Amber Archive Apr 2016: by subject

[AMBER] [cpptraj] Automating pcmin/pcmax selection of modes command
- Daniel Roe (Tue Apr 19 2016 - 08:49:31 PDT)
- Eiros Zamora, Juan (Tue Apr 19 2016 - 04:52:01 PDT)
[AMBER] A contrarian note about gravity potentials in MD
- David A Case (Fri Apr 01 2016 - 09:21:01 PDT)
[AMBER] accelerated MD on set of dihedrals
- Giuseppina La Sala (Fri Apr 29 2016 - 15:15:52 PDT)
- Giuseppina La Sala (Fri Apr 29 2016 - 15:14:06 PDT)
- giulia palermo (Fri Apr 29 2016 - 11:47:21 PDT)
- Daniel Roe (Fri Apr 29 2016 - 10:18:41 PDT)
- Giuseppina La Sala (Fri Apr 29 2016 - 09:56:00 PDT)
[AMBER] Alanine Scanning ERROR!!!
- Jag Silwal (Thu Apr 14 2016 - 04:46:49 PDT)
- Jason Swails (Wed Apr 13 2016 - 19:01:46 PDT)
- Jag Silwal (Wed Apr 13 2016 - 15:22:39 PDT)
- Jason Swails (Wed Apr 13 2016 - 09:53:29 PDT)
- Jag Silwal (Mon Apr 11 2016 - 19:11:17 PDT)
[AMBER] Amber custom hardware setup
- Jason Swails (Wed Apr 13 2016 - 19:05:44 PDT)
- Leonardo Lazzaro (Wed Apr 13 2016 - 17:39:55 PDT)
[AMBER] AMBER Project
- Daniel Roe (Tue Apr 26 2016 - 11:54:23 PDT)
- Niharikav Veeresh (Tue Apr 26 2016 - 11:52:30 PDT)
[AMBER] Amber script to delete all hydrogen atoms from protein?
- Michael Shokhen (Sun Apr 10 2016 - 05:25:45 PDT)
- Arati Paudyal (Sun Apr 10 2016 - 04:22:31 PDT)
- Marcelo Andrade Chagas (Sun Apr 10 2016 - 04:05:38 PDT)
- Michael Shokhen (Sun Apr 10 2016 - 02:11:18 PDT)
[AMBER] amber v16
- Hai Nguyen (Mon Apr 18 2016 - 12:43:04 PDT)
- Arjun Sharma (Mon Apr 18 2016 - 12:38:01 PDT)
[AMBER] Amber14/AmberTools15 compliation error
- Kris Feher (Tue Apr 12 2016 - 01:19:19 PDT)
- Jason Swails (Wed Apr 06 2016 - 07:42:00 PDT)
- Kris Feher (Wed Apr 06 2016 - 07:34:04 PDT)
[AMBER] Amber: .rst file not created
- Jason Swails (Thu Apr 07 2016 - 09:28:33 PDT)
- ABHIJEET CHOWDHURY (Thu Apr 07 2016 - 04:47:27 PDT)
- Marcelo Andrade Chagas (Wed Apr 06 2016 - 07:42:30 PDT)
- ABHIJEET CHOWDHURY (Wed Apr 06 2016 - 05:08:56 PDT)
[AMBER] ambpdb error
- Jason Swails (Fri Apr 29 2016 - 10:22:33 PDT)
- Daniel Roe (Fri Apr 29 2016 - 10:14:31 PDT)
- Arati Paudyal (Fri Apr 29 2016 - 10:01:20 PDT)
- Daniel Roe (Fri Apr 29 2016 - 09:17:28 PDT)
- Daