Amber Archive Nov 2014: by subject

Elham tazikeh (Thu Nov 27 2014 - 00:57:29 PST)
[AMBER] (no subject)
- Jason Swails (Thu Nov 27 2014 - 03:49:52 PST)
[AMBER] 100ps long minimization script
- David A Case (Sun Nov 30 2014 - 12:38:21 PST)
- Carlos Simmerling (Sun Nov 30 2014 - 05:53:13 PST)
- pradeep pant (Sun Nov 30 2014 - 05:38:01 PST)
[AMBER] 4x GTX 980
- Ross Walker (Sun Nov 23 2014 - 18:03:50 PST)
- Ross Walker (Sun Nov 23 2014 - 18:02:57 PST)
- Ross Walker (Sun Nov 23 2014 - 18:01:29 PST)
- Scott Le Grand (Sun Nov 23 2014 - 17:34:40 PST)
- Parker de Waal (Sun Nov 23 2014 - 17:32:46 PST)
- Scott Le Grand (Sun Nov 23 2014 - 17:26:41 PST)
- Parker de Waal (Sun Nov 23 2014 - 16:51:16 PST)
- Scott Le Grand (Sun Nov 23 2014 - 16:32:38 PST)
- Scott Le Grand (Sun Nov 23 2014 - 16:31:34 PST)
- Parker de Waal (Sun Nov 23 2014 - 16:22:22 PST)
- Scott Le Grand (Mon Nov 17 2014 - 14:42:53 PST)
- James Maier (Sun Nov 16 2014 - 20:16:18 PST)
- James Maier (Sun Nov 16 2014 - 20:13:24 PST)
- Parker de Waal (Sun Nov 16 2014 - 18:28:07 PST)
[AMBER] [Amber] Amber14 does not find parameters for Mg2+, please help
- Genin, Nicolas J (Wed Nov 12 2014 - 11:29:09 PST)
- Jason Swails (Wed Nov 12 2014 - 08:34:58 PST)
- Genin, Nicolas J (Wed Nov 12 2014 - 07:35:49 PST)
[AMBER] [q4md-fft] FAD wrong geometry in F-90 project
- FyD (Sat Nov 01 2014 - 13:50:17 PDT)
[AMBER] a problem on heating the system
- Jason Swails (Wed Nov 12 2014 - 04:34:10 PST)
- David A Case (Wed Nov 12 2014 - 04:15:11 PST)
- ZHAO Ruisheng (Tue Nov 11 2014 - 04:53:02 PST)
- David A Case (Tue Nov 11 2014 - 03:54:32 PST)
- ZHAO Ruisheng (Tue Nov 11 2014 - 00:32:16 PST)
- David A Case (Mon Nov 10 2014 - 06:01:54 PST)
- Jason Swails (Mon Nov 10 2014 - 05:30:06 PST)
- ZHAO Ruisheng (Mon Nov 10 2014 - 05:25:56 PST)
[AMBER] about nab
- David A Case (Fri Nov 21 2014 - 04:36:23 PST)
- m13654940810 (Fri Nov 21 2014 - 03:12:07 PST)
[AMBER] adQM/MM vlimit exceeded problem
- Andreas Goetz (Mon Nov 24 2014 - 13:44:25 PST)
- Andreas Goetz (Sun Nov 23 2014 - 21:30:49 PST)
- Aixiao Li (Thu Nov 20 2014 - 02:32:49 PST)
[AMBER] AM1-BCC dipole moment
- Hannes Loeffler (Mon Nov 10 2014 - 07:59:09 PST)
- CHAMI F. (Mon Nov 10 2014 - 07:10:10 PST)
- Jason Swails (Mon Nov 10 2014 - 06:01:52 PST)
- CHAMI F. (Mon Nov 10 2014 - 05:51:33 PST)
- Jason Swails (Wed Nov 05 2014 - 07:21:05 PST)
- David A Case (Wed Nov 05 2014 - 07:10:11 PST)
- CHAMI F. (Wed Nov 05 2014 - 04:20:04 PST)
[AMBER] Amber 14 and NetCDF installation issue
- Jason Swails (Thu Nov 27 2014 - 03:55:11 PST)
- Fernando Ezequiel Chain (Thu Nov 27 2014 - 01:14:37 PST)
[AMBER] Amber 14 installation problems
- David A Case (Fri Nov 14 2014 - 04:55:33 PST)
- 汪小涧 (Thu Nov 13 2014 - 19:07:29 PST)
[AMBER] AMBER Digest, Vol 1041, Issue 1
- Jason Swails (Tue Nov 18 2014 - 08:32:04 PST)
- Robin Jain (Tue Nov 18 2014 - 07:34:02 PST)
[AMBER] AMBER Digest, Vol 1044, Issue 1
- Jason Swails (Mon Nov 24 2014 - 02:44:31 PST)
- Abhishek TYAGI (Sun Nov 23 2014 - 22:08:48 PST)
[AMBER] AMBER Digest, Vol 1045, Issue 1
- David A Case (Sat Nov 22 2014 - 04:39:51 PST)
- Robin Jain (Sat Nov 22 2014 - 00:25:58 PST)
[AMBER] amber error about protein containing heme
- David A Case (Sat Nov 22 2014 - 04:35:03 PST)
