Amber Archive Oct 2014: by subject

[AMBER] 3D Histogram in cpptraj
- Daniel Roe (Fri Oct 31 2014 - 09:53:42 PDT)
- CHAMI F. (Thu Oct 30 2014 - 10:31:17 PDT)
- Asaminew Haile (Thu Oct 30 2014 - 10:25:55 PDT)
- CHAMI F. (Thu Oct 30 2014 - 10:18:44 PDT)
[AMBER] About error of the Pmemd.cuda (14)/ aMD
- Daniel Roe (Sun Oct 12 2014 - 09:34:59 PDT)
- Yeng-Tseng Wang (Sun Oct 12 2014 - 07:15:07 PDT)
[AMBER] About geometry of FAD in the F-90 project of http://q4md-forcefieldtools.org/
- Emilio Lence (Fri Oct 31 2014 - 05:47:31 PDT)
[AMBER] Amber 14 compile error
- David A Case (Mon Oct 13 2014 - 18:10:12 PDT)
- 汪盛 (Mon Oct 13 2014 - 15:12:26 PDT)
[AMBER] Amber for beginner
- Raman Parkesh (Tue Oct 14 2014 - 20:01:55 PDT)
- Jonathan Gough (Tue Oct 14 2014 - 18:01:40 PDT)
- Suraya Abdul Sani (Tue Oct 14 2014 - 17:21:29 PDT)
[AMBER] AMBER GAUSSIAN QM/MM
- Ayesha Fatima (Fri Oct 24 2014 - 01:52:46 PDT)
- Marc van der Kamp (Fri Oct 24 2014 - 01:07:50 PDT)
- Ayesha Fatima (Fri Oct 24 2014 - 00:23:29 PDT)
[AMBER] amber-Gaussian
- 王珍 (Thu Oct 16 2014 - 05:41:43 PDT)
[AMBER] amber12 Installation Error MAC OS X
- BERGY (Tue Oct 07 2014 - 15:12:11 PDT)
- BERGY (Tue Oct 07 2014 - 14:46:12 PDT)
- David A Case (Tue Oct 07 2014 - 13:27:14 PDT)
- BERGY (Tue Oct 07 2014 - 12:14:34 PDT)
[AMBER] ANTECHAMBER tutorial
- Sourav Purohit (Wed Oct 22 2014 - 05:43:29 PDT)
- Jason Swails (Wed Oct 22 2014 - 05:41:57 PDT)
- Sourav Purohit (Wed Oct 22 2014 - 03:35:04 PDT)
[AMBER] atom coordinate disagreement with sander TI
- Hannes Loeffler (Thu Oct 09 2014 - 08:15:30 PDT)
- David A Case (Thu Oct 09 2014 - 05:25:52 PDT)
- Hannes Loeffler (Thu Oct 09 2014 - 04:15:27 PDT)
[AMBER] ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 46946 0
- David A Case (Mon Oct 13 2014 - 18:02:29 PDT)
- Hirdesh Kumar (Mon Oct 13 2014 - 13:41:58 PDT)
- David A Case (Mon Oct 13 2014 - 13:28:37 PDT)
- Hirdesh Kumar (Mon Oct 13 2014 - 13:19:50 PDT)
[AMBER] BSUB on LSF cluster
- Jason Swails (Tue Oct 21 2014 - 17:56:05 PDT)
- D.A. Ragland (Tue Oct 21 2014 - 17:18:47 PDT)
- D.A. Ragland (Tue Oct 21 2014 - 17:12:02 PDT)
- Jason Swails (Tue Oct 21 2014 - 17:10:02 PDT)
- D.A. Ragland (Tue Oct 21 2014 - 14:54:55 PDT)
[AMBER] Building Amber 14 for Intel PHIs
- Baker D.J. (Tue Oct 14 2014 - 01:44:18 PDT)
- Ross Walker (Mon Oct 13 2014 - 11:31:09 PDT)
- Baker D.J. (Mon Oct 13 2014 - 02:10:31 PDT)
[AMBER] Calcium possibly replaced by carbon with MCPB
- Pengfei Li (Tue Oct 14 2014 - 21:17:05 PDT)
- mmaestre.gate.sinica.edu.tw (Tue Oct 14 2014 - 18:25:07 PDT)
- mmaestre.gate.sinica.edu.tw (Tue Oct 14 2014 - 15:11:34 PDT)
- Pengfei Li (Tue Oct 14 2014 - 08:30:12 PDT)
- Pengfei Li (Tue Oct 14 2014 - 08:26:44 PDT)
- mmaestre.gate.sinica.edu.tw (Mon Oct 13 2014 - 16:28:38 PDT)
- mmaestre.gate.sinica.edu.tw (Mon Oct 13 2014 - 16:22:45 PDT)
- mmaestre.gate.sinica.edu.tw (Mon Oct 13 2014 - 16:19:41 PDT)
- FyD (Mon Oct 13 2014 - 12:40:29 PDT)
- Pengfei Li (Mon Oct 13 2014 - 07:45:43 PDT)
- Ken Merz (Mon Oct 13 2014 - 07:39:03 PDT)
- mmaestre.gate.sinica.edu.tw (Mon Oct 13 2014 - 07:22:03 PDT)
- Ken Merz (Mon Oct 13 2014 - 05:06:03 PDT)
- mmaestre.gate.sinica.edu.tw (Sun Oct 12 2014 - 17:00:12 PDT)
[AMBER] carbon and nitrogen chemical shift restraints
- Alexandra Balaceanu (Fri Oct 03 2014 - 12:03:59 PDT)
- David A Case (Fri Oct 03 2014 - 06:32:15 PDT)
