jun 21 2013 - 00:02:50 PDT)
- Pranjal Mahanta (Thu Jun 20 2013 - 11:34:30 PDT)
[AMBER] Amber 12 bugfix 18 ?
- Marek Maly (Sat Jun 01 2013 - 14:19:47 PDT)
- Jason Swails (Sat Jun 01 2013 - 14:24:33 PDT)
- Jason Swails (Sat Jun 01 2013 - 14:23:26 PDT)
- Marek Maly (Sat Jun 01 2013 - 13:26:32 PDT)
- ET (Sat Jun 01 2013 - 13:27:18 PDT)
- Marek Maly (Sat Jun 01 2013 - 11:22:53 PDT)
[AMBER] Amber compile, number of files
- Jason Swails (Tue Jun 18 2013 - 11:14:38 PDT)
- Hunter Brown (Tue Jun 18 2013 - 10:15:25 PDT)
[AMBER] Amber to Charmm
- Jason Swails (Thu Jun 13 2013 - 18:23:00 PDT)
- Manikanthan Bhavaraju (Thu Jun 13 2013 - 17:42:53 PDT)
[AMBER] Amber updater issues
- David A Case (Wed Jun 26 2013 - 04:20:05 PDT)
- eneas.usal.es (Tue Jun 25 2013 - 10:25:52 PDT)
- Jason Swails (Tue Jun 25 2013 - 10:18:40 PDT)
- eneas.usal.es (Tue Jun 25 2013 - 09:58:26 PDT)
- David A Case (Tue Jun 25 2013 - 09:29:01 PDT)
- Jason Swails (Tue Jun 25 2013 - 09:21:37 PDT)
- eneas.usal.es (Tue Jun 25 2013 - 09:04:22 PDT)
[AMBER] amber2accent perl script
- Manikanthan Bhavaraju (Thu Jun 13 2013 - 14:03:38 PDT)
- Jason Swails (Thu Jun 13 2013 - 13:56:18 PDT)
- Manikanthan Bhavaraju (Thu Jun 13 2013 - 10:59:09 PDT)
[AMBER] AmberTools 13 igb=8 CalcError: $AMBERHOME/bin/mmpbsa_py_energy failed with prmtop complex.top!
- psu4.uic.edu (Fri Jun 07 2013 - 17:14:13 PDT)
- Jason Swails (Wed Jun 05 2013 - 11:26:55 PDT)
- psu4.uic.edu (Wed Jun 05 2013 - 11:03:04 PDT)
- Jason Swails (Tue Jun 04 2013 - 17:34:26 PDT)
- Hai Nguyen (Tue Jun 04 2013 - 17:26:49 PDT)
- psu4.uic.edu (Tue Jun 04 2013 - 14:44:48 PDT)
[AMBER] Antechamber atom types and all_nuc94.in atom descriptions
- Kamali Sripathi (Thu Jun 27 2013 - 08:00:04 PDT)
- FyD (Thu Jun 27 2013 - 06:48:19 PDT)
- Kamali Sripathi (Wed Jun 26 2013 - 20:07:46 PDT)
- FyD (Wed Jun 26 2013 - 01:43:06 PDT)
- Kamali Sripathi (Tue Jun 25 2013 - 05:53:25 PDT)
- FyD (Tue Jun 25 2013 - 00:55:08 PDT)
- Kamali Sripathi (Mon Jun 24 2013 - 20:26:34 PDT)
- Kamali Sripathi (Mon Jun 24 2013 - 19:01:46 PDT)
- Kamali Sripathi (Sun Jun 23 2013 - 16:10:40 PDT)
- Kamali Sripathi (Sun Jun 23 2013 - 05:06:29 PDT)
- FyD (Wed Jun 19 2013 - 01:13:12 PDT)
- Kamali Sripathi (Tue Jun 18 2013 - 13:06:44 PDT)
- FyD (Tue Jun 18 2013 - 00:31:30 PDT)
- Kamali Sripathi (Sat Jun 15 2013 - 20:26:12 PDT)
[AMBER] Any tips on setting up a cluster to run amber?
- ET (Wed Jun 05 2013 - 14:32:53 PDT)
- Jan-Philip Gehrcke (Wed Jun 05 2013 - 02:55:00 PDT)
- Daniel Sindhikara (Wed Jun 05 2013 - 02:52:17 PDT)
- Josh Berryman (Wed Jun 05 2013 - 02:38:00 PDT)
[AMBER] Anyone running machines with Quad GPU setups
- ET (Mon Jun 24 2013 - 23:09:40 PDT)
- ET (Mon Jun 24 2013 - 22:56:41 PDT)
- Ross Walker (Mon Jun 24 2013 - 22:36:19 PDT)
- ET (Mon Jun 24 2013 - 22:29:20 PDT)
- ET (Mon Jun 24 2013 - 22:19:56 PDT)
- ET (Mon Jun 24 2013 - 20:06:40 PDT)
- Ross Walker (Mon Jun 24 2013 - 16:58:57 PDT)
- Kevin Hauser (Mon Jun 24 2013 - 16:40:03 PDT)
- ET (Mon Jun 24 2013 - 11:48:16 PDT)
- deeptinayar.gmail.com (Mon Jun 24 2013 - 19:44:54 PDT)
- Ross Walker (Sun Jun 23 2013 - 17:21:25 PDT)
- ET (Sat Jun 22 2013 - 22:36:41 PDT)
- Scott Le Grand (Sat Jun 22 2013 - 13:31:48 PDT)
- ET (Sat Jun 22 2013 - 13:26:04 PDT)
- Ross Walker (Sat Jun 22 2013 - 13:12:26 PDT)
- ET (Sat Jun 22 2013 - 12:45:20 PDT)
- Scott Le Grand (Sat Jun 22 2013 - 11:31:27 PDT)
- Divi/GMAIL (Sat Jun 22 2013 - 11:30:28 PDT)
- ET (Sat Jun 22 2013 - 10:40:25 PDT)
- Jan-Philip Gehrcke (Sat Jun 22 2013 - 10:36:25 PDT)
- Jan-Philip Gehrcke (Sat Jun 22 2013 - 10:29:18 PDT)
- ET (Sat Jun 22 2013 - 10:10:18 PDT)
- Jan-Philip Gehrcke (Sat Jun 22 2013 - 08:32:39 PDT)
- Scott Le Grand (Sat Jun 22 2013 - 08:15:08 PDT)
- Divi/GMAIL (Fri Jun 21 2013 - 16:07:44 PDT)
- ET (Fri Jun 21 2013 - 14:04:21 PDT)
- ET (Thu Jun 20 2013 - 17:18:59 PDT)
[AMBER] Assessing Antechamber temporary files
- Kamali Sripathi (Mon Jun 17 2013 - 05:03:11 PDT)
[AMBER] avgcoord in AT13
- Daniel Roe (Fri Jun 28 2013 - 13:31:17 PDT)
- Jason Swails (Fri Jun 28 2013 - 13:30:56 PDT)
- Hongyi WU (Fri Jun 28 2013 - 12:51:19 PDT)
[AMBER] bad atom type: N3 (In MMGBSA decomp calculations)
- Jason Swails (Thu Jun 13 2013 - 10:43:07 PDT)
- Jason Slingsby (Wed Jun 12 2013 - 15:38:29 PDT)
[AMBER] Binding energy
- steinbrt.rci.rutgers.edu (Thu Jun 27 2013 - 02:34:27 PDT)
- eneas.usal.es (Thu Jun 27 2013 - 01:26:37 PDT)
[AMBER] Building CUDA-enabled Amber11 (pmemd.cuda) * (Amber 11 only)
- David A Case (Fri Jun 14 2013 - 04:42:19 PDT)
- Changqing Yan (Fri Jun 14 2013 - 02:29:18 PDT)
[AMBER] by pmemd.cuda runs
- Cenk $Jenk$ Andac (Sat Jun 01 2013 - 03:09:38 PDT)
- Cenk $Jenk$ Andac (Sat Jun 01 2013 - 03:08:42 PDT)
- Cenk $Jenk$ Andac (Sat Jun 01 2013 - 03:05:31 PDT)
[AMBER] Calculating harmonic potential in umbrella sampling
- Sajeewa Pemasinghe (Mon Jun 10 2013 - 21:11:15 PDT)
- Jason Swails (Mon Jun 10 2013 - 20:14:59 PDT)
- Sajeewa Pemasinghe (Mon Jun 10 2013 - 11:25:31 PDT)
[AMBER] Calculating Hydrophobic Interaction
- ET (Mon Jun 24 2013 - 11:51:02 PDT)
- Ravi Tripathi (Fri Jun 21 2013 - 05:31:24 PDT)
[AMBER] Can RMSF be at least 2 times larger than RMSD?