- Fatemeh Sadat Alavi (Sat Nov 22 2014 - 00:04:33 PST)
- Jason Swails (Tue Nov 18 2014 - 06:56:15 PST)
- David A Case (Tue Nov 18 2014 - 04:38:56 PST)
- Fatemeh Sadat Alavi (Tue Nov 18 2014 - 02:37:16 PST)
- Fatemeh Sadat Alavi (Tue Nov 18 2014 - 02:31:57 PST)
[AMBER] AMBER error: peek_ewald_inpcrd: SHOULD NOT BE HERE
- David A Case (Sat Nov 22 2014 - 11:35:45 PST)
- Hadeer ELHabashy (Sat Nov 22 2014 - 07:43:24 PST)
[AMBER] AMBER Question: Setting box angle in tleap
- David A Case (Wed Nov 05 2014 - 04:00:44 PST)
- 曲薇 (Wed Nov 05 2014 - 01:22:48 PST)
[AMBER] AMBER Unique atom types
- FyD (Sat Nov 22 2014 - 23:45:25 PST)
- David A Case (Sat Nov 22 2014 - 18:28:26 PST)
- Brittany Boykin (Sat Nov 22 2014 - 14:45:39 PST)
[AMBER] AmberTools13
- Jason Swails (Thu Nov 27 2014 - 03:58:55 PST)
- Ibrahim Said (Thu Nov 27 2014 - 02:01:57 PST)
- David A Case (Wed Nov 26 2014 - 10:31:59 PST)
- Jason Swails (Wed Nov 26 2014 - 10:28:26 PST)
- Daniel Roe (Wed Nov 26 2014 - 09:54:27 PST)
- Ibrahim Said (Wed Nov 26 2014 - 09:32:44 PST)
[AMBER] aMD error
- maryam azimzadehirani (Wed Nov 05 2014 - 00:37:43 PST)
- Jason Swails (Tue Nov 04 2014 - 04:35:55 PST)
- maryam azimzadehirani (Mon Nov 03 2014 - 23:23:10 PST)
[AMBER] aMD on Amber 12
- Daniel Roe (Tue Nov 18 2014 - 09:47:25 PST)
- Aldo Segura (Tue Nov 18 2014 - 08:49:14 PST)
- Daniel Roe (Tue Nov 18 2014 - 07:01:20 PST)
- Aldo Segura (Mon Nov 17 2014 - 21:53:21 PST)
[AMBER] Binding energy using mm_pbsa.pl
- Wong, Sook (NIH/NCATS) [V] (Fri Nov 07 2014 - 13:15:03 PST)
- Jason Swails (Thu Nov 06 2014 - 13:55:10 PST)
- Aron Broom (Thu Nov 06 2014 - 13:50:38 PST)
- Wong, Sook (NIH/NCATS) [V] (Thu Nov 06 2014 - 12:54:14 PST)
- Jason Swails (Thu Nov 06 2014 - 12:34:39 PST)
- Wong, Sook (NIH/NCATS) [V] (Thu Nov 06 2014 - 12:24:03 PST)
- Jason Swails (Thu Nov 06 2014 - 12:18:46 PST)
- Aron Broom (Thu Nov 06 2014 - 12:14:04 PST)
- Wong, Sook (NIH/NCATS) [V] (Thu Nov 06 2014 - 12:05:34 PST)
- Aron Broom (Thu Nov 06 2014 - 11:51:30 PST)
- Wong, Sook (NIH/NCATS) [V] (Thu Nov 06 2014 - 08:28:57 PST)
[AMBER] bond distances in amber
- Mary Varughese (Sun Nov 09 2014 - 01:59:20 PST)
- David A Case (Sat Nov 08 2014 - 17:10:50 PST)
- Niel Henriksen (Sat Nov 08 2014 - 15:31:08 PST)
- Mary Varughese (Sat Nov 08 2014 - 09:15:21 PST)
- Jason Swails (Fri Nov 07 2014 - 04:55:38 PST)
- Mary Varughese (Fri Nov 07 2014 - 01:47:53 PST)
[AMBER] box size changing during equilibration
- Daniel Roe (Wed Nov 19 2014 - 07:26:45 PST)
- Robin Jain (Wed Nov 19 2014 - 07:20:29 PST)
[AMBER] bug in pmemd softcore TI with SHAKE
- Hannes Loeffler (Tue Nov 04 2014 - 02:07:39 PST)
[AMBER] Bug Report
- Jason Swails (Fri Nov 21 2014 - 02:30:30 PST)
- Liu, Hui (Thu Nov 20 2014 - 23:38:52 PST)
[AMBER] Calcium parameters in calmodulin
- Jason Swails (Thu Nov 13 2014 - 08:58:19 PST)
- bharat lakhani (Thu Nov 13 2014 - 08:16:59 PST)
[AMBER] Calcium vdW parameters
- Ken Merz (Sat Nov 29 2014 - 05:07:38 PST)
- mmaestre.gate.sinica.edu.tw (Fri Nov 28 2014 - 19:15:03 PST)
- Caitlin Scott (Fri Nov 28 2014 - 16:14:40 PST)
[AMBER] Calculating Normalised electron density for DOPC.
- Him Shweta (Sat Nov 01 2014 - 06:10:58 PDT)
[AMBER] Can you use cholesterol lipid 11 parameters and lipid 14 lipid parameters?
- Jonathan Gough (Thu Nov 20 2014 - 12:06:19 PST)
[AMBER] CHAMBER error
- Jason Swails (Wed Nov 26 2014 - 18:56:39 PST)
- Abhishek TYAGI (Mon Nov 24 2014 - 20:37:46 PST)
[AMBER] citation for mdout_analyser.py
- Jason Swails (Tue Nov 18 2014 - 06:49:03 PST)
- Krisztina Feher (Tue Nov 18 2014 - 05:14:33 PST)
[AMBER] confirm b31b76c2dc0c4f0c33e4cac638252d6c6723f46d
- vojtech.mlynsky.upol.cz (Wed Nov 26 2014 - 01:43:56 PST)
- Zgarbova Marie (Mon Nov 24 2014 - 12:56:57 PST)
[AMBER] Constant pH MD with CUDA not working
- BATUHAN KAV (Mon Nov 10 2014 - 12:05:55 PST)
[AMBER] Correct script for B-factor
- Daniel Roe (Sun Nov 30 2014 - 10:33:05 PST)
- Soumendranath Bhakat (Fri Nov 28 2014 - 19:37:22 PST)
- David A Case (Fri Nov 28 2014 - 09:22:10 PST)
- Marcus Arieno (Fri Nov 28 2014 - 08:06:43 PST)
- Soumendranath Bhakat (Fri Nov 28 2014 - 07:38:19 PST)
[AMBER] Counseling about the GPU series supporting PMEMD
- Ross Walker (Sun Nov 23 2014 - 23:11:56 PST)
- geyushu.ustc.edu.cn (Sun Nov 23 2014 - 23:06:03 PST)
[AMBER] cpptraj
- Daniel Roe (Tue Nov 11 2014 - 12:04:38 PST)
- Sylvester Tumusiime (Tue Nov 11 2014 - 11:58:39 PST)
- nabil bennenni (Tue Nov 11 2014 - 11:55:42 PST)
- Daniel Roe (Tue Nov 11 2014 - 11:46:03 PST)
- Sylvester Tumusiime (Tue Nov 11 2014 - 11:30:23 PST)
[AMBER] cpptraj hist 3D
- andrea spitaleri (Thu Nov 06 2014 - 11:54:52 PST)
- Jason Swails (Thu Nov 06 2014 - 11:36:39 PST)
- andrea spitaleri (Thu Nov 06 2014 - 10:39:55 PST)
- Daniel Roe (Thu Nov 06 2014 - 09:35:46 PST)
- andrea spitaleri (Thu Nov 06 2014 - 06:38:23 PST)
- Jason Swails (Thu Nov 06 2014 - 06:29:21 PST)
- CHAMI F. (Thu Nov 06 2014 - 04:54:58 PST)
[AMBER] cut value in minimisation
- David A Case (Fri Nov 21 2014 - 04:26:26 PST)
- Jason Swails (Fri Nov 21 2014 - 02:18:44 PST)
- Robin Jain (Thu Nov 20 2014 - 23:17:49 PST)
[AMBER] cyclic peptide side chains
- David A Case (Fri Nov 21 2014 - 04:29:02 PST)
- Maria Diaz (Fri Nov 21 2014 - 02:43:50 PST)
[AMBER] determine free available space in simulation box
- Iqbal, Muhammad Sajid (Thu Nov 06 2014 - 11:04:12 PST)
[AMBER] Different PCA results when loading trajectories in a different order
- Daniel Roe (Wed Nov 26 2014 - 09:52:04 PST)
- Daniel Roe (Wed Nov 26 2014 - 07:36:50 PST)
- Guillaume Roellinger (Wed Nov 26 2014 - 01:58:43 PST)
- Daniel Roe (Tue Nov 25 2014 - 10:08:33 PST)
- Daniel Roe (Tue Nov 25 2014 - 10:03:42 PST)
- Guillaume Roellinger (Tue Nov 25 2014 - 09:49:05 PST)
[AMBER] doubt in RMD
- Mary Varughese (Sat Nov 29 2014 - 04:40:02 PST)
- Jason Swails (Fri Nov 28 2014 - 19:17:02 PST)
- Mary Varughese (Thu Nov 27 2014 - 09:40:22 PST)
- Jason Swails (Thu Nov 27 2014 - 03:48:15 PST)
- Mary Varughese (Wed Nov 26 2014 - 21:58:04 PST)
- Jason Swails (Wed Nov 26 2014 - 14:58:27 PST)
- Mary Varughese (Mon Nov 24 2014 - 23:57:32 PST)
[AMBER] DRUG_PROTEIN INTERACTIOM
- Jason Swails (Fri Nov 07 2014 - 04:31:14 PST)
- Wei Ye (Fri Nov 07 2014 - 04:28:06 PST)
- Ruchika Bhat (Fri Nov 07 2014 - 01:00:58 PST)
- Wei Ye (Thu Nov 06 2014 - 23:57:40 PST)
- Ruchika Bhat (Thu Nov 06 2014 - 22:53:11 PST)
[AMBER] Entropy using Nmode
- Jason Swails (Fri Nov 14 2014 - 20:14:46 PST)
- Wong, Sook (NIH/NCATS) [V] (Fri Nov 14 2014 - 10:57:38 PST)
[AMBER] ERROR atom with mass 1 has type alreadydesignated as non-hydrogen type
- Abhishek TYAGI (Wed Nov 19 2014 - 19:01:08 PST)
[AMBER] ERROR DURING "TESTING" OF AMBER INSTALLATION
- ROOPALI VERMA (Wed Nov 19 2014 - 22:55:27 PST)
- Amihai (Wed Nov 19 2014 - 04:21:25 PST)
- David A Case (Wed Nov 19 2014 - 04:08:00 PST)
- ROOPALI VERMA (Tue Nov 18 2014 - 22:43:38 PST)
- David A Case (Tue Nov 18 2014 - 04:34:10 PST)
- ROOPALI VERMA (Mon Nov 17 2014 - 23:47:31 PST)
[AMBER] Error in CHAMBER output
- Robin Betz (Wed Nov 19 2014 - 22:23:33 PST)
- Abhishek TYAGI (Wed Nov 19 2014 - 22:18:25 PST)
[AMBER] error in mmpbsa calculation
- Abdul wadood (Fri Nov 14 2014 - 08:37:42 PST)
- Jason Swails (Thu Nov 13 2014 - 09:02:51 PST)
- Abdul wadood (Thu Nov 13 2014 - 08:30:40 PST)
[AMBER] Error logs
- James Starlight (Tue Nov 04 2014 - 00:24:15 PST)
[AMBER] error message of addLJType of parmed: Action addLJType failed. UnhandledArgumentWarning: 0.0 0.0
- Jason Swails (Tue Nov 04 2014 - 04:33:54 PST)
- Ying-Chieh Sun (Mon Nov 03 2014 - 18:40:24 PST)
- Jason Swails (Mon Nov 03 2014 - 09:09:25 PST)
- sun (Mon Nov 03 2014 - 08:11:57 PST)
[AMBER] Errors compiling Amber 14 after applying update 7
- Ross Walker (Thu Nov 20 2014 - 12:38:46 PST)
- David A Case (Thu Nov 20 2014 - 12:33:32 PST)
- Jason Swails (Thu Nov 20 2014 - 12:17:51 PST)
- Bob Healey (Thu Nov 20 2014 - 09:45:08 PST)
[AMBER] errors in qm/mm
- Ayesha Fatima (Mon Nov 24 2014 - 05:56:29 PST)
- Gustavo Seabra (Mon Nov 24 2014 - 05:53:42 PST)
- Ayesha Fatima (Mon Nov 24 2014 - 05:27:50 PST)
- Gustavo Seabra (Mon Nov 24 2014 - 04:43:18 PST)
- Ayesha Fatima (Mon Nov 24 2014 - 01:22:47 PST)
- Marc van der Kamp (Mon Nov 24 2014 - 00:03:32 PST)
- Ayesha Fatima (Sun Nov 23 2014 - 23:02:47 PST)
- Ayesha Fatima (Sun Nov 23 2014 - 22:39:49 PST)
- Andreas Goetz (Sun Nov 23 2014 - 22:27:33 PST)
- Ayesha Fatima (Sun Nov 23 2014 - 22:10:57 PST)
[AMBER] Failure of antechamber with c -1 m 2
- Francesco Pietra (Mon Nov 17 2014 - 08:55:07 PST)
- David A Case (Mon Nov 17 2014 - 08:01:25 PST)
- Francesco Pietra (Sun Nov 16 2014 - 13:57:15 PST)
- David A Case (Sun Nov 16 2014 - 13:20:04 PST)
- Francesco Pietra (Sun Nov 16 2014 - 09:35:45 PST)
[AMBER] Forcefield for DNA
- Baifan Wang (Tue Nov 25 2014 - 04:29:09 PST)
- Petr Jurecka (Tue Nov 25 2014 - 01:52:22 PST)
- Baifan Wang (Mon Nov 24 2014 - 06:55:15 PST)
[AMBER] Free energy landscape
- anu chandra (Thu Nov 27 2014 - 03:44:44 PST)
- Carlos Simmerling (Wed Nov 26 2014 - 09:12:53 PST)
- Daniel Roe (Wed Nov 26 2014 - 09:01:33 PST)
- anu chandra (Wed Nov 26 2014 - 03:07:19 PST)
[AMBER] Fully random MPI error after updating CentOS from release 6.5 to 6.6
- Massimiliano Porrini (Mon Nov 03 2014 - 08:25:52 PST)
- Jason Swails (Mon Nov 03 2014 - 04:36:57 PST)
- Massimiliano Porrini (Mon Nov 03 2014 - 02:54:20 PST)
[AMBER] Fwd: InputError when running MMBPSA.py
- Jason Swails (Fri Nov 21 2014 - 21:49:30 PST)
- HERBERT MAX VENTHUR PE¥A (Fri Nov 21 2014 - 19:28:58 PST)
[AMBER] generate topology file and parameter file for complex with dummy atoms
- Jorgen Simonsen (Sat Nov 29 2014 - 16:08:00 PST)
- Jason Swails (Fri Nov 28 2014 - 15:53:21 PST)
- Jorgen Simonsen (Fri Nov 28 2014 - 15:45:21 PST)
[AMBER] Glycan bond error leap
- maryam azimzadehirani (Mon Nov 24 2014 - 20:51:35 PST)
- Lachele Foley (Mon Nov 24 2014 - 10:18:56 PST)
- Jason Swails (Mon Nov 24 2014 - 08:20:03 PST)
- maryam azimzadehirani (Mon Nov 24 2014 - 00:11:31 PST)
[AMBER] GPU enabled Hardware specification
- M. Reza Ganjalikhany (Mon Nov 17 2014 - 12:28:15 PST)
- Ross Walker (Mon Nov 17 2014 - 11:35:24 PST)
- M. Reza Ganjalikhany (Mon Nov 17 2014 - 01:17:18 PST)
- Ross Walker (Sun Nov 16 2014 - 12:22:46 PST)
- M. Reza Ganjalikhany (Sat Nov 15 2014 - 23:49:46 PST)
- Ross Walker (Sat Nov 15 2014 - 12:49:49 PST)
- M. Reza Ganjalikhany (Sat Nov 15 2014 - 02:41:01 PST)
[AMBER] GTX 780 Ti & GTX 980
- Ross Walker (Wed Nov 26 2014 - 13:18:39 PST)
- Jordi Bujons (Wed Nov 26 2014 - 09:35:06 PST)
[AMBER] H-REMD
- Jason Swails (Wed Nov 05 2014 - 09:05:07 PST)
- Carlos Simmerling (Wed Nov 05 2014 - 08:52:48 PST)
- Mele N. (Wed Nov 05 2014 - 08:20:33 PST)
[AMBER] hbonds
- Mary Varughese (Sat Nov 08 2014 - 09:23:36 PST)
- Jason Swails (Fri Nov 07 2014 - 05:02:11 PST)
- Mary Varughese (Fri Nov 07 2014 - 02:27:10 PST)
[AMBER] HEAT and PROD files for 10 ns run
- Jason Swails (Sat Nov 08 2014 - 09:11:34 PST)
- Ruchika Bhat (Sat Nov 08 2014 - 08:45:44 PST)
[AMBER] help
- Jason Swails (Mon Nov 17 2014 - 10:48:24 PST)
- Robin Jain (Mon Nov 17 2014 - 09:30:41 PST)
- David A Case (Thu Nov 13 2014 - 03:57:42 PST)
- Robin Jain (Wed Nov 12 2014 - 21:59:24 PST)
[AMBER] Help generating Heme parameters
- Pengfei Li (Fri Nov 21 2014 - 07:18:00 PST)
- 杨川 (Tue Nov 18 2014 - 23:20:29 PST)
[AMBER] help in MD
- Ayesha Fatima (Thu Nov 13 2014 - 03:09:10 PST)
- Robin Jain (Wed Nov 12 2014 - 23:48:20 PST)
[AMBER] Help needed regarding Ligand Protein MD studies
- Ruchika Bhat (Sat Nov 08 2014 - 07:47:27 PST)
- David A Case (Sat Nov 08 2014 - 07:14:42 PST)
- Ruchika Bhat (Fri Nov 07 2014 - 10:16:27 PST)
- Ruchika Bhat (Fri Nov 07 2014 - 10:11:11 PST)
- Wei Ye (Fri Nov 07 2014 - 06:52:31 PST)
- Ruchika Bhat (Fri Nov 07 2014 - 06:47:01 PST)
- Gulsevin,Alican (Fri Nov 07 2014 - 06:38:48 PST)
- Wei Ye (Fri Nov 07 2014 - 06:17:02 PST)
- Jason Swails (Fri Nov 07 2014 - 06:12:48 PST)
- Ruchika Bhat (Fri Nov 07 2014 - 05:39:07 PST)
[AMBER] heme amber parameter
- David A Case (Sat Nov 15 2014 - 17:58:46 PST)
- Fatemeh Sadat Alavi (Sat Nov 15 2014 - 07:56:27 PST)
[AMBER] How to restrain atoms
- Akihiro Yamane (Fri Nov 28 2014 - 04:57:26 PST)
- David A Case (Wed Nov 26 2014 - 05:11:30 PST)
- Akihiro Yamane (Tue Nov 25 2014 - 22:03:13 PST)
[AMBER] How to seperate a protein-protein complex in PRMTOP and INPCRD files?
- Daniel Roe (Mon Nov 24 2014 - 07:26:46 PST)
- Jason Swails (Sun Nov 23 2014 - 17:42:54 PST)
- LI An-Bang (Sun Nov 23 2014 - 16:27:56 PST)
[AMBER] hydophobicity
- Daniel Roe (Sun Nov 30 2014 - 10:42:13 PST)
- Mary Varughese (Thu Nov 27 2014 - 09:43:11 PST)
- Jason Swails (Thu Nov 27 2014 - 03:34:51 PST)
- Mary Varughese (Wed Nov 26 2014 - 22:00:03 PST)
- Jason Swails (Wed Nov 26 2014 - 15:28:04 PST)
- Mary Varughese (Mon Nov 24 2014 - 23:59:24 PST)
[AMBER] Imaging
- Daniel Roe (Mon Nov 03 2014 - 10:45:09 PST)
[AMBER] Implicit simulation and MMPBSA/GBSA caculations
- Aron Broom (Sun Nov 09 2014 - 11:53:58 PST)
- Jason Swails (Sun Nov 09 2014 - 06:10:58 PST)
- Bajarang Kumbhar (Sat Nov 08 2014 - 22:26:51 PST)
[AMBER] InputError when running MMBPSA.py
- Jason Swails (Tue Nov 18 2014 - 22:52:46 PST)
- HERBERT MAX VENTHUR PE¥A (Tue Nov 18 2014 - 18:16:54 PST)
[AMBER] Installation error: recipe for target 'pupildata.o' failed
- Parker de Waal (Sun Nov 23 2014 - 18:18:10 PST)
- Jason Swails (Sun Nov 23 2014 - 17:36:22 PST)
- Parker de Waal (Sun Nov 23 2014 - 13:59:02 PST)
- Jason Swails (Sun Nov 23 2014 - 09:55:57 PST)
- Parker de Waal (Sun Nov 23 2014 - 08:24:25 PST)
- Jason Swails (Sat Nov 22 2014 - 20:58:01 PST)
- Parker de Waal (Sat Nov 22 2014 - 19:47:44 PST)
- David A Case (Sat Nov 22 2014 - 18:09:49 PST)
- Parker de Waal (Sat Nov 22 2014 - 17:03:29 PST)
- Parker de Waal (Sat Nov 22 2014 - 14:37:30 PST)
[AMBER] installing amber12 in GPU
- Jason Swails (Fri Nov 28 2014 - 15:31:46 PST)
- Vijay Achari (Fri Nov 28 2014 - 05:49:35 PST)
[AMBER] Interaction energy between two dimer unit
- Jason Swails (Fri Nov 28 2014 - 16:03:44 PST)
- Soumendranath Bhakat (Thu Nov 27 2014 - 21:26:21 PST)
[AMBER] Is it possible to extract atomic charge information from the trajectory?
- Jason Swails (Tue Nov 18 2014 - 22:47:21 PST)
- Yip Yew Mun (Tue Nov 18 2014 - 18:53:20 PST)
[AMBER] Is there a tool to calculate electron density maps averaged over a trajectory?
- Pawel Janowski (Mon Nov 24 2014 - 14:43:57 PST)
- Jose Borreguero (Sat Nov 15 2014 - 06:58:23 PST)
- David A Case (Fri Nov 14 2014 - 18:31:54 PST)
- Jose Borreguero (Fri Nov 14 2014 - 15:16:10 PST)
[AMBER] Issue with DFTB-MD trajectory
- Perry, Jamin W. (Sun Nov 16 2014 - 22:19:05 PST)
- David A Case (Tue Nov 11 2014 - 03:56:44 PST)
- Perry, Jamin W. (Sun Nov 09 2014 - 14:02:08 PST)
[AMBER] Issues with Cholesterol lipid11, lipid14 and lipid14_supp.lib
- Jonathan Gough (Fri Nov 21 2014 - 10:15:02 PST)
[AMBER] Metal parameterization
- Ken Merz (Sat Nov 29 2014 - 05:11:56 PST)
- sailu (Fri Nov 28 2014 - 20:50:46 PST)
[AMBER] minimization problem
- Emilio Angelina (Fri Nov 14 2014 - 06:49:18 PST)
- David A Case (Fri Nov 14 2014 - 04:59:56 PST)
- Emilio Angelina (Thu Nov 13 2014 - 12:52:28 PST)
[AMBER] minimization question
- Carlos Romero (Fri Nov 28 2014 - 07:38:53 PST)
- David A Case (Fri Nov 28 2014 - 07:32:41 PST)
- Carlos Romero (Fri Nov 28 2014 - 07:03:37 PST)
[AMBER] MMPBSA warning : No skew or curtosis when zero variance in moment
- Jason Swails (Mon Nov 17 2014 - 05:57:32 PST)
- Mina Madah (Mon Nov 17 2014 - 00:23:22 PST)
[AMBER] MMPBSA.py
- Jason Swails (Sun Nov 09 2014 - 14:49:26 PST)
- Sourav Purohit (Sun Nov 09 2014 - 11:20:22 PST)
[AMBER] MMPBSA.py bug with amber mask for stability/QH calculations
- Jason Swails (Thu Nov 20 2014 - 15:47:42 PST)
- Lawrenz, Morgan (Thu Nov 20 2014 - 15:34:06 PST)
[AMBER] MMPBSA.py nmode
- Jason Swails (Mon Nov 17 2014 - 06:02:28 PST)
- Sourav Purohit (Sun Nov 16 2014 - 18:13:37 PST)
[AMBER] MMPBSA.py normal mode analysis
- Sourav Purohit (Mon Nov 17 2014 - 12:08:53 PST)
- Jason Swails (Mon Nov 17 2014 - 12:08:39 PST)
- Sourav Purohit (Mon Nov 17 2014 - 12:00:19 PST)
[AMBER] Monitoring pi-cationic interaction
- Daniel Roe (Sun Nov 30 2014 - 11:01:11 PST)
- asdda asa (Fri Nov 28 2014 - 23:12:14 PST)
[AMBER] nativecontacts in ambertools14
- Daniel Roe (Tue Nov 11 2014 - 11:55:40 PST)
- Asmita Gupta (Tue Nov 11 2014 - 09:03:31 PST)
[AMBER] NBCR AMBER Workshop - UCSD - Mon Dec 15th to Thur Dec 18th 2014 - Registration open.