- Alexandra Balaceanu (Fri Oct 03 2014 - 01:54:45 PDT)
[AMBER] Carboxyl and Carboxylate groups with GLYCAM
- sa (Tue Oct 21 2014 - 14:24:21 PDT)
- Lachele Foley (Tue Oct 21 2014 - 13:57:27 PDT)
- sa (Tue Oct 21 2014 - 13:32:59 PDT)
- Lachele Foley (Tue Oct 21 2014 - 13:06:12 PDT)
- sa (Tue Oct 21 2014 - 11:33:36 PDT)
- Lachele Foley (Tue Oct 21 2014 - 10:44:32 PDT)
- sa (Mon Oct 20 2014 - 08:52:47 PDT)
[AMBER] Chains missing during the simulation
- Harshavardhan Khare (Wed Oct 22 2014 - 04:23:31 PDT)
- Jason Swails (Tue Oct 21 2014 - 04:39:46 PDT)
- Harshavardhan Khare (Tue Oct 21 2014 - 00:56:58 PDT)
[AMBER] Chloroform box
- Jason Swails (Tue Oct 07 2014 - 04:52:18 PDT)
- David A Case (Tue Oct 07 2014 - 04:30:20 PDT)
- Neha Gandhi (Tue Oct 07 2014 - 00:49:12 PDT)
[AMBER] Cluster RMSD
- Daniel Roe (Fri Oct 03 2014 - 07:15:58 PDT)
- Soumendranath Bhakat (Fri Oct 03 2014 - 02:48:54 PDT)
[AMBER] Complex MD with protein ligand covalent bond
- David A Case (Mon Oct 20 2014 - 05:10:28 PDT)
- Bikash Ranjan Sahoo (Mon Oct 20 2014 - 00:01:36 PDT)
[AMBER] cpptraj hbond: query on output
- Daniel Roe (Thu Oct 09 2014 - 18:14:53 PDT)
- George Tzotzos (Thu Oct 09 2014 - 17:00:58 PDT)
- Daniel Roe (Thu Oct 09 2014 - 15:24:35 PDT)
- George Tzotzos (Thu Oct 09 2014 - 13:33:25 PDT)
[AMBER] cpptraj Tutorial C1
- Daniel Roe (Fri Oct 03 2014 - 11:57:56 PDT)
- Jason Swails (Fri Oct 03 2014 - 11:50:06 PDT)
- George Tzotzos (Fri Oct 03 2014 - 11:36:40 PDT)
- George Tzotzos (Fri Oct 03 2014 - 11:25:11 PDT)
[AMBER] Cpptraj: Move origin to specific coordinates
- Daniel Roe (Tue Oct 21 2014 - 09:07:31 PDT)
- Waldner, Birgit (Tue Oct 21 2014 - 08:37:15 PDT)
- Daniel Roe (Tue Oct 21 2014 - 08:06:58 PDT)
- Waldner, Birgit (Tue Oct 21 2014 - 06:09:31 PDT)
[AMBER] crashing multisander with TI/dummy
- Hannes Loeffler (Fri Oct 10 2014 - 04:11:21 PDT)
[AMBER] CUDA test failed
- Jason Swails (Fri Oct 10 2014 - 09:25:21 PDT)
- Niels Geudens (Fri Oct 10 2014 - 03:42:56 PDT)
[AMBER] dendrimer-query
- Vishal Maingi (Thu Oct 16 2014 - 08:03:09 PDT)
- Daniel Roe (Tue Oct 14 2014 - 13:49:24 PDT)
- Vishal Maingi (Mon Oct 13 2014 - 08:33:34 PDT)
- Daniel Roe (Sun Oct 12 2014 - 10:14:57 PDT)
- Martiniano Bello Ramirez (Sun Oct 12 2014 - 09:59:42 PDT)
[AMBER] Desmond trajectory use with AMBER
- Daniel Roe (Sun Oct 19 2014 - 12:20:01 PDT)
- D.A. Ragland (Sun Oct 19 2014 - 12:09:36 PDT)
- Daniel Roe (Sun Oct 19 2014 - 12:06:49 PDT)
- D.A. Ragland (Sun Oct 19 2014 - 11:53:11 PDT)
[AMBER] DFTB3 in Amber
- Gustavo Seabra (Mon Oct 13 2014 - 05:50:07 PDT)
- Eric Lang (Sun Oct 12 2014 - 20:26:02 PDT)
[AMBER] Dummy atom and PMEMD
- Jason Swails (Mon Oct 06 2014 - 04:26:38 PDT)
- Miroslav Krepl (Mon Oct 06 2014 - 01:13:10 PDT)
- Jason Swails (Sun Oct 05 2014 - 18:02:01 PDT)
- Miroslav Krepl (Sun Oct 05 2014 - 13:11:58 PDT)
[AMBER] Entropy calculation
- asdda asa (Wed Oct 29 2014 - 20:31:58 PDT)
- Jason Swails (Wed Oct 29 2014 - 10:44:29 PDT)
- asdda asa (Tue Oct 28 2014 - 19:38:13 PDT)
[AMBER] Error: FFTW configure returned 77 during AMBER 12 installation
- sunita.tifrh.res.in (Thu Oct 09 2014 - 06:02:20 PDT)
- Jason Swails (Thu Oct 09 2014 - 05:30:53 PDT)
- sunita.tifrh.res.in (Thu Oct 09 2014 - 00:11:14 PDT)
[AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer
- Pablo Ródenas (Tue Oct 28 2014 - 01:39:25 PDT)
- Scott Le Grand (Tue Oct 14 2014 - 09:11:37 PDT)