- Yip Yew Mun (Sat Jun 15 2013 - 06:26:02 PDT)
- Daniel Roe (Fri Jun 14 2013 - 09:34:19 PDT)
- Carlos Simmerling (Fri Jun 14 2013 - 09:10:32 PDT)
- Yip Yew Mun (Fri Jun 14 2013 - 08:57:07 PDT)
[AMBER] Cannot find Sander in Amber13
- Michelle Mukonyora (Fri Jun 14 2013 - 04:47:33 PDT)
- David A Case (Fri Jun 14 2013 - 04:44:49 PDT)
- steinbrt.rci.rutgers.edu (Fri Jun 14 2013 - 04:06:32 PDT)
- Michelle Mukonyora (Fri Jun 14 2013 - 03:06:15 PDT)
[AMBER] Cellulose NVE with pmemd.cuda.MPI
- Nakashima, Yoshihisa (Wed Jun 19 2013 - 19:28:01 PDT)
- Scott Le Grand (Wed Jun 19 2013 - 10:07:31 PDT)
- Ross Walker (Wed Jun 19 2013 - 05:19:12 PDT)
- Nakashima, Yoshihisa (Mon Jun 17 2013 - 23:19:50 PDT)
[AMBER] counterions in md simulation
- Mary Varughese (Tue Jun 11 2013 - 02:03:13 PDT)
- Marc van der Kamp (Tue Jun 11 2013 - 01:42:44 PDT)
- Dr. Vitaly Chaban (Tue Jun 11 2013 - 01:40:27 PDT)
- Mary Varughese (Tue Jun 11 2013 - 01:27:45 PDT)
[AMBER] cpptraj diffusion ambertool13
- Daniel Roe (Fri Jun 07 2013 - 07:42:25 PDT)
- Asmita Gupta (Fri Jun 07 2013 - 05:04:49 PDT)
[AMBER] cpptraj grid water density
- Asmita Gupta (Sun Jun 16 2013 - 06:01:26 PDT)
[AMBER] cpptraj: can we retrieve the minimal distance between two sets of residues?
- Daniel Roe (Tue Jun 18 2013 - 08:22:14 PDT)
- Jan-Philip Gehrcke (Tue Jun 18 2013 - 06:56:46 PDT)
[AMBER] csh problem
- David A Case (Wed Jun 12 2013 - 18:43:14 PDT)
- Albert (Wed Jun 12 2013 - 10:44:08 PDT)
[AMBER] Cu+2 problem
- FyD (Mon Jun 03 2013 - 23:24:27 PDT)
- Francesco Pietra (Mon Jun 03 2013 - 08:22:49 PDT)
- ros (Mon Jun 03 2013 - 07:51:06 PDT)
- Fabian Glaser (Mon Jun 03 2013 - 04:40:21 PDT)
[AMBER] CUDA install fails due to undefined netcdf definitions
- Matthew Wampole (Fri Jun 14 2013 - 07:39:32 PDT)
- Jason Swails (Tue Jun 11 2013 - 13:38:42 PDT)
- Matthew Wampole (Tue Jun 11 2013 - 13:25:17 PDT)
- Daniel Roe (Thu Jun 06 2013 - 14:26:45 PDT)
- Matthew Wampole (Thu Jun 06 2013 - 14:12:10 PDT)
- Jason Swails (Thu Jun 06 2013 - 08:51:06 PDT)
- Matthew Wampole (Thu Jun 06 2013 - 08:28:29 PDT)
[AMBER] CUDA install fails on ubuntu 12.04 using GNU compiler
- ET (Mon Jun 03 2013 - 18:17:52 PDT)
- Ayesha Fatima (Mon Jun 03 2013 - 18:02:03 PDT)
- ET (Mon Jun 03 2013 - 14:26:42 PDT)
- ET (Mon Jun 03 2013 - 14:06:18 PDT)
- ET (Mon Jun 03 2013 - 13:49:03 PDT)
[AMBER] Cupper cluster parametrization with MCPB
- mmaestre.gate.sinica.edu.tw (Wed Jun 26 2013 - 19:41:11 PDT)
- mmaestre.gate.sinica.edu.tw (Wed Jun 26 2013 - 18:42:25 PDT)
[AMBER] Curious behavior of cpptraj in ambertools 13.1
- Jason Swails (Wed Jun 19 2013 - 19:45:18 PDT)
- Fabrício Bracht (Wed Jun 19 2013 - 19:18:39 PDT)
- Jason Swails (Wed Jun 19 2013 - 10:39:55 PDT)
- Daniel Roe (Wed Jun 19 2013 - 10:10:56 PDT)
- Fabrício Bracht (Wed Jun 19 2013 - 09:49:28 PDT)
[AMBER] Custom topology parameter usage
- FyD (Wed Jun 26 2013 - 01:48:20 PDT)
- Daniel Roe (Tue Jun 25 2013 - 21:37:48 PDT)
- Parker de Waal (Tue Jun 25 2013 - 21:18:39 PDT)
[AMBER] Cutoff smoothing
- George Tzotzos (Tue Jun 25 2013 - 09:41:41 PDT)
- tec3.utah.edu (Tue Jun 25 2013 - 09:31:21 PDT)
- George Tzotzos (Tue Jun 25 2013 - 09:17:24 PDT)
[AMBER] D amino acids
- Krisztina Feher (Tue Jun 18 2013 - 08:48:58 PDT)
- David A Case (Tue Jun 18 2013 - 08:19:58 PDT)
- Krisztina Feher (Tue Jun 18 2013 - 08:12:47 PDT)
- FyD (Tue Jun 18 2013 - 07:33:18 PDT)
- Krisztina Feher (Tue Jun 18 2013 - 07:11:47 PDT)
[AMBER] Difficulty compiling amber12/ambertools13
- Jason Swails (Mon Jun 17 2013 - 10:42:02 PDT)
- Jason Swails (Mon Jun 17 2013 - 09:48:45 PDT)
- Jason Swails (Mon Jun 17 2013 - 09:48:09 PDT)
- Daniel Roe (Mon Jun 17 2013 - 09:46:00 PDT)
- Hunter Brown (Mon Jun 17 2013 - 09:44:16 PDT)
- Daniel Roe (Mon Jun 17 2013 - 09:10:44 PDT)
- Jan-Philip Gehrcke (Mon Jun 17 2013 - 08:45:04 PDT)
- Hunter Brown (Mon Jun 17 2013 - 07:33:19 PDT)
- Jason Swails (Fri Jun 14 2013 - 17:49:36 PDT)
- Bill Ross (Fri Jun 14 2013 - 16:10:57 PDT)
- Hunter Brown (Fri Jun 14 2013 - 15:41:11 PDT)
[AMBER] Difficulty in reading .mdcrd file in VMD
- Jason Swails (Thu Jun 20 2013 - 04:23:58 PDT)
- Yan Duan (Mon Jun 17 2013 - 16:07:31 PDT)
[AMBER] Difficulty running sander
- Jason Swails (Wed Jun 19 2013 - 12:34:00 PDT)
- Hunter Brown (Wed Jun 19 2013 - 11:10:35 PDT)
[AMBER] enegy minimization with restrain
- Rasha Alqus (Tue Jun 04 2013 - 03:01:32 PDT)
[AMBER] energy analysis in amber
- Jason Swails (Fri Jun 28 2013 - 07:34:29 PDT)
- Asmita Gupta (Thu Jun 27 2013 - 23:11:08 PDT)
[AMBER] entropy calculation starts from where it stops
- psu4.uic.edu (Tue Jun 25 2013 - 13:00:23 PDT)
- Jason Swails (Tue Jun 25 2013 - 11:59:34 PDT)
- psu4.uic.edu (Tue Jun 25 2013 - 11:09:57 PDT)
- Jason Swails (Tue Jun 25 2013 - 10:47:16 PDT)
- psu4.uic.edu (Tue Jun 25 2013 - 10:34:15 PDT)
[AMBER] error energy minimization with restrain
- Jason Swails (Wed Jun 05 2013 - 12:23:19 PDT)
- Rasha Alqus (Wed Jun 05 2013 - 11:59:22 PDT)
[AMBER] Error in mm_pbsa
- Chinh Su Tran To (Tue Jun 11 2013 - 20:56:09 PDT)
- Jason Swails (Tue Jun 11 2013 - 05:38:37 PDT)
- Chinh Su Tran To (Tue Jun 11 2013 - 02:09:38 PDT)
[AMBER] error in running MMPBSA.MPI
- onetwo (Sun Jun 30 2013 - 07:50:28 PDT)
[AMBER] error of PBSA calculation
- Bill Miller III (Mon Jun 24 2013 - 05:11:34 PDT)
- Changqing Yan (Mon Jun 24 2013 - 01:03:45 PDT)