- Ross Walker (Wed Nov 05 2014 - 12:40:05 PST)
[AMBER] nmr restraints and periodic boundary conditions
- David A Case (Tue Nov 18 2014 - 17:50:37 PST)
- Niel Henriksen (Tue Nov 18 2014 - 15:02:07 PST)
- Jason Swails (Tue Nov 18 2014 - 14:57:54 PST)
- Chris Moth (Tue Nov 18 2014 - 14:20:06 PST)
[AMBER] NVT and NPT ensemble
- Sangita Kachhap (Mon Nov 03 2014 - 06:20:37 PST)
- Jason Swails (Mon Nov 03 2014 - 06:23:17 PST)
- Sangita Kachhap (Mon Nov 03 2014 - 05:56:21 PST)
- Jason Swails (Mon Nov 03 2014 - 04:53:42 PST)
- Sangita Kachhap (Sun Nov 02 2014 - 21:07:05 PST)
[AMBER] options "-ext" and "-pqr" of ambpdb are exlusive
- LI An-Bang (Sun Nov 16 2014 - 16:21:34 PST)
- David A Case (Fri Nov 14 2014 - 05:19:36 PST)
- Daniel Roe (Wed Nov 12 2014 - 07:27:02 PST)
- LI An-Bang (Tue Nov 11 2014 - 19:48:52 PST)
[AMBER] Pairwise vs Sander with imin=5
- Daniel Roe (Thu Nov 20 2014 - 10:01:58 PST)
- kurisaki (Wed Nov 19 2014 - 22:02:00 PST)
- Daniel Roe (Wed Nov 19 2014 - 21:14:27 PST)
- kurisaki (Wed Nov 19 2014 - 18:01:08 PST)
[AMBER] PARALLEL INSTALLATION ERROR
- Jason Swails (Sun Nov 30 2014 - 04:46:59 PST)
- Nalini Chauhan (Sun Nov 30 2014 - 03:47:23 PST)
[AMBER] PBSA error
- Ray Luo, Ph.D. (Thu Nov 20 2014 - 14:49:07 PST)
- Kshatresh Dutta Dubey (Thu Nov 20 2014 - 12:52:22 PST)
- Kshatresh Dutta Dubey (Thu Nov 20 2014 - 12:45:49 PST)
- David A Case (Thu Nov 20 2014 - 12:42:25 PST)
- David A Case (Thu Nov 20 2014 - 12:32:45 PST)
- Jason Swails (Thu Nov 20 2014 - 12:21:23 PST)
- Kshatresh Dutta Dubey (Thu Nov 20 2014 - 10:10:08 PST)
[AMBER] pmemd.MPI thermodynamic integration (TI) relative binding free energy set up
- hannes.loeffler.stfc.ac.uk (Sat Nov 15 2014 - 00:40:15 PST)
- psu4.uic.edu (Fri Nov 14 2014 - 14:32:49 PST)
[AMBER] Postdoctoral Position at the U.S. Army Research Laboratory in Coarse-Grain Modeling and Simulation
- Izvyekov, Sergiy (Sergey) CIV USARMY ARL (US) (Fri Nov 14 2014 - 13:11:51 PST)
[AMBER] Prmtop
- Jason Swails (Sat Nov 15 2014 - 09:51:34 PST)
- Sylvester Tumusiime (Sat Nov 15 2014 - 08:55:40 PST)
[AMBER] Problem regarding Chamber and psf file
- Pete Kekenes-Huskey (Sun Nov 02 2014 - 17:18:23 PST)
- Jason Swails (Sat Nov 01 2014 - 15:35:39 PDT)
[AMBER] problem reimaging after strip WAT
- nabil bennenni (Tue Nov 11 2014 - 09:16:06 PST)
- Pablo D. Dans Puiggròs (Tue Nov 11 2014 - 08:24:03 PST)
- Daniel Roe (Tue Nov 11 2014 - 08:05:15 PST)
- Pablo D. Dans Puiggròs (Tue Nov 11 2014 - 07:59:36 PST)
- Jason Swails (Tue Nov 11 2014 - 07:28:09 PST)
- Pablo D. Dans Puiggròs (Tue Nov 11 2014 - 07:24:34 PST)
[AMBER] problem using pmemd.cuda with barostat=2 option
- Sorensen, Jesper (Wed Nov 05 2014 - 12:27:36 PST)
- Jason Swails (Wed Nov 05 2014 - 10:47:20 PST)
- Ross Walker (Wed Nov 05 2014 - 09:41:58 PST)
- Scott Le Grand (Wed Nov 05 2014 - 10:23:44 PST)
- Sorensen, Jesper (Wed Nov 05 2014 - 10:18:57 PST)
[AMBER] Problem with triangular point in parameter file
- Jorgen Simonsen (Sun Nov 30 2014 - 14:53:42 PST)
- David A Case (Sun Nov 30 2014 - 12:43:36 PST)
- Jorgen Simonsen (Sun Nov 30 2014 - 09:52:56 PST)
[AMBER] Problems of pdb file convertion by pdb4amber and mmtsb
- Jason Swails (Mon Nov 10 2014 - 04:42:29 PST)
- David A Case (Mon Nov 10 2014 - 04:12:02 PST)
- LI An-Bang (Sun Nov 09 2014 - 18:31:43 PST)
[AMBER] Problems on PRMTOP file generation under ff02pol.r1
- Wei Ye (Fri Nov 07 2014 - 06:01:54 PST)
- David A Case (Fri Nov 07 2014 - 05:53:09 PST)
- Wei Ye (Thu Nov 06 2014 - 20:09:02 PST)
[AMBER] Problems with AmberTools test suite
- David A Case (Thu Nov 20 2014 - 08:15:31 PST)
[AMBER] QM/MM adaptive biased MD_ABMD
- Aixiao Li (Fri Nov 28 2014 - 12:32:36 PST)
- David A Case (Fri Nov 28 2014 - 09:28:25 PST)
- Aixiao Li (Fri Nov 28 2014 - 08:36:12 PST)
[AMBER] Questions regarding GB simulations in Amber14 - ff14SBonlysc vs ff14SB - igb1 vs igb8 - hydrphobic force
- Marek Maly (Sun Nov 23 2014 - 18:40:49 PST)
- Carlos Simmerling (Fri Nov 21 2014 - 18:35:02 PST)
- Marek Maly (Fri Nov 21 2014 - 17:58:14 PST)
[AMBER] Regarding pairdist function in cpptraj
- DEBOSTUTI GHOSHDASTIDAR (Mon Nov 17 2014 - 21:56:15 PST)
- Daniel Roe (Mon Nov 17 2014 - 07:17:31 PST)
- DEBOSTUTI GHOSHDASTIDAR (Mon Nov 17 2014 - 06:49:06 PST)
[AMBER] Reminder: NBCR AMBER Workshop - UCSD - Mon Dec 15th to Thur Dec 18th 2014 - Registration open.