- Pablo Ródenas (Tue Oct 14 2014 - 07:03:02 PDT)
- Scott Le Grand (Tue Oct 14 2014 - 06:54:15 PDT)
- Pablo Ródenas (Tue Oct 14 2014 - 00:44:23 PDT)
- Pablo Ródenas (Sun Oct 12 2014 - 23:45:34 PDT)
- Scott Le Grand (Fri Oct 10 2014 - 12:16:41 PDT)
- Pablo Ródenas (Thu Oct 09 2014 - 23:36:43 PDT)
- Scott Le Grand (Thu Oct 09 2014 - 09:06:43 PDT)
- Scott Le Grand (Thu Oct 09 2014 - 08:54:42 PDT)
- Pablo Ródenas (Thu Oct 09 2014 - 08:54:37 PDT)
- Pablo Ródenas (Thu Oct 09 2014 - 08:44:42 PDT)
- Scott Le Grand (Thu Oct 09 2014 - 08:25:28 PDT)
- Scott Le Grand (Thu Oct 09 2014 - 08:23:37 PDT)
- Pablo Ródenas (Thu Oct 09 2014 - 08:20:38 PDT)
- Scott Le Grand (Thu Oct 09 2014 - 08:09:46 PDT)
- Scott Le Grand (Thu Oct 09 2014 - 08:06:14 PDT)
- Scott Le Grand (Thu Oct 09 2014 - 07:58:26 PDT)
- Pablo Ródenas (Thu Oct 09 2014 - 07:22:37 PDT)
[AMBER] Errors while attempting .prmtop file production
- David A Case (Tue Oct 14 2014 - 12:12:15 PDT)
- Evans, Shalton (Tue Oct 14 2014 - 09:09:02 PDT)
[AMBER] force field for lithium ion
- Mohd Farid Ismail (Thu Oct 09 2014 - 16:38:58 PDT)
- Evans, Shalton (Thu Oct 09 2014 - 16:11:11 PDT)
[AMBER] Forcefield for RNA
- Asfa Ali (Sat Oct 25 2014 - 04:19:22 PDT)
- Jason Swails (Fri Oct 24 2014 - 06:19:43 PDT)
- Asfa Ali (Fri Oct 24 2014 - 05:46:02 PDT)
- Jiri Sponer (Thu Oct 23 2014 - 14:15:20 PDT)
- koushik (Thu Oct 23 2014 - 14:06:58 PDT)
- koushik (Thu Oct 23 2014 - 14:03:54 PDT)
- Jiri Sponer (Thu Oct 23 2014 - 13:58:58 PDT)
- pavel.banas.upol.cz (Thu Oct 23 2014 - 13:54:28 PDT)
- David A Case (Thu Oct 23 2014 - 04:54:12 PDT)
- Asfa Ali (Thu Oct 23 2014 - 04:26:48 PDT)
- Jason Swails (Thu Oct 23 2014 - 04:07:19 PDT)
- Ilyas Yildirim (Thu Oct 23 2014 - 02:26:01 PDT)
- Jiri Sponer (Thu Oct 23 2014 - 01:12:50 PDT)
- Jiri Sponer (Thu Oct 23 2014 - 00:57:06 PDT)
- Asfa Ali (Wed Oct 22 2014 - 22:52:47 PDT)
[AMBER] Forcefield_PTM
- Sourav Purohit (Tue Oct 21 2014 - 08:35:00 PDT)
- David A Case (Tue Oct 21 2014 - 07:47:22 PDT)
- Jason Swails (Tue Oct 21 2014 - 06:02:30 PDT)
- Sourav Purohit (Tue Oct 21 2014 - 05:25:40 PDT)
- Sourav Purohit (Mon Oct 13 2014 - 02:35:31 PDT)
- Ying-Chieh Sun (Sun Oct 12 2014 - 20:04:21 PDT)
- Adrian Roitberg (Sat Oct 11 2014 - 15:54:09 PDT)
- Sourav Purohit (Sat Oct 11 2014 - 11:22:12 PDT)
[AMBER] Fwd: Desmond trajectory use with AMBER
- jojartb.jgypk.u-szeged.hu (Sun Oct 19 2014 - 21:15:39 PDT)
- Daniel Roe (Sun Oct 19 2014 - 11:49:37 PDT)
- D.A. Ragland (Sun Oct 19 2014 - 11:26:28 PDT)
[AMBER] Fwd: parallel amber installation failed
- Fabian Gmail (Tue Oct 07 2014 - 11:14:39 PDT)
- Jason Swails (Tue Oct 07 2014 - 10:58:59 PDT)
- Jason Swails (Tue Oct 07 2014 - 10:55:49 PDT)
- David A Case (Tue Oct 07 2014 - 10:53:30 PDT)
- Fabian Glaser (Tue Oct 07 2014 - 09:42:58 PDT)
- Daniel Roe (Tue Oct 07 2014 - 07:29:17 PDT)
- Fabian (Tue Oct 07 2014 - 06:45:39 PDT)
[AMBER] GIST dx files
- Gard Nelson (Tue Oct 14 2014 - 15:23:51 PDT)
- Nguyen, Crystal (Tue Oct 14 2014 - 12:31:59 PDT)
- Jonathan Gough (Tue Oct 14 2014 - 12:34:28 PDT)
- Gard Nelson (Tue Oct 14 2014 - 11:42:35 PDT)
[AMBER] GPU enabled Hardware specification
- Ross Walker (Tue Oct 28 2014 - 14:02:49 PDT)
- Scott Le Grand (Tue Oct 28 2014 - 12:59:37 PDT)
- M. Reza Ganjalikhany (Tue Oct 28 2014 - 12:50:36 PDT)
- Ross Walker (Tue Oct 28 2014 - 07:53:31 PDT)