[AMBER] ERROR: GPU runs fail with nfft Error only when running 2x geforce TITANS in same machine
- ET (Thu Jun 20 2013 - 12:07:12 PDT)
- Scott Le Grand (Thu Jun 20 2013 - 12:02:23 PDT)
- ET (Thu Jun 20 2013 - 11:42:42 PDT)
- Ross Walker (Thu Jun 20 2013 - 09:37:06 PDT)
- Ross Walker (Thu Jun 20 2013 - 07:58:28 PDT)
- ET (Thu Jun 20 2013 - 07:56:37 PDT)
- Scott Le Grand (Wed Jun 19 2013 - 10:15:34 PDT)
- ET (Mon Jun 17 2013 - 22:24:17 PDT)
- ET (Mon Jun 17 2013 - 22:21:49 PDT)
[AMBER] errors compiling
- Jonathan Gough (Wed Jun 05 2013 - 12:30:10 PDT)
- Jason Swails (Wed Jun 05 2013 - 12:11:13 PDT)
- Jonathan Gough (Wed Jun 05 2013 - 12:03:28 PDT)
- Daniel Roe (Wed Jun 05 2013 - 11:47:25 PDT)
- Jonathan Gough (Wed Jun 05 2013 - 11:23:54 PDT)
[AMBER] example karplus.txt file for cpptraj jcoupling command
- Daniel Roe (Tue Jun 04 2013 - 12:21:41 PDT)
- Duggan, Brendan (Tue Jun 04 2013 - 11:42:49 PDT)
[AMBER] Experience with terachem and amber12
- Fabrício Bracht (Sat Jun 15 2013 - 21:49:50 PDT)
- Jason Swails (Sat Jun 15 2013 - 13:59:05 PDT)
- Fabrício Bracht (Fri Jun 14 2013 - 23:36:14 PDT)
[AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
- Ross Walker (Wed Jun 26 2013 - 16:02:48 PDT)
- Scott Le Grand (Wed Jun 26 2013 - 15:12:54 PDT)
- Jonathan Gough (Wed Jun 26 2013 - 14:22:38 PDT)
- Marek Maly (Thu Jun 20 2013 - 11:05:00 PDT)
- Ross Walker (Thu Jun 20 2013 - 10:36:25 PDT)
- Scott Le Grand (Thu Jun 20 2013 - 10:26:58 PDT)
- Marek Maly (Thu Jun 20 2013 - 09:57:09 PDT)
- Scott Le Grand (Thu Jun 20 2013 - 09:57:18 PDT)
- ET (Thu Jun 20 2013 - 09:51:27 PDT)
- Marek Maly (Thu Jun 20 2013 - 09:03:04 PDT)
- Scott Le Grand (Thu Jun 20 2013 - 08:25:05 PDT)
- Marek Maly (Thu Jun 20 2013 - 06:58:00 PDT)
- Ross Walker (Wed Jun 19 2013 - 19:25:07 PDT)
- Scott Le Grand (Wed Jun 19 2013 - 11:33:58 PDT)
- Scott Le Grand (Wed Jun 19 2013 - 11:29:50 PDT)
- Marek Maly (Wed Jun 19 2013 - 11:08:08 PDT)
- Marek Maly (Wed Jun 19 2013 - 10:55:46 PDT)
- Robert Konecny (Wed Jun 19 2013 - 11:12:02 PDT)
- Daniel Roe (Wed Jun 19 2013 - 10:50:35 PDT)
- Marek Maly (Wed Jun 19 2013 - 10:17:50 PDT)
- Scott Le Grand (Wed Jun 19 2013 - 10:23:31 PDT)
- Scott Le Grand (Wed Jun 19 2013 - 10:21:53 PDT)
- Marek Maly (Wed Jun 19 2013 - 10:00:59 PDT)
- Marek Maly (Wed Jun 19 2013 - 09:55:32 PDT)
- Scott Le Grand (Wed Jun 19 2013 - 10:03:18 PDT)
- Jonathan Gough (Wed Jun 19 2013 - 09:34:36 PDT)
- Scott Le Grand (Wed Jun 19 2013 - 08:50:51 PDT)
- Marek Maly (Wed Jun 19 2013 - 08:20:15 PDT)
- Marek Maly (Wed Jun 12 2013 - 11:16:46 PDT)
- Scott Le Grand (Wed Jun 12 2013 - 10:07:49 PDT)
- filip fratev (Tue Jun 11 2013 - 04:38:56 PDT)
- Marek Maly (Tue Jun 11 2013 - 03:23:29 PDT)
- Scott Le Grand (Mon Jun 10 2013 - 21:31:37 PDT)
- ET (Sun Jun 09 2013 - 08:22:58 PDT)
- Scott Le Grand (Fri Jun 07 2013 - 15:50:05 PDT)
- filip fratev (Fri Jun 07 2013 - 15:41:20 PDT)
- Jonathan Gough (Fri Jun 07 2013 - 15:11:48 PDT)
- Scott Le Grand (Fri Jun 07 2013 - 15:05:43 PDT)
- Jonathan Gough (Fri Jun 07 2013 - 14:40:53 PDT)
- Marek Maly (Fri Jun 07 2013 - 14:16:47 PDT)
- Scott Le Grand (Fri Jun 07 2013 - 14:32:57 PDT)
- Jonathan Gough (Fri Jun 07 2013 - 14:00:23 PDT)
- Scott Le Grand (Fri Jun 07 2013 - 13:46:42 PDT)
- Scott Le Grand (Fri Jun 07 2013 - 13:45:50 PDT)
- filip fratev (Fri Jun 07 2013 - 13:34:26 PDT)
- Jonathan Gough (Fri Jun 07 2013 - 12:48:36 PDT)
- Marek Maly (Thu Jun 06 2013 - 07:29:03 PDT)
- Marek Maly (Thu Jun 06 2013 - 07:27:28 PDT)
- Jonathan Gough (Thu Jun 06 2013 - 07:37:03 PDT)
- Scott Le Grand (Thu Jun 06 2013 - 07:23:30 PDT)
- Marek Maly (Thu Jun 06 2013 - 03:40:55 PDT)
- Jonathan Gough (Thu Jun 06 2013 - 03:01:35 PDT)
- Marek Maly (Wed Jun 05 2013 - 15:45:13 PDT)
- Jonathan Gough (Wed Jun 05 2013 - 15:34:39 PDT)
- Marek Maly (Wed Jun 05 2013 - 10:29:36 PDT)
- Scott Le Grand (Wed Jun 05 2013 - 09:15:48 PDT)
- Marek Maly (Wed Jun 05 2013 - 06:18:00 PDT)
- filip fratev (Wed Jun 05 2013 - 06:29:55 PDT)
- ET (Wed Jun 05 2013 - 06:25:33 PDT)
- filip fratev (Wed Jun 05 2013 - 05:23:41 PDT)
- Marek Maly (Wed Jun 05 2013 - 03:33:07 PDT)
- filip fratev (Wed Jun 05 2013 - 02:12:54 PDT)
- Marek Maly (Tue Jun 04 2013 - 15:20:35 PDT)
- Scott Le Grand (Tue Jun 04 2013 - 13:36:00 PDT)
- ET (Tue Jun 04 2013 - 06:23:37 PDT)
- Marek Maly (Tue Jun 04 2013 - 04:39:57 PDT)
- Jonathan Gough (Tue Jun 04 2013 - 04:54:09 PDT)
- Marek Maly (Mon Jun 03 2013 - 21:14:28 PDT)
- Scott Le Grand (Mon Jun 03 2013 - 19:51:08 PDT)
- ET (Mon Jun 03 2013 - 13:18:20 PDT)
- Marek Maly (Mon Jun 03 2013 - 12:31:03 PDT)
- Ross Walker (Mon Jun 03 2013 - 12:17:23 PDT)
- Marek Maly (Mon Jun 03 2013 - 11:47:36 PDT)
- Scott Le Grand (Mon Jun 03 2013 - 11:12:04 PDT)
- Marek Maly (Mon Jun 03 2013 - 09:42:24 PDT)
- Marek Maly (Mon Jun 03 2013 - 04:21:43 PDT)
- ET (Mon Jun 03 2013 - 04:31:09 PDT)
- Marek Maly (Mon Jun 03 2013 - 03:34:15 PDT)
- Marek Maly (Mon Jun 03 2013 - 03:31:08 PDT)
- ET (Mon Jun 03 2013 - 02:51:46 PDT)
- ET (Mon Jun 03 2013 - 02:28:39 PDT)
- Divi/GMAIL (Sun Jun 02 2013 - 17:38:00 PDT)
- Marek Maly (Sun Jun 02 2013 - 16:57:36 PDT)
- ET (Sun Jun 02 2013 - 16:20:27 PDT)
- ET (Sun Jun 02 2013 - 15:34:57 PDT)
- Scott Le Grand (Sun Jun 02 2013 - 12:49:41 PDT)
- ET (Sun Jun 02 2013 - 11:02:21 PDT)
- Marek Maly (Sun Jun 02 2013 - 10:37:15 PDT)
- ET (Sun Jun 02 2013 - 10:53:21 PDT)
- Marek Maly (Sun Jun 02 2013 - 10:22:54 PDT)
- Scott Le Grand (Sun Jun 02 2013 - 10:15:23 PDT)