- Ross Walker (Wed Nov 19 2014 - 21:39:51 PST)
[AMBER] Representing Sphere and Its parameterization in Amber.
- ATUL KUMAR (Thu Nov 13 2014 - 04:21:35 PST)
- ATUL KUMAR (Tue Nov 11 2014 - 22:30:38 PST)
- David A Case (Tue Nov 11 2014 - 03:47:48 PST)
- ATUL KUMAR (Mon Nov 10 2014 - 22:42:50 PST)
[AMBER] restart file position
- Jason Swails (Sun Nov 02 2014 - 06:15:49 PST)
- Fabian Glaser (Sun Nov 02 2014 - 05:57:19 PST)
[AMBER] Running explicit solvent CpHMD on GPUs
- Garrido Ruiz, Diego (Wed Nov 12 2014 - 11:40:52 PST)
[AMBER] simulation of peptide in alkane slab
- samarprit chakraborty (Sun Nov 09 2014 - 02:38:23 PST)
- nabil bennenni (Sat Nov 08 2014 - 11:15:49 PST)
- samarprit chakraborty (Sat Nov 08 2014 - 09:43:30 PST)
[AMBER] single dimension PMF calculation
- joan.montesdeoca.uns.edu.ar (Mon Nov 03 2014 - 16:32:59 PST)
[AMBER] small molecules
- David A Case (Mon Nov 10 2014 - 14:11:34 PST)
- Lara rajam (Mon Nov 10 2014 - 12:46:02 PST)
[AMBER] Strange behavior AMBER12
- IBRAHIM M ABDELRADY (Mon Nov 03 2014 - 08:15:12 PST)
- IBRAHIM M ABDELRADY (Mon Nov 03 2014 - 07:57:51 PST)
- Jason Swails (Mon Nov 03 2014 - 07:56:40 PST)
- Adrian Roitberg (Mon Nov 03 2014 - 07:55:22 PST)
- IBRAHIM M ABDELRADY (Mon Nov 03 2014 - 07:52:59 PST)
[AMBER] The error when install amber12+AmberTools13 on Ubuntucd
- Biao Ma (Mon Nov 24 2014 - 18:26:25 PST)
- Jason Swails (Thu Nov 20 2014 - 19:06:29 PST)
- Biao Ma (Thu Nov 20 2014 - 18:31:18 PST)
[AMBER] The question about REMD exchange ratio
- 王漠野 (Thu Nov 13 2014 - 17:34:09 PST)
- Jason Swails (Thu Nov 13 2014 - 05:17:18 PST)
- Carlos Simmerling (Thu Nov 13 2014 - 03:35:05 PST)
- 王漠野 (Wed Nov 12 2014 - 22:43:55 PST)
- Jason Swails (Mon Nov 03 2014 - 06:03:25 PST)
- 王漠野 (Mon Nov 03 2014 - 05:12:50 PST)
[AMBER] Thermodynamic integration: Delta G of less soft core atoms is different from the one with more soft core atoms
- Hannes Loeffler (Mon Nov 24 2014 - 08:21:51 PST)
- sun (Mon Nov 24 2014 - 08:10:22 PST)
[AMBER] time correlation function
- Daniel Roe (Thu Nov 13 2014 - 07:09:54 PST)
- giulia palermo (Thu Nov 13 2014 - 03:44:52 PST)
- Daniel Roe (Wed Nov 12 2014 - 10:37:44 PST)
- giulia palermo (Wed Nov 12 2014 - 10:04:00 PST)
[AMBER] tleap not found in parallel amber14
- Jason Swails (Tue Nov 18 2014 - 06:53:47 PST)
- Amihai (Tue Nov 18 2014 - 06:12:45 PST)
[AMBER] Transition state
- Jason Swails (Thu Nov 13 2014 - 05:24:30 PST)
- Mahmood Jasim (Thu Nov 13 2014 - 01:43:51 PST)
- John Smith (Mon Nov 10 2014 - 10:13:36 PST)
[AMBER] Which force field is "the best"
- Gonzalo Jimenez (Mon Nov 10 2014 - 04:20:55 PST)
- David A Case (Sun Nov 09 2014 - 14:29:46 PST)
- Gonzalo Jimenez (Sun Nov 09 2014 - 11:10:41 PST)
[AMBER] writing out restart files in netcdf format
- Christina Bergonzo (Fri Nov 07 2014 - 08:39:24 PST)
- Sylvester Tumusiime (Fri Nov 07 2014 - 08:33:13 PST)
- Christina Bergonzo (Fri Nov 07 2014 - 08:30:36 PST)
- Sylvester Tumusiime (Fri Nov 07 2014 - 08:24:41 PST)
[AMBER] xLEaP Na+ Cl-
- Asaminew Haile (Thu Nov 27 2014 - 04:05:42 PST)
- Weinzierl, Robert O J (Thu Nov 27 2014 - 04:01:03 PST)
[q4md-fft] FAD wrong geometry in F-90 project
- FyD (Sat Nov 01 2014 - 22:39:35 PDT)

Amber Archive Nov 2014 by subject