- Jonathan Gough (Tue Oct 28 2014 - 07:42:41 PDT)
- Jonathan Gough (Tue Oct 28 2014 - 06:35:20 PDT)
- M. Reza Ganjalikhany (Tue Oct 28 2014 - 02:41:10 PDT)
- Scott Le Grand (Mon Oct 27 2014 - 14:19:45 PDT)
- M. Reza Ganjalikhany (Mon Oct 27 2014 - 13:39:41 PDT)
[AMBER] Heating Problem
- Daniel Roe (Sun Oct 19 2014 - 12:01:39 PDT)
- jinfeng liu (Sun Oct 19 2014 - 11:49:21 PDT)
[AMBER] help: MD on DNA
- Jason Swails (Fri Oct 03 2014 - 09:23:37 PDT)
- pradeep pant (Fri Oct 03 2014 - 07:15:58 PDT)
- David A Case (Thu Oct 02 2014 - 05:17:00 PDT)
- pradeep pant (Thu Oct 02 2014 - 03:33:58 PDT)
[AMBER] Heme Parameters
- David A Case (Fri Oct 24 2014 - 05:29:17 PDT)
- Jason Swails (Fri Oct 24 2014 - 04:44:57 PDT)
- 杨川 (Fri Oct 24 2014 - 01:08:42 PDT)
[AMBER] How can I do MD simulation of a protein-ligand complex where the ligand is covalently attached to the protein
- Bikash Ranjan Sahoo (Wed Oct 15 2014 - 17:50:03 PDT)
- Bikash Ranjan Sahoo (Wed Oct 15 2014 - 06:01:49 PDT)
- Bikash Ranjan Sahoo (Tue Oct 14 2014 - 21:04:54 PDT)
[AMBER] How can I get amber know calcium
- mmaestre.gate.sinica.edu.tw (Mon Oct 20 2014 - 16:15:09 PDT)
- Pengfei Li (Mon Oct 20 2014 - 14:08:33 PDT)
- Chinthaka Ratnaweera (Mon Oct 20 2014 - 12:09:44 PDT)
- Ken Merz (Mon Oct 20 2014 - 11:50:47 PDT)
- Pengfei Li (Mon Oct 20 2014 - 11:50:18 PDT)
- Chinthaka Ratnaweera (Mon Oct 20 2014 - 11:47:19 PDT)
- Pengfei Li (Mon Oct 20 2014 - 11:38:20 PDT)
- Chinthaka Ratnaweera (Mon Oct 20 2014 - 11:28:01 PDT)
- jinfeng liu (Mon Oct 20 2014 - 10:57:29 PDT)
- Jason Swails (Mon Oct 20 2014 - 10:44:23 PDT)
- Sajeewa Pemasinghe (Mon Oct 20 2014 - 10:41:44 PDT)
- jinfeng liu (Mon Oct 20 2014 - 09:35:44 PDT)
[AMBER] How do MCPB make sidechain.bcl?
- Pengfei Li (Wed Oct 29 2014 - 12:50:22 PDT)
- Saeed Nasiri (Tue Oct 28 2014 - 21:31:30 PDT)
[AMBER] How to install sander.MPI?
- David A Case (Mon Oct 13 2014 - 18:05:55 PDT)
- Zhong, Roger (Mon Oct 13 2014 - 13:50:11 PDT)
[AMBER] Imaging
- Sylvester Tumusiime (Thu Oct 30 2014 - 14:51:19 PDT)
- Daniel Roe (Thu Oct 30 2014 - 13:33:06 PDT)
- Thomas Cheatham (Thu Oct 30 2014 - 13:27:37 PDT)
- Sylvester Tumusiime (Thu Oct 30 2014 - 12:23:55 PDT)
- Sylvester Tumusiime (Wed Oct 29 2014 - 14:29:24 PDT)
- Daniel Roe (Wed Oct 29 2014 - 13:31:17 PDT)
- Sylvester Tumusiime (Wed Oct 29 2014 - 09:22:13 PDT)
- Sylvester Tumusiime (Wed Oct 29 2014 - 09:11:05 PDT)
- Daniel Roe (Wed Oct 29 2014 - 08:53:42 PDT)
- Sylvester Tumusiime (Wed Oct 29 2014 - 08:38:36 PDT)
- Daniel Roe (Wed Oct 29 2014 - 08:20:16 PDT)
- Sylvester Tumusiime (Wed Oct 29 2014 - 08:10:36 PDT)
[AMBER] Implementing parameterized heme?
- Pengfei Li (Thu Oct 30 2014 - 12:18:20 PDT)
- Pengfei Li (Thu Oct 30 2014 - 12:15:27 PDT)
- Yarrow Madrona (Wed Oct 29 2014 - 17:46:23 PDT)
- Yarrow Madrona (Wed Oct 29 2014 - 17:34:21 PDT)
- Pengfei Li (Wed Oct 29 2014 - 12:44:02 PDT)
- Pengfei Li (Wed Oct 29 2014 - 12:35:07 PDT)
- Kevin Murphy (Wed Oct 29 2014 - 10:21:21 PDT)
[AMBER] Info About GPU and PMEMD versions
- Ross Walker (Wed Oct 22 2014 - 07:56:30 PDT)
- Jason Swails (Wed Oct 22 2014 - 05:55:33 PDT)
- Lorenzo Gontrani (Wed Oct 22 2014 - 01:55:50 PDT)
[AMBER] install error after updates
- Daniel Roe (Thu Oct 16 2014 - 12:24:57 PDT)
- Nihal Korkmaz (Thu Oct 16 2014 - 11:22:42 PDT)
[AMBER] Is there a way to maintain pdb coordinates into leap?
- Jonathan Gough (Wed Oct 08 2014 - 18:10:21 PDT)
- David A Case (Wed Oct 08 2014 - 14:19:56 PDT)
- Bill Ross (Wed Oct 08 2014 - 11:48:12 PDT)
- Jonathan Gough (Wed Oct 08 2014 - 11:14:22 PDT)
[AMBER] Jarzynski SMD
- Jason Swails (Fri Oct 17 2014 - 14:38:47 PDT)
- George Tzotzos (Fri Oct 17 2014 - 12:39:19 PDT)
[AMBER] key word to pull out eigenvalues
- newamber list (Tue Sep 30 2014 - 16:30:11 PDT)
[AMBER] Lambda Exchange
- Jason Swails (Wed Oct 08 2014 - 12:29:53 PDT)
- Jeff Wereszczynski (Wed Oct 08 2014 - 11:50:31 PDT)
- Jason Swails (Wed Oct 08 2014 - 11:30:40 PDT)
- Jeff Wereszczynski (Wed Oct 08 2014 - 10:23:22 PDT)
- Jason Swails (Wed Oct 08 2014 - 05:18:38 PDT)
- Jeff Wereszczynski (Tue Oct 07 2014 - 19:19:29 PDT)
[AMBER] Langevin thermostat in vacuu simulation o ..High RMSF of TEMP
- Jason Swails (Sun Oct 05 2014 - 19:24:56 PDT)
- CHAMI F. (Sun Oct 05 2014 - 10:21:34 PDT)
[AMBER] LIE FUNCTION
- Jason Swails (Wed Oct 01 2014 - 08:17:30 PDT)
- Jason Swails (Wed Oct 01 2014 - 04:20:17 PDT)
- Loïc Etheve (Wed Oct 01 2014 - 02:21:48 PDT)
[AMBER] loading force field ff14SB
- Jiri Sponer (Tue Oct 28 2014 - 09:17:05 PDT)
- Vlad Cojocaru (Tue Oct 28 2014 - 08:56:57 PDT)
- Christina Bergonzo (Tue Oct 28 2014 - 08:31:19 PDT)
- Jason Swails (Tue Oct 28 2014 - 08:36:05 PDT)
- Vlad Cojocaru (Tue Oct 28 2014 - 08:12:18 PDT)
[AMBER] Loadpdb in Tleap takes forever
- Daniel Roe (Thu Oct 16 2014 - 12:55:26 PDT)
- Ahmed Ayoub (Thu Oct 16 2014 - 11:16:44 PDT)
[AMBER] Looking force field for beta-peptide
- David A Case (Fri Oct 31 2014 - 10:26:51 PDT)
- MOHD HOMAIDUR RAHMAN (Fri Oct 31 2014 - 06:25:54 PDT)
[AMBER] Loss of secondary structure in GB simulations
- Nhai (Wed Oct 15 2014 - 15:49:34 PDT)
- Nihal Korkmaz (Wed Oct 15 2014 - 14:29:51 PDT)
- Hai Nguyen (Tue Oct 14 2014 - 22:00:49 PDT)
- Nihal Korkmaz (Tue Oct 14 2014 - 18:32:32 PDT)
- Carlos Simmerling (Tue Oct 14 2014 - 17:19:14 PDT)
- Nihal Korkmaz (Tue Oct 14 2014 - 13:50:13 PDT)
[AMBER] MMGBSA & igb 8
- Carlos Simmerling (Mon Oct 20 2014 - 07:43:06 PDT)
- Jason Swails (Mon Oct 20 2014 - 07:34:01 PDT)
- jojartb.jgypk.u-szeged.hu (Mon Oct 20 2014 - 03:01:27 PDT)
[AMBER] MMGBSA doesn't finish
- Jason Swails (Fri Oct 24 2014 - 04:53:10 PDT)
- Bernhard Poll (Thu Oct 23 2014 - 23:22:40 PDT)
[AMBER] MMPBSA Error: PB Bomb in pb_atmlist(): maxnba too short
- Jason Swails (Mon Oct 27 2014 - 05:19:41 PDT)
- MOHD HOMAIDUR RAHMAN (Mon Oct 27 2014 - 00:27:34 PDT)
[AMBER] Multiple timecorr commands in one cpptraj script
- George M Giambasu (Thu Oct 30 2014 - 11:29:36 PDT)
- Eugene Yedvabny (Thu Oct 30 2014 - 09:54:51 PDT)
[AMBER] Need help for retrained MD
- Daniel Roe (Tue Oct 07 2014 - 07:36:41 PDT)
- Jason Swails (Tue Oct 07 2014 - 04:55:58 PDT)
- Sudhanshu Shanker (Tue Oct 07 2014 - 03:37:59 PDT)
[AMBER] Need help for retrained MD (Daniel Roe)
- Daniel Roe (Fri Oct 17 2014 - 06:54:54 PDT)
- Sudhanshu Shanker (Fri Oct 17 2014 - 00:20:40 PDT)
[AMBER] No AMBERHOME/dat/mtkpp folder
- Jason Swails (Wed Oct 08 2014 - 16:56:08 PDT)
- mmaestre.gate.sinica.edu.tw (Wed Oct 08 2014 - 16:35:44 PDT)
- David A Case (Wed Oct 08 2014 - 05:03:26 PDT)
- Jason Swails (Wed Oct 08 2014 - 04:56:03 PDT)
- mmaestre.gate.sinica.edu.tw (Tue Oct 07 2014 - 20:15:54 PDT)
[AMBER] Number of water hits and density
- Suhaib Shekfeh (Sun Oct 26 2014 - 06:50:42 PDT)
- Thomas Cheatham (Thu Oct 23 2014 - 10:19:06 PDT)
- Carlos Simmerling (Thu Oct 23 2014 - 10:18:00 PDT)
- Suhaib Shekfeh (Thu Oct 23 2014 - 08:01:05 PDT)
[AMBER] On the enthropy estimation in MMPBSA
- James Starlight (Wed Oct 08 2014 - 01:30:55 PDT)
- James Starlight (Tue Oct 07 2014 - 00:39:51 PDT)
[AMBER] Parameters for Boron atom
- David A Case (Mon Oct 20 2014 - 05:06:08 PDT)
- 王璇 (Sun Oct 19 2014 - 18:26:39 PDT)
[AMBER] PDB to P2N conversion
- ABEL Stephane 175950 (Sat Oct 25 2014 - 12:09:28 PDT)
- Sylvester Tumusiime (Sat Oct 25 2014 - 09:14:53 PDT)
[AMBER] peptideligandParameters
- FyD (Fri Oct 24 2014 - 22:17:11 PDT)
- Jason Swails (Fri Oct 24 2014 - 05:48:15 PDT)
- zayan alhalabi (Thu Oct 23 2014 - 01:58:08 PDT)
[AMBER] Plotting Issue
- Jason Swails (Thu Oct 16 2014 - 07:55:18 PDT)
- Soumendranath Bhakat (Thu Oct 16 2014 - 07:26:49 PDT)
[AMBER] principal axes cpptraj
- Daniel Roe (Tue Oct 14 2014 - 13:44:30 PDT)
- Asmita Gupta (Tue Oct 14 2014 - 04:25:59 PDT)
[AMBER] Problem about "Too many dipole_dipole interactions for allocated" in heat simulation
- Tong Zhu (Tue Oct 28 2014 - 22:23:48 PDT)
[AMBER] Problem about "Too many dipole_dipole interactions for allocated" when heat
- Ya Gao (Wed Oct 29 2014 - 05:31:16 PDT)
- Lorenzo Gontrani (Wed Oct 29 2014 - 04:58:33 PDT)
- David A Case (Wed Oct 29 2014 - 04:38:52 PDT)
- Ya Gao (Tue Oct 28 2014 - 19:30:34 PDT)
[AMBER] problem in DNA-ligand trajectory
- Jason Swails (Wed Oct 29 2014 - 10:22:57 PDT)
- Mina Madah (Wed Oct 29 2014 - 03:54:31 PDT)
[AMBER] Problem installing amber14
- 肖立 (Mon Oct 13 2014 - 11:08:44 PDT)
[AMBER] Problem on generating topology file of lithium based electrolyte using GAFF
- Debashis Kundu (Wed Oct 08 2014 - 16:56:47 PDT)
[AMBER] Problem regarding Chamber
- Jason Swails (Mon Oct 27 2014 - 09:04:26 PDT)
- Shubhadip Das (Sun Oct 26 2014 - 21:28:54 PDT)
- Jason Swails (Fri Oct 24 2014 - 08:14:56 PDT)
- Jason Swails (Thu Oct 23 2014 - 00:45:33 PDT)
- Jason Swails (Mon Oct 20 2014 - 07:32:12 PDT)
- Shubhadip Das (Mon Oct 20 2014 - 04:28:43 PDT)
[AMBER] Problem regarding Chamber and psf file
- Pete Kekenes-Huskey (Fri Oct 31 2014 - 13:36:06 PDT)
- Jason Swails (Fri Oct 31 2014 - 08:51:40 PDT)
- Caitlin Scott (Fri Oct 31 2014 - 07:20:04 PDT)
- Jason Swails (Mon Oct 27 2014 - 06:52:50 PDT)
- Caitlin Scott (Mon Oct 27 2014 - 06:25:45 PDT)
[AMBER] problem with extra-point
- David A Case (Sat Oct 25 2014 - 13:05:01 PDT)
- Emilio Angelina (Sat Oct 25 2014 - 09:38:55 PDT)
[AMBER] Problem with input coordinates file
- Francesco Gentile (Tue Oct 21 2014 - 13:05:00 PDT)
- Francesco Gentile (Fri Oct 17 2014 - 13:01:13 PDT)
- Daniel Roe (Fri Oct 17 2014 - 12:23:17 PDT)
- Daniel Roe (Thu Oct 16 2014 - 14:36:01 PDT)
- Francesco Gentile (Thu Oct 16 2014 - 14:06:54 PDT)
- Daniel Roe (Thu Oct 16 2014 - 12:52:36 PDT)
- Francesco Gentile (Thu Oct 16 2014 - 10:55:19 PDT)
[AMBER] Problem with lone pair
- Jason Swails (Tue Oct 14 2014 - 14:37:17 PDT)
- Giachetti Andrea - CERM (Mon Oct 13 2014 - 01:23:03 PDT)
[AMBER] problems with "Could not find vdW"
- Investigador Química (Thu Oct 09 2014 - 07:18:20 PDT)
- Daniel Roe (Thu Oct 09 2014 - 07:08:02 PDT)
- Investigador Química (Thu Oct 09 2014 - 06:59:17 PDT)
- Daniel Roe (Wed Oct 08 2014 - 08:15:45 PDT)
- Jason Swails (Wed Oct 08 2014 - 08:13:59 PDT)
- Investigador Química (Wed Oct 08 2014 - 08:07:36 PDT)
- Jason Swails (Wed Oct 08 2014 - 07:51:00 PDT)
- Investigador Química (Wed Oct 08 2014 - 07:40:50 PDT)
[AMBER] Problems with MMPBSA.py.MPI
- James Starlight (Fri Oct 03 2014 - 00:30:23 PDT)
[AMBER] Processing of the trajectories using ptraj
- Daniel Roe (Mon Oct 06 2014 - 07:59:34 PDT)
- James Starlight (Mon Oct 06 2014 - 00:15:41 PDT)
- Daniel Roe (Fri Oct 03 2014 - 07:09:22 PDT)
- James Starlight (Fri Oct 03 2014 - 05:13:18 PDT)
[AMBER] pyroglutamic acid or 5-oxoproline
- Yves Boulard (Fri Oct 31 2014 - 04:08:52 PDT)
[AMBER] QM/MM in amber, PME when qm_theory='extern'
- Andreas Goetz (Tue Oct 14 2014 - 22:00:19 PDT)
- Brian Radak (Mon Oct 06 2014 - 14:27:59 PDT)
- Aixiao Li (Fri Oct 03 2014 - 06:57:28 PDT)
[AMBER] Questions about restarting REMD simulations
- Jason Swails (Fri Oct 10 2014 - 19:01:49 PDT)
- 王漠野 (Fri Oct 10 2014 - 19:01:00 PDT)
- 王漠野 (Fri Oct 10 2014 - 18:54:26 PDT)
- Jason Swails (Fri Oct 10 2014 - 12:41:17 PDT)
- Daniel Roe (Fri Oct 10 2014 - 06:48:16 PDT)
- 王漠野 (Thu Oct 09 2014 - 23:25:58 PDT)
[AMBER] RAM error during multiple MMGBSA runs
- James Starlight (Fri Oct 03 2014 - 01:45:17 PDT)
- Ray Luo, Ph.D. (Thu Oct 02 2014 - 13:24:05 PDT)
- James Starlight (Thu Oct 02 2014 - 00:36:05 PDT)
[AMBER] Regarding dihedrals in GAFF need clarification
- Jason Swails (Wed Oct 08 2014 - 07:35:22 PDT)
- Arun Srikanth (Wed Oct 08 2014 - 07:32:45 PDT)
- Jason Swails (Wed Oct 08 2014 - 07:19:58 PDT)
- Arun Srikanth (Wed Oct 08 2014 - 07:09:37 PDT)
[AMBER] Regarding impropers from parmed.py and guessing from bond topology
- Arun Srikanth (Sun Oct 19 2014 - 23:24:39 PDT)
- Jason Swails (Sun Oct 19 2014 - 23:08:30 PDT)
- Arun Srikanth (Sun Oct 19 2014 - 21:45:08 PDT)
- Jason Swails (Sun Oct 19 2014 - 21:27:52 PDT)
- Arun Srikanth (Sun Oct 19 2014 - 21:16:10 PDT)
- Jason Swails (Sat Oct 18 2014 - 21:52:51 PDT)
- Arun Srikanth (Sat Oct 18 2014 - 20:20:41 PDT)
- David A Case (Sat Oct 18 2014 - 18:13:59 PDT)
- Jason Swails (Sat Oct 18 2014 - 16:27:12 PDT)
- Daniel Roe (Sat Oct 18 2014 - 16:24:23 PDT)
- Arun Srikanth (Sat Oct 18 2014 - 14:38:36 PDT)
[AMBER] Regarding Protein-ligand MD
- FyD (Tue Oct 28 2014 - 02:02:22 PDT)
- Bikash Ranjan Sahoo (Mon Oct 27 2014 - 20:17:02 PDT)
- Robin Betz (Mon Oct 27 2014 - 20:02:48 PDT)
- Bikash Ranjan Sahoo (Mon Oct 27 2014 - 19:58:33 PDT)
[AMBER] restart file position
- Jason Swails (Wed Oct 29 2014 - 10:17:22 PDT)
- Fabian Glaser (Wed Oct 29 2014 - 08:31:42 PDT)
[AMBER] Restarting MD production run
- Daniel Roe (Sat Oct 11 2014 - 10:07:07 PDT)
- Soumendranath Bhakat (Sat Oct 11 2014 - 05:21:41 PDT)
[AMBER] RNA with Malachite Green simulation
- Kasprzak, Wojciech (NIH/NCI) [C] (Tue Oct 07 2014 - 13:15:31 PDT)
[AMBER] Running G03
- FyD (Mon Oct 27 2014 - 23:50:10 PDT)
- Kshatresh Dutta Dubey (Mon Oct 27 2014 - 13:19:53 PDT)
- Brittany Boykin (Mon Oct 27 2014 - 12:14:43 PDT)
[AMBER] Setting exclusions - am i overcounting ?