- Marek Maly (Sun Jun 02 2013 - 09:44:23 PDT)
- Scott Le Grand (Sun Jun 02 2013 - 09:57:08 PDT)
- ET (Sun Jun 02 2013 - 09:49:00 PDT)
- Scott Le Grand (Sun Jun 02 2013 - 09:42:31 PDT)
- Scott Le Grand (Sun Jun 02 2013 - 09:33:52 PDT)
- Scott Le Grand (Sun Jun 02 2013 - 09:31:17 PDT)
- Scott Le Grand (Sun Jun 02 2013 - 09:07:14 PDT)
- Marek Maly (Sun Jun 02 2013 - 07:58:38 PDT)
- ET (Sun Jun 02 2013 - 06:29:49 PDT)
- Scott Le Grand (Sat Jun 01 2013 - 22:45:53 PDT)
- ET (Sat Jun 01 2013 - 20:29:35 PDT)
- Scott Le Grand (Sat Jun 01 2013 - 19:36:32 PDT)
- ET (Sat Jun 01 2013 - 18:45:05 PDT)
- ET (Sat Jun 01 2013 - 18:30:22 PDT)
- Marek Maly (Sat Jun 01 2013 - 16:49:47 PDT)
- Marek Maly (Sat Jun 01 2013 - 16:35:20 PDT)
- Marek Maly (Sat Jun 01 2013 - 16:30:43 PDT)
- Scott Le Grand (Sat Jun 01 2013 - 16:38:34 PDT)
- Scott Le Grand (Sat Jun 01 2013 - 16:25:44 PDT)
- Marek Maly (Sat Jun 01 2013 - 15:41:13 PDT)
- Scott Le Grand (Sat Jun 01 2013 - 15:28:45 PDT)
- ET (Sat Jun 01 2013 - 14:42:34 PDT)
- Marek Maly (Sat Jun 01 2013 - 14:13:07 PDT)
- ET (Sat Jun 01 2013 - 14:12:26 PDT)
- Marek Maly (Sat Jun 01 2013 - 13:32:15 PDT)
- ET (Sat Jun 01 2013 - 13:18:34 PDT)
- Marek Maly (Sat Jun 01 2013 - 12:34:17 PDT)
- Scott Le Grand (Sat Jun 01 2013 - 12:48:06 PDT)
- Marek Maly (Sat Jun 01 2013 - 12:26:42 PDT)
- Marek Maly (Sat Jun 01 2013 - 12:09:46 PDT)
- Scott Le Grand (Sat Jun 01 2013 - 12:20:49 PDT)
- Scott Le Grand (Sat Jun 01 2013 - 12:16:29 PDT)
- Jan-Philip Gehrcke (Sat Jun 01 2013 - 12:04:52 PDT)
- Scott Le Grand (Sat Jun 01 2013 - 11:48:12 PDT)
- Scott Le Grand (Sat Jun 01 2013 - 11:46:29 PDT)
- ET (Sat Jun 01 2013 - 11:26:16 PDT)
[AMBER] Experiences with GTX 780 in the framework of Amber calculations ?
- Gould, Ian R (Thu Jun 20 2013 - 07:05:55 PDT)
- ET (Thu Jun 20 2013 - 06:33:40 PDT)
- filip fratev (Wed Jun 19 2013 - 12:58:45 PDT)
- Marek Maly (Wed Jun 19 2013 - 12:14:29 PDT)
- Scott Le Grand (Wed Jun 19 2013 - 11:39:09 PDT)
- Gould, Ian R (Wed Jun 19 2013 - 11:35:31 PDT)
- Gould, Ian R (Wed Jun 19 2013 - 11:34:15 PDT)
- Marek Maly (Wed Jun 19 2013 - 10:35:58 PDT)
[AMBER] FATAL: Atom XXX does not have a type
- FyD (Fri Jun 28 2013 - 00:04:37 PDT)
- Karl N. Kirschner (Thu Jun 27 2013 - 23:28:02 PDT)
- sunyeping.aliyun.com (Thu Jun 27 2013 - 11:58:16 PDT)
[AMBER] Fluctuation of density during equilibration phase
- Jason Swails (Fri Jun 21 2013 - 20:16:27 PDT)
- Ibrahim Said (Fri Jun 21 2013 - 13:23:54 PDT)
[AMBER] Force-field for non-native peptide containing fluoride
- Alessandro Contini (Wed Jun 26 2013 - 08:56:39 PDT)
- Cheng-I Lee (Wed Jun 26 2013 - 08:19:20 PDT)
- Karl N. Kirschner (Wed Jun 26 2013 - 02:41:42 PDT)
- Cheng-I Lee (Wed Jun 26 2013 - 02:14:43 PDT)
[AMBER] Fwd: Cu+2 problem
- Francesco Pietra (Mon Jun 03 2013 - 08:25:17 PDT)
[AMBER] gaff atom type
- inhee park (Tue Jun 18 2013 - 12:39:26 PDT)
[AMBER] GAFF atom type for CO
- David A Case (Sun Jun 23 2013 - 18:28:10 PDT)
- Krisztina Feher (Sat Jun 22 2013 - 11:22:50 PDT)
- David A Case (Sat Jun 22 2013 - 09:59:22 PDT)
- Krisztina Feher (Sat Jun 22 2013 - 07:03:42 PDT)
- David A Case (Sat Jun 22 2013 - 05:48:39 PDT)
- FyD (Fri Jun 21 2013 - 09:18:16 PDT)
- Karl N. Kirschner (Fri Jun 21 2013 - 03:02:33 PDT)
- Krisztina Feher (Fri Jun 21 2013 - 02:51:56 PDT)
- Krisztina Feher (Fri Jun 21 2013 - 01:59:41 PDT)
- FyD (Thu Jun 20 2013 - 23:49:44 PDT)
- David A Case (Thu Jun 20 2013 - 13:55:19 PDT)
- Krisztina Feher (Thu Jun 20 2013 - 11:16:17 PDT)
[AMBER] glycame06_carbohydrate_hydrogen bond pattern
- Karl N. Kirschner (Thu Jun 13 2013 - 03:57:55 PDT)
- Rasha Alqus (Thu Jun 13 2013 - 02:26:22 PDT)
[AMBER] Graphene topology from GAFF
- Dan Piraner (Tue Jun 18 2013 - 17:05:27 PDT)
- Hector A. Baldoni (Tue Jun 18 2013 - 14:40:11 PDT)
- Dan Piraner (Tue Jun 18 2013 - 02:47:06 PDT)
- Karl N. Kirschner (Tue Jun 18 2013 - 01:17:45 PDT)
- FyD (Tue Jun 18 2013 - 00:20:52 PDT)
- David A Case (Mon Jun 17 2013 - 17:33:00 PDT)
- dpiraner.caltech.edu (Mon Jun 17 2013 - 11:48:48 PDT)
[AMBER] GTX780
- Ross Walker (Wed Jun 26 2013 - 20:19:01 PDT)
- Fabrício Bracht (Wed Jun 26 2013 - 19:33:32 PDT)
[AMBER] GTX780 News
- ET (Thu Jun 27 2013 - 13:43:59 PDT)
- Ross Walker (Thu Jun 27 2013 - 11:43:34 PDT)
- ET (Thu Jun 27 2013 - 12:15:45 PDT)
- Scott Le Grand (Thu Jun 27 2013 - 11:36:33 PDT)
- ET (Thu Jun 27 2013 - 11:20:22 PDT)
- Scott Le Grand (Thu Jun 27 2013 - 10:50:02 PDT)
- ET (Wed Jun 26 2013 - 19:13:41 PDT)
- Scott Le Grand (Wed Jun 26 2013 - 17:47:32 PDT)
- Ross Walker (Wed Jun 26 2013 - 16:31:26 PDT)
[AMBER] hbond in ptraj and cpptraj
- Daniel Roe (Mon Jun 03 2013 - 06:43:51 PDT)
- pmaj.nencki.gov.pl (Mon Jun 03 2013 - 05:19:39 PDT)
- pmaj.nencki.gov.pl (Mon Jun 03 2013 - 03:12:06 PDT)
[AMBER] help
- 徐俊 (Fri Jun 14 2013 - 03:56:57 PDT)
[AMBER] Help regarding Mn parameters
- Daniel Roe (Fri Jun 07 2013 - 14:02:29 PDT)
- Mallipeddi, Premalatha (Fri Jun 07 2013 - 11:07:30 PDT)
[AMBER] How can I calculate the individual PBSA energies of a large set
- Changqing Yan (Sun Jun 16 2013 - 17:41:01 PDT)
[AMBER] how does leap-prmtop calculate residues in water
- Jonathan Gough (Tue Jun 11 2013 - 13:45:29 PDT)
- Jason Swails (Tue Jun 11 2013 - 13:22:28 PDT)
- Jonathan Gough (Tue Jun 11 2013 - 13:13:05 PDT)
[AMBER] How to avoid tleap error *** Error: tl_getline(): not interactive, use stdio.
- Niel Henriksen (Mon Jun 10 2013 - 12:13:22 PDT)
- David A Case (Mon Jun 10 2013 - 11:53:37 PDT)
- kurisaki (Mon Jun 10 2013 - 06:20:20 PDT)
- ET (Mon Jun 10 2013 - 06:12:24 PDT)
- Jason Swails (Mon Jun 10 2013 - 06:06:19 PDT)
- kurisaki (Mon Jun 10 2013 - 05:15:04 PDT)
[AMBER] How to define reaction coordinate in Umbrella sampeling
- Sindrila Dutta banik (Sat Jun 29 2013 - 19:32:19 PDT)
- Jason Swails (Sat Jun 29 2013 - 06:13:07 PDT)
- David A Case (Sat Jun 29 2013 - 06:08:53 PDT)
- Sindrila Dutta banik (Fri Jun 28 2013 - 22:52:09 PDT)
- Jason Swails (Fri Jun 28 2013 - 20:41:22 PDT)
- Sindrila Dutta banik (Fri Jun 28 2013 - 19:19:44 PDT)
- Jason Swails (Fri Jun 28 2013 - 13:24:42 PDT)
- Sindrila Dutta banik (Fri Jun 28 2013 - 12:35:46 PDT)
- Jason Swails (Fri Jun 28 2013 - 06:06:13 PDT)
- Sindrila Dutta banik (Fri Jun 28 2013 - 00:42:08 PDT)
[AMBER] How to define restraint for Umbrella sampling
- Marc van der Kamp (Fri Jun 21 2013 - 08:28:54 PDT)
- Brian Radak (Fri Jun 21 2013 - 06:45:56 PDT)
- Sindrila Dutta banik (Fri Jun 21 2013 - 00:46:17 PDT)
[AMBER] How to get correlation matrix of center of mass of partial atoms for residues?
- Daniel Roe (Sat Jun 29 2013 - 15:42:32 PDT)
- Baogen Duan (Fri Jun 28 2013 - 23:44:28 PDT)
[AMBER] How to make a specific non-bonded interaction off
- kurisaki (Thu Jun 13 2013 - 22:01:51 PDT)
- Jason Swails (Thu Jun 13 2013 - 20:56:40 PDT)
- kurisaki (Thu Jun 13 2013 - 20:21:12 PDT)
- kurisaki (Mon Jun 10 2013 - 06:33:01 PDT)
- Jason Swails (Mon Jun 10 2013 - 06:00:46 PDT)
- kurisaki (Mon Jun 10 2013 - 03:22:53 PDT)
[AMBER] How to modify/add velocity entries in .inpcrd file?
- Jason Swails (Thu Jun 13 2013 - 16:18:32 PDT)
- Yan Duan (Thu Jun 13 2013 - 15:56:52 PDT)
[AMBER] hydrogen bond pattern
- David A Case (Tue Jun 18 2013 - 06:52:11 PDT)
- Rasha Alqus (Tue Jun 18 2013 - 04:51:31 PDT)
[AMBER] In regards to my previous question
- Hunter Brown (Fri Jun 14 2013 - 15:45:22 PDT)
[AMBER] inhomogeneous solvent mixture
- Daniel Roe (Sat Jun 22 2013 - 09:38:44 PDT)
- Chinthaka Ratnaweera (Sat Jun 22 2013 - 08:09:38 PDT)
- David A Case (Sat Jun 22 2013 - 05:48:03 PDT)
- Chinthaka Ratnaweera (Fri Jun 21 2013 - 22:52:56 PDT)
- Chinthaka Ratnaweera (Fri Jun 21 2013 - 21:36:01 PDT)
[AMBER] iron-sulfur parameterization
- francesco oteri (Thu Jun 06 2013 - 00:19:46 PDT)
- Sergio R Aragon (Wed Jun 05 2013 - 15:08:48 PDT)
- francesco oteri (Wed Jun 05 2013 - 14:18:01 PDT)
- Sergio R Aragon (Wed Jun 05 2013 - 13:16:17 PDT)
- case (Wed Jun 05 2013 - 12:40:40 PDT)
- venkatesh s (Wed Jun 05 2013 - 11:52:59 PDT)
[AMBER] Is per atome decomposition in MM-PBSA possible?
- Alexander Metz (Thu Jun 20 2013 - 03:37:06 PDT)
- Jason Swails (Thu Jun 20 2013 - 03:11:55 PDT)
- Haralambos Tzoupis (Thu Jun 20 2013 - 02:37:11 PDT)
[AMBER] Is that a way to generate free energy landscapes with ptraj?
- Jason Swails (Sat Jun 15 2013 - 11:47:36 PDT)
- Yip Yew Mun (Sat Jun 15 2013 - 06:29:38 PDT)
[AMBER] Is there any major change of MMPBSA.py in AmberTools 13?
- hannes.loeffler.stfc.ac.uk (Sun Jun 30 2013 - 01:35:57 PDT)
- Ray Luo, Ph.D. (Fri Jun 28 2013 - 10:47:53 PDT)
- Hannes Loeffler (Fri Jun 28 2013 - 08:13:45 PDT)
- Jason Swails (Fri Jun 28 2013 - 07:16:25 PDT)
- Hannes Loeffler (Fri Jun 28 2013 - 01:22:29 PDT)
- Jason Swails (Thu Jun 27 2013 - 09:44:21 PDT)
- psu4.uic.edu (Thu Jun 27 2013 - 09:02:42 PDT)
[AMBER] issue in tleap
- Jason Swails (Mon Jun 24 2013 - 14:32:06 PDT)
- Rejwan (Mon Jun 24 2013 - 14:25:27 PDT)
[AMBER] Job stops due to INFO: Old style inpcrd file read
- Jason Swails (Tue Jun 18 2013 - 12:03:29 PDT)
- Aditya Padhi (Tue Jun 18 2013 - 11:23:38 PDT)
- Jason Swails (Tue Jun 18 2013 - 09:14:14 PDT)
- Aditya Padhi (Tue Jun 18 2013 - 08:32:28 PDT)
[AMBER] Karplus.txt file for nucleic acid residues
- case (Thu Jun 06 2013 - 06:09:39 PDT)
- Indrajit Deb (Thu Jun 06 2013 - 02:02:30 PDT)
[AMBER] LEaP & improper parameters
- FyD (Wed Jun 05 2013 - 23:52:01 PDT)
- Jason Swails (Wed Jun 05 2013 - 07:16:10 PDT)
- FyD (Wed Jun 05 2013 - 00:05:37 PDT)
[AMBER] Lipid11 DMPC
- Dickson, Callum (Fri Jun 07 2013 - 02:21:49 PDT)
- Kanin Wichapong (Thu Jun 06 2013 - 07:56:54 PDT)
[AMBER] membrane-protein simulation with AMBER lipid11 FF
- Rejwan (Fri Jun 21 2013 - 09:30:24 PDT)
[AMBER] Methylated histidine lib and frcomd files
- FyD (Thu Jun 06 2013 - 00:17:04 PDT)
- FyD (Tue Jun 04 2013 - 05:03:49 PDT)
- George Patargias (Tue Jun 04 2013 - 04:26:04 PDT)
- FyD (Mon Jun 03 2013 - 06:52:43 PDT)
- George Patargias (Mon Jun 03 2013 - 06:33:46 PDT)
[AMBER] mmGBSA bondi/mbondi2 and force field questions
- Hai Nguyen (Mon Jun 03 2013 - 15:23:56 PDT)
- psu4.uic.edu (Mon Jun 03 2013 - 09:42:26 PDT)
[AMBER] MMPBSA Alanine scan terminal residues
- Jason Swails (Tue Jun 11 2013 - 05:34:53 PDT)
- Jason Swails (Mon Jun 10 2013 - 20:16:51 PDT)
- BERGY (Sat Jun 08 2013 - 23:23:48 PDT)
[AMBER] mmpbsa not included in Amber11?
- Changqing Yan (Thu Jun 27 2013 - 20:10:20 PDT)
- Jason Swails (Thu Jun 27 2013 - 20:00:40 PDT)
- Bill Miller III (Thu Jun 27 2013 - 20:03:48 PDT)
- Changqing Yan (Thu Jun 27 2013 - 19:55:27 PDT)
[AMBER] MMPBSA per-residue stuck forever without output even for 3 frames only
- M Elkot (Mon Jun 24 2013 - 07:48:28 PDT)
- Jason Swails (Mon Jun 24 2013 - 07:31:00 PDT)
- Jason Swails (Mon Jun 24 2013 - 06:34:09 PDT)
- Vaibhav Dixit (Mon Jun 24 2013 - 05:46:47 PDT)
- Jason Swails (Sat Jun 22 2013 - 08:06:25 PDT)
- M Elkot (Sat Jun 22 2013 - 07:36:53 PDT)
[AMBER] MMPBSA results for DNA-ligand system
- Sorensen, Jesper (Mon Jun 17 2013 - 07:32:38 PDT)
- Josh Berryman (Mon Jun 17 2013 - 01:14:47 PDT)
- deeptinayar.gmail.com (Mon Jun 17 2013 - 12:21:59 PDT)
- Sorensen, Jesper (Sun Jun 16 2013 - 22:33:48 PDT)
[AMBER] mmpbsa-with and without entropy
- colvin (Wed Jun 26 2013 - 03:19:22 PDT)
[AMBER] MMPBSA.py and cpptraj error
- Jason Swails (Thu Jun 20 2013 - 11:06:13 PDT)
- Sorensen, Jesper (Thu Jun 20 2013 - 10:56:48 PDT)
- Jason Swails (Thu Jun 20 2013 - 10:07:22 PDT)
- Sorensen, Jesper (Thu Jun 20 2013 - 09:43:59 PDT)
- Jason Swails (Wed Jun 19 2013 - 18:23:48 PDT)
- Sorensen, Jesper (Wed Jun 19 2013 - 16:08:33 PDT)
- Jason Swails (Wed Jun 19 2013 - 03:12:38 PDT)
- Sorensen, Jesper (Tue Jun 18 2013 - 19:37:46 PDT)
- Sorensen, Jesper (Tue Jun 18 2013 - 19:12:23 PDT)
- David A Case (Tue Jun 18 2013 - 04:54:16 PDT)
- Sorensen, Jesper (Mon Jun 17 2013 - 20:35:08 PDT)
[AMBER] MMPBSA.py error
- Jason Swails (Tue Jun 25 2013 - 10:45:48 PDT)
- Jason Swails (Tue Jun 25 2013 - 09:45:18 PDT)
- eneas.usal.es (Tue Jun 25 2013 - 09:37:33 PDT)
- Daniel Roe (Mon Jun 10 2013 - 08:43:24 PDT)
- Senthil Natesan (Mon Jun 10 2013 - 06:18:01 PDT)
- Daniel Roe (Fri Jun 07 2013 - 07:22:24 PDT)
- Senthil Natesan (Fri Jun 07 2013 - 06:06:04 PDT)
- Jason Swails (Thu Jun 06 2013 - 08:56:40 PDT)
- Senthil Natesan (Thu Jun 06 2013 - 08:46:12 PDT)
[AMBER] MMPBSA.py problem
- David A Case (Wed Jun 26 2013 - 04:40:50 PDT)
- Asmita Gupta (Wed Jun 26 2013 - 01:43:51 PDT)
- Hai Nguyen (Tue Jun 25 2013 - 13:28:36 PDT)
- Jason Swails (Tue Jun 25 2013 - 04:48:45 PDT)
- Asmita Gupta (Tue Jun 25 2013 - 00:07:05 PDT)
[AMBER] MPI Compilation problems Amber 12 on CentOS 6.2
- Frank Thommen (Thu Jun 13 2013 - 06:27:21 PDT)
- David A Case (Thu Jun 13 2013 - 05:35:37 PDT)
- Frank Thommen (Thu Jun 13 2013 - 05:03:03 PDT)
- David A Case (Thu Jun 13 2013 - 04:47:37 PDT)
- Frank Thommen (Thu Jun 13 2013 - 01:36:43 PDT)
[AMBER] NAB extract residue from molecule
- David A Case (Thu Jun 20 2013 - 08:21:45 PDT)
- Le,Huy Tuan (Wed Jun 19 2013 - 11:31:12 PDT)
[AMBER] nab in AmberTools13: documentation of newton() and getpdb_prm() sample
- David A Case (Tue Jun 11 2013 - 18:42:38 PDT)
- Chris Moth (Tue Jun 11 2013 - 13:49:13 PDT)
[AMBER] Need a higher value for SKINNB
- Scott Le Grand (Fri Jun 21 2013 - 10:31:41 PDT)
- Scott Le Grand (Wed Jun 19 2013 - 15:08:36 PDT)
- Hailin Huang (Wed Jun 19 2013 - 14:48:42 PDT)
- Scott Le Grand (Wed Jun 19 2013 - 14:23:54 PDT)
- Hailin Huang (Wed Jun 19 2013 - 13:34:43 PDT)
- Scott Le Grand (Wed Jun 19 2013 - 13:03:39 PDT)
- Hailin Huang (Wed Jun 19 2013 - 12:14:29 PDT)
- Scott Le Grand (Wed Jun 19 2013 - 11:59:02 PDT)
- Hailin Huang (Wed Jun 19 2013 - 10:43:47 PDT)
- Scott Le Grand (Wed Jun 19 2013 - 10:16:02 PDT)
- Hailin Huang (Wed Jun 19 2013 - 05:33:55 PDT)
- Jason Swails (Mon Jun 17 2013 - 16:31:37 PDT)
- Hailin Huang (Mon Jun 17 2013 - 15:20:57 PDT)
[AMBER] new AmberTools13 update has error in configure2 - needs changing
- Jason Swails (Mon Jun 03 2013 - 19:40:58 PDT)
- ET (Mon Jun 03 2013 - 13:13:25 PDT)
- Jason Swails (Mon Jun 03 2013 - 11:57:39 PDT)
- ET (Mon Jun 03 2013 - 11:02:23 PDT)
[AMBER] Nonbond cells need to be recalculated, restart simulation from previous checkpoint with a higher value for skinnb.
- Jason Swails (Wed Jun 19 2013 - 03:20:53 PDT)
- 涂志萍 (Wed Jun 19 2013 - 02:35:01 PDT)
[AMBER] ntt=2 on gpu
- Ross Walker (Wed Jun 12 2013 - 11:01:21 PDT)
- Sarah Graham (Mon Jun 10 2013 - 11:34:53 PDT)
- Ross Walker (Mon Jun 10 2013 - 07:12:36 PDT)
- Sarah Graham (Mon Jun 10 2013 - 05:26:21 PDT)
- Sarah Graham (Thu Jun 06 2013 - 12:36:34 PDT)
[AMBER] Parameters for Aluminum Ion
- Jason Swails (Fri Jun 14 2013 - 08:42:25 PDT)
[AMBER] parameters of ions for TIP5P water box
- Xioling Chuang (Wed Jun 12 2013 - 18:49:33 PDT)
- David A Case (Wed Jun 12 2013 - 04:58:32 PDT)
- Xioling Chuang (Tue Jun 11 2013 - 20:21:58 PDT)
- tec3.utah.edu (Tue Jun 11 2013 - 14:29:42 PDT)
- Xioling Chuang (Tue Jun 11 2013 - 03:54:57 PDT)
[AMBER] PB Bomb in pb_aaradi() - missing ff12SB atom types
- Jason Swails (Tue Jun 25 2013 - 08:55:22 PDT)
- Hannes Loeffler (Tue Jun 25 2013 - 08:29:16 PDT)
- Jason Swails (Tue Jun 25 2013 - 05:39:37 PDT)
- Hannes Loeffler (Tue Jun 25 2013 - 05:28:09 PDT)
- Jason Swails (Tue Jun 25 2013 - 04:59:08 PDT)
- Hannes Loeffler (Tue Jun 25 2013 - 03:05:39 PDT)
[AMBER] PEG
- Bailey, Steven (Tue Jun 18 2013 - 08:25:07 PDT)
- David A Case (Tue Jun 18 2013 - 08:15:32 PDT)
- Bailey, Steven (Tue Jun 18 2013 - 07:24:48 PDT)
- David A Case (Tue Jun 18 2013 - 06:56:16 PDT)
- Anselm Horn (Tue Jun 18 2013 - 05:54:14 PDT)
- FyD (Tue Jun 18 2013 - 05:36:28 PDT)
- Bailey, Steven (Tue Jun 18 2013 - 05:18:24 PDT)
[AMBER] Per-residue decomposition output file format looks unfriendly
- Mahmoud Soliman (Tue Jun 25 2013 - 05:00:10 PDT)
- Jason Swails (Tue Jun 25 2013 - 04:52:03 PDT)
- Jan-Philip Gehrcke (Tue Jun 25 2013 - 04:22:13 PDT)
- Kshatresh Dutta Dubey (Tue Jun 25 2013 - 04:03:52 PDT)
- Mahmoud Soliman (Tue Jun 25 2013 - 01:53:51 PDT)
[AMBER] PM6 and PM3
- me, Nancy (Thu Jun 06 2013 - 14:23:42 PDT)
- Brian Radak (Thu Jun 06 2013 - 12:22:31 PDT)
- me, Nancy (Thu Jun 06 2013 - 11:55:25 PDT)
- Brian Radak (Thu Jun 06 2013 - 11:34:11 PDT)
- me, Nancy (Thu Jun 06 2013 - 11:11:01 PDT)
[AMBER] post-clustering calculation of DBI and pSF
- Amparo Garcia Lopez (Sat Jun 22 2013 - 10:46:08 PDT)
- Thomas Cheatham (Fri Jun 21 2013 - 09:25:49 PDT)
- Daniel Roe (Fri Jun 21 2013 - 09:03:13 PDT)
- Amparo Garcia Lopez (Fri Jun 21 2013 - 08:18:23 PDT)
- Daniel Roe (Fri Jun 21 2013 - 07:30:55 PDT)
- Amparo Garcia Lopez (Fri Jun 21 2013 - 06:34:26 PDT)
[AMBER] Potential smoothing
- George Tzotzos (Tue Jun 04 2013 - 09:48:21 PDT)
[AMBER] print forces experienced by molecule during simulation
- Jason Swails (Fri Jun 14 2013 - 13:18:25 PDT)
- ET (Fri Jun 14 2013 - 07:02:54 PDT)
- Jason Swails (Fri Jun 14 2013 - 06:30:12 PDT)
- ET (Fri Jun 14 2013 - 05:22:53 PDT)
[AMBER] prmtop
- David A Case (Wed Jun 12 2013 - 09:53:32 PDT)
- Jason Swails (Wed Jun 12 2013 - 09:17:31 PDT)
- Sarah Graham (Wed Jun 12 2013 - 09:04:06 PDT)
- Bailey, Steven (Wed Jun 12 2013 - 08:49:22 PDT)
- cieplak.cgl.ucsf.edu (Wed Jun 12 2013 - 08:33:15 PDT)
- Karl N. Kirschner (Wed Jun 12 2013 - 07:02:44 PDT)
- Bailey, Steven (Wed Jun 12 2013 - 06:42:46 PDT)
[AMBER] prmtop for stripped down coordinates
- Paul Driscoll (Mon Jun 03 2013 - 06:34:36 PDT)
- Jason Swails (Mon Jun 03 2013 - 06:18:16 PDT)
- Marc van der Kamp (Mon Jun 03 2013 - 05:45:57 PDT)
- Paul Driscoll (Mon Jun 03 2013 - 05:38:17 PDT)
[AMBER] problem with MM-PBSA
- Jason Swails (Sat Jun 29 2013 - 10:32:05 PDT)
- Maryam Hamzehee (Sat Jun 29 2013 - 08:27:49 PDT)
[AMBER] problem with parmchk and a big organic molecule
- Jason Swails (Fri Jun 14 2013 - 08:24:29 PDT)
[AMBER] Problem with PDB files in LEaP
- David A Case (Fri Jun 28 2013 - 10:19:53 PDT)
- Daniel Roe (Fri Jun 28 2013 - 09:43:31 PDT)
- Hunter Brown (Fri Jun 28 2013 - 08:09:58 PDT)
[AMBER] problem with restart file in amber 11
- Jason Swails (Thu Jun 13 2013 - 18:19:26 PDT)
- Edward Pate (Thu Jun 13 2013 - 17:10:33 PDT)
[AMBER] Problem with SMD
- Jason Swails (Mon Jun 10 2013 - 21:08:16 PDT)
- moitrayee.mbu.iisc.ernet.in (Sun Jun 09 2013 - 02:06:55 PDT)
[AMBER] problem with tleap
- FyD (Fri Jun 21 2013 - 00:11:17 PDT)
- Bill Ross (Wed Jun 19 2013 - 13:31:03 PDT)
- Rejwan (Wed Jun 19 2013 - 08:06:05 PDT)
- Rejwan (Tue Jun 18 2013 - 18:46:29 PDT)
- Jason Swails (Tue Jun 18 2013 - 14:09:21 PDT)
- Rejwan (Tue Jun 18 2013 - 13:06:45 PDT)
[AMBER] Problematic PDB files
- Daniel Roe (Fri Jun 28 2013 - 13:22:39 PDT)
- Daniel Roe (Fri Jun 28 2013 - 12:35:43 PDT)
[AMBER] Protein leaving periodic box
- Daniel Roe (Wed Jun 19 2013 - 12:30:17 PDT)
- Hailin Huang (Wed Jun 19 2013 - 11:28:44 PDT)
- Daniel Roe (Wed Jun 12 2013 - 14:33:36 PDT)
- Hailin Huang (Wed Jun 12 2013 - 13:56:58 PDT)
[AMBER] Provisional GTX780 Numbers
- ET (Wed Jun 26 2013 - 15:47:24 PDT)
- Michael Lerner (Wed Jun 26 2013 - 13:04:45 PDT)
- Ross Walker (Wed Jun 26 2013 - 12:56:28 PDT)
- Michael Lerner (Wed Jun 26 2013 - 12:38:05 PDT)
- ET (Tue Jun 25 2013 - 10:56:06 PDT)
- Ross Walker (Tue Jun 25 2013 - 09:26:14 PDT)
- ET (Tue Jun 25 2013 - 00:28:06 PDT)
- Ross Walker (Mon Jun 24 2013 - 14:23:02 PDT)
[AMBER] ptraj error
- Daniel Roe (Mon Jun 03 2013 - 06:50:41 PDT)
- Sushil Mishra (Mon Jun 03 2013 - 05:39:36 PDT)
- parul sharma (Mon Jun 03 2013 - 04:14:13 PDT)
[AMBER] qmcut in QM/MM simulation with AMBER/GAUSSIAN
- Eric Berquist (Wed Jun 19 2013 - 07:01:52 PDT)
- Tamara Meirelles (Mon Jun 17 2013 - 17:39:00 PDT)
[AMBER] Questions about installation of Amber11
- Jason Swails (Fri Jun 14 2013 - 20:24:15 PDT)
- Changqing Yan (Fri Jun 14 2013 - 19:57:08 PDT)
- David A Case (Fri Jun 14 2013 - 04:41:20 PDT)
- Changqing Yan (Fri Jun 14 2013 - 01:16:44 PDT)
[AMBER] Questions about installing Amber 11
- David A Case (Fri Jun 14 2013 - 04:38:17 PDT)
- Changqing Yan (Fri Jun 14 2013 - 00:03:54 PDT)
[AMBER] Questions about ncsu_smd in Amber12
- moitrayee.mbu.iisc.ernet.in (Mon Jun 24 2013 - 20:51:34 PDT)
[AMBER] Questions about SMD using jar=1
- moitrayee.mbu.iisc.ernet.in (Tue Jun 25 2013 - 18:11:33 PDT)
- Jason Swails (Tue Jun 25 2013 - 14:28:05 PDT)
- moitrayee.mbu.iisc.ernet.in (Tue Jun 25 2013 - 12:23:24 PDT)
[AMBER] RADIAL ptraj vs cpptraj
- Daniel Roe (Tue Jun 18 2013 - 10:50:10 PDT)
- Domenico Marson (Tue Jun 18 2013 - 09:42:08 PDT)
[AMBER] receiving amber digest not separate subject wise as earlier
- Vaibhav Dixit (Fri Jun 21 2013 - 00:33:50 PDT)
- Ross Walker (Thu Jun 20 2013 - 09:32:41 PDT)
- Vaibhav Dixit (Thu Jun 20 2013 - 01:15:07 PDT)
[AMBER] reference group and pulled group in umbrella sampling
- Jason Swails (Wed Jun 05 2013 - 18:57:32 PDT)
- Jio M (Wed Jun 05 2013 - 12:51:25 PDT)
- Jio M (Sun Jun 02 2013 - 01:42:54 PDT)
- Jason Swails (Sat Jun 01 2013 - 21:29:21 PDT)
[AMBER] result of molsurf calculation
- Daniel Roe (Thu Jun 06 2013 - 08:08:44 PDT)
- Marcus Arieno (Thu Jun 06 2013 - 08:05:05 PDT)
- setyanto md (Thu Jun 06 2013 - 07:36:10 PDT)
[AMBER] Running MD NPT Ensemble Error
- ET (Wed Jun 12 2013 - 20:24:13 PDT)
- ET (Wed Jun 12 2013 - 20:11:08 PDT)
- Benjamin Grant (Wed Jun 12 2013 - 14:07:58 PDT)
[AMBER] search for a method name: 'targeted molecular dynamics'?