- Jason Swails (Wed Oct 15 2014 - 17:51:12 PDT)
- Arun Srikanth (Wed Oct 15 2014 - 17:05:23 PDT)
- Daniel Roe (Wed Oct 15 2014 - 15:57:55 PDT)
- Arun Srikanth (Wed Oct 15 2014 - 14:56:12 PDT)
[AMBER] Setting exclusions - am i overcounting ?-Last question
- Arun Srikanth (Wed Oct 15 2014 - 22:35:59 PDT)
- Jason Swails (Wed Oct 15 2014 - 21:24:38 PDT)
- Arun Srikanth (Wed Oct 15 2014 - 19:54:42 PDT)
[AMBER] Setting exclusions correctly
- Jason Swails (Wed Oct 15 2014 - 20:42:33 PDT)
- Arun Srikanth (Tue Oct 14 2014 - 15:38:33 PDT)
- Daniel Roe (Tue Oct 14 2014 - 14:13:38 PDT)
- Jason Swails (Tue Oct 14 2014 - 14:12:28 PDT)
- Arun Srikanth (Mon Oct 13 2014 - 00:12:15 PDT)
[AMBER] Small NAB program: Not getting desired output
- David A Case (Fri Oct 17 2014 - 05:30:41 PDT)
- Himanshu Joshi (Fri Oct 17 2014 - 00:45:39 PDT)
- David A Case (Thu Oct 16 2014 - 05:11:07 PDT)
- Himanshu Joshi (Wed Oct 15 2014 - 23:23:00 PDT)
- Himanshu Joshi (Wed Oct 15 2014 - 22:41:28 PDT)
[AMBER] solvation free energy
- David A Case (Tue Oct 14 2014 - 05:27:23 PDT)
- kirtana S (Mon Oct 13 2014 - 22:07:27 PDT)
- kirtana S (Mon Oct 13 2014 - 21:53:58 PDT)
- David A Case (Sun Oct 12 2014 - 13:44:03 PDT)
- kirtana S (Sun Oct 12 2014 - 12:58:06 PDT)
- David A Case (Sun Oct 12 2014 - 05:38:04 PDT)
- kirtana S (Sat Oct 11 2014 - 22:15:17 PDT)
[AMBER] solvation of a pdb file
- David A Case (Sun Oct 19 2014 - 10:47:46 PDT)
- Robin Jain (Sun Oct 19 2014 - 08:19:37 PDT)
[AMBER] source leaprc.constph error
- jinfeng liu (Thu Oct 16 2014 - 18:12:49 PDT)
- Jason Swails (Thu Oct 16 2014 - 17:51:37 PDT)
- jinfeng liu (Thu Oct 16 2014 - 17:29:35 PDT)
- Jason Swails (Thu Oct 16 2014 - 16:11:24 PDT)
- jinfeng liu (Thu Oct 16 2014 - 15:07:24 PDT)
[AMBER] switch from digest
- Jason Swails (Thu Oct 02 2014 - 19:49:40 PDT)
- amirhossein taghavi (Wed Oct 01 2014 - 23:55:45 PDT)
[AMBER] Temperature not correctly maintained using AMBER14
- Ross Walker (Sun Oct 26 2014 - 18:57:13 PDT)
- Gonzalo Jimenez (Sun Oct 26 2014 - 14:15:46 PDT)
- Ross Walker (Sun Oct 26 2014 - 13:22:33 PDT)
- Gonzalo Jimenez (Sat Oct 25 2014 - 19:41:52 PDT)
- Ross Walker (Sat Oct 25 2014 - 18:44:59 PDT)
- Gonzalo Jimenez (Sat Oct 25 2014 - 18:07:38 PDT)
[AMBER] Tethering water molecules in the receptor
- Jason Swails (Sat Oct 04 2014 - 20:50:54 PDT)
- George Tzotzos (Sat Oct 04 2014 - 16:14:06 PDT)
- Jason Swails (Sat Oct 04 2014 - 14:09:00 PDT)
- George Tzotzos (Sat Oct 04 2014 - 12:37:01 PDT)
[AMBER] thanks
- zayan alhalabi (Sat Oct 18 2014 - 07:45:10 PDT)
[AMBER] TI and FEW
- Nadine Homeyer (Mon Oct 20 2014 - 06:38:12 PDT)
- David A Case (Thu Oct 16 2014 - 06:32:42 PDT)
- sabine.ruppel.boehringer-ingelheim.com (Thu Oct 16 2014 - 06:03:57 PDT)
- David A Case (Wed Oct 15 2014 - 17:57:07 PDT)
- sabine.ruppel.boehringer-ingelheim.com (Wed Oct 15 2014 - 13:11:22 PDT)
[AMBER] Torsion Scan
- Dwight McGee (Wed Oct 08 2014 - 23:24:11 PDT)
- Zachary Davis (Wed Oct 08 2014 - 20:31:24 PDT)
[AMBER] Trouble making frcmod file (ultimately to create prmtop file)
- Brian Radak (Mon Oct 06 2014 - 14:35:01 PDT)
- Jason Swails (Mon Oct 06 2014 - 13:42:53 PDT)
- Evans, Shalton (Mon Oct 06 2014 - 13:34:12 PDT)
[AMBER] using multiple force fields in a simulation
- Carlos Simmerling (Thu Oct 30 2014 - 08:00:06 PDT)
- Hannes Loeffler (Thu Oct 30 2014 - 02:26:37 PDT)
- Bhushan (Thu Oct 30 2014 - 00:45:40 PDT)
[AMBER] visualize CPPTRAJ clculated modes
- Daniel Roe (Thu Oct 30 2014 - 07:34:28 PDT)
- Vlad Cojocaru (Thu Oct 30 2014 - 07:15:50 PDT)
- Jason Swails (Thu Oct 30 2014 - 04:33:21 PDT)
- Vlad Cojocaru (Thu Oct 30 2014 - 02:35:20 PDT)
[AMBER] Which GPU is recommended?
- Jason Swails (Wed Oct 22 2014 - 05:37:00 PDT)
- Alexander Metz (Wed Oct 22 2014 - 03:54:31 PDT)
- Ross Walker (Fri Oct 17 2014 - 12:16:04 PDT)
- xueqiaoup.gmail.com (Thu Oct 16 2014 - 22:29:52 PDT)
[AMBER] why total energy of the system is on the rise in NVE ensemble
- David A Case (Wed Oct 15 2014 - 05:58:12 PDT)
- Hector A. Baldoni (Tue Oct 14 2014 - 16:34:16 PDT)
- James Maier (Sun Oct 12 2014 - 19:52:58 PDT)
- zhangmk (Sun Oct 12 2014 - 19:43:03 PDT)
[AMBER] writing trr trajectory
- Daniel Roe (Wed Oct 01 2014 - 07:11:50 PDT)
- newamber list (Tue Sep 30 2014 - 16:16:50 PDT)
[AMBER] Zinc Parameterization
- Patrick Appiah-Kubi (Thu Oct 09 2014 - 08:26:14 PDT)
[AMBER] Zinc Paramitarization
- Pengfei Li (Thu Oct 09 2014 - 08:25:50 PDT)
- Patrick Appiah-Kubi (Thu Oct 09 2014 - 01:02:28 PDT)

Amber Archive Oct 2014 by subject