- Jan-Philip Gehrcke (Wed Jun 05 2013 - 03:19:20 PDT)
- Daniel Sindhikara (Wed Jun 05 2013 - 00:59:38 PDT)
- Jan-Philip Gehrcke (Wed Jun 05 2013 - 00:16:32 PDT)
- Jan-Philip Gehrcke (Sat Jun 01 2013 - 07:08:36 PDT)
[AMBER] selective aMD
- Romelia Salomon (Tue Jun 18 2013 - 11:07:40 PDT)
- Chris Moth (Mon Jun 17 2013 - 08:16:50 PDT)
- Daniel Roe (Sun Jun 16 2013 - 19:13:15 PDT)
- Thomas Evangelidis (Sun Jun 16 2013 - 09:43:30 PDT)
[AMBER] solvatebox membrane
- Igor Marques (Thu Jun 06 2013 - 02:56:06 PDT)
- Kanin Wichapong (Thu Jun 06 2013 - 02:53:40 PDT)
[AMBER] Step by step tutorial to using Ptraj in generating DCCM
- Yip Yew Mun (Sat Jun 15 2013 - 06:27:13 PDT)
- Daniel Roe (Thu Jun 13 2013 - 08:17:27 PDT)
- #YIP YEW MUN# (Wed Jun 12 2013 - 18:22:20 PDT)
[AMBER] surf in cpptraj doesn't support 'stripped' trajectories?
- Marc van der Kamp (Wed Jun 05 2013 - 14:19:40 PDT)
- Daniel Roe (Tue Jun 04 2013 - 14:01:40 PDT)
- Daniel Roe (Tue Jun 04 2013 - 13:12:14 PDT)
- Marc van der Kamp (Tue Jun 04 2013 - 13:10:55 PDT)
- Marc van der Kamp (Tue Jun 04 2013 - 11:38:30 PDT)
- Daniel Roe (Tue Jun 04 2013 - 11:02:34 PDT)
- Marc van der Kamp (Tue Jun 04 2013 - 09:32:18 PDT)
[AMBER] Thanks
- Hunter Brown (Wed Jun 19 2013 - 09:07:07 PDT)
[AMBER] TI calculations and autocorrelation time
- steinbrt.rci.rutgers.edu (Thu Jun 27 2013 - 10:18:14 PDT)
- Kepa K. Burusco (Thu Jun 27 2013 - 07:56:48 PDT)
[AMBER] tleap and ff02pol.r1
- live (Mon Jun 03 2013 - 05:15:21 PDT)
- Jason Swails (Sun Jun 02 2013 - 14:35:42 PDT)
- live (Sun Jun 02 2013 - 09:59:21 PDT)
[AMBER] tleap has error by applying amber ff03ua
- David A Case (Wed Jun 19 2013 - 05:25:11 PDT)
- Chris Moth (Tue Jun 18 2013 - 15:56:25 PDT)
[AMBER] To all K20 - K20x "positive" Amber users
- Marek Maly (Sat Jun 01 2013 - 13:22:21 PDT)
[AMBER] Troubles running LEaP
- Daniel Roe (Fri Jun 21 2013 - 12:08:55 PDT)
- Hunter Brown (Fri Jun 21 2013 - 11:57:39 PDT)
[AMBER] unable to compile amberTools12
- Christopher Neale (Wed Jun 26 2013 - 18:40:05 PDT)
- Jason Swails (Wed Jun 26 2013 - 05:03:57 PDT)
- David A Case (Wed Jun 26 2013 - 04:37:40 PDT)
- Christopher Neale (Tue Jun 25 2013 - 12:38:44 PDT)
[AMBER] unable to run minimizations after new installation of amber11
- Amparo Garcia Lopez (Tue Jun 11 2013 - 05:54:08 PDT)
- Jason Swails (Mon Jun 10 2013 - 21:00:37 PDT)
- Amparo Garcia Lopez (Sat Jun 08 2013 - 09:09:22 PDT)
- David A Case (Fri Jun 07 2013 - 12:01:05 PDT)
- Amparo Garcia Lopez (Fri Jun 07 2013 - 09:58:21 PDT)
- David A Case (Fri Jun 07 2013 - 09:01:05 PDT)
- Amparo Garcia Lopez (Thu Jun 06 2013 - 11:59:25 PDT)
[AMBER] Unfolding a protein using Accelerated Molecular Dynamics
- sunita gupta (Sat Jun 01 2013 - 04:11:51 PDT)
[AMBER] Unknown redidue when using tleap
- David A Case (Fri Jun 21 2013 - 05:33:34 PDT)
- FyD (Fri Jun 21 2013 - 04:31:34 PDT)
- Dongshan Wei (Fri Jun 21 2013 - 02:12:08 PDT)
- Dongshan Wei (Thu Jun 13 2013 - 06:49:46 PDT)
- FyD (Thu Jun 13 2013 - 00:37:22 PDT)
- ET (Wed Jun 12 2013 - 19:56:29 PDT)
- Dongshan Wei (Wed Jun 12 2013 - 18:40:42 PDT)
[AMBER] Update 10 for AmberTools 13: CPPTRAJ
- Jan-Philip Gehrcke (Wed Jun 19 2013 - 11:06:07 PDT)
- Daniel Roe (Wed Jun 19 2013 - 10:03:01 PDT)
[AMBER] using ntt=2 on gpu
- Sarah Graham (Thu Jun 06 2013 - 08:43:29 PDT)
[AMBER] Warnings in leap about lipid11
- Åge Aleksander Skjevik (Thu Jun 27 2013 - 14:55:03 PDT)
- eneas.usal.es (Thu Jun 27 2013 - 08:01:54 PDT)
[AMBER] What are the controls parameters for the nmode command line tool
- Jose Borreguero (Tue Jun 25 2013 - 07:18:58 PDT)
- David A Case (Tue Jun 25 2013 - 04:30:03 PDT)
- Jason Swails (Tue Jun 25 2013 - 04:28:33 PDT)
- Jose Borreguero (Mon Jun 24 2013 - 16:39:21 PDT)
[AMBER] What bugfix.18 actually does to correct the problem in NPT simulations on GPU?
- Takato Sato (Mon Jun 17 2013 - 01:54:00 PDT)
[AMBER] What is minimum GPU bandwidth to get AMBER to run properly?
- Jan-Philip Gehrcke (Mon Jun 10 2013 - 08:18:05 PDT)
- ET (Mon Jun 10 2013 - 07:59:48 PDT)
- Ross Walker (Mon Jun 10 2013 - 07:10:31 PDT)
- ET (Mon Jun 10 2013 - 06:32:26 PDT)
- Ross Walker (Sun Jun 09 2013 - 10:02:12 PDT)
- ET (Sun Jun 09 2013 - 07:46:31 PDT)
[AMBER] Which is the best compiler to use with AMBER 12
- ET (Sun Jun 02 2013 - 03:23:32 PDT)
- Jan-Philip Gehrcke (Sun Jun 02 2013 - 02:58:26 PDT)
- Ross Walker (Sat Jun 01 2013 - 22:05:51 PDT)
- ET (Sat Jun 01 2013 - 21:28:51 PDT)
- Jason Swails (Sat Jun 01 2013 - 21:21:50 PDT)
- ET (Sat Jun 01 2013 - 20:47:05 PDT)
[AMBER] 答复: avgcoord in AT13
- Jason Swails (Sat Jun 29 2013 - 07:34:36 PDT)
- Hongyi WU (Fri Jun 28 2013 - 18:50:12 PDT)
- Hongyi WU (Fri Jun 28 2013 - 18:43:23 PDT)
] Amber updater issues
- Jason Swails (Tue Jun 25 2013 - 09:34:35 PDT)
- eneas.usal.es (Tue Jun 25 2013 - 09:28:09 PDT)
FATAL: Atom XXX does not have a type
- FyD (Sat Jun 29 2013 - 02:35:59 PDT)
- sunyeping.aliyun.com (Fri Jun 28 2013 - 09:05:16 PDT)
Graphene topology from GAFF
- FyD (Wed Jun 26 2013 - 02:02:29 PDT)
- FyD (Thu Jun 20 2013 - 07:02:04 PDT)
Is it a bug? Compilation Error in Ambertools
- David A Case (Tue Jun 25 2013 - 07:44:09 PDT)
- Matthias Bohner (Tue Jun 25 2013 - 05:56:53 PDT)
- Matthias Bohner (Tue Jun 25 2013 - 05:54:08 PDT)
- Jason Swails (Tue Jun 25 2013 - 04:55:43 PDT)
- David A Case (Tue Jun 25 2013 - 04:49:48 PDT)
- Matthias Bohner (Tue Jun 25 2013 - 00:40:37 PDT)

Amber Archive Jun 2013 by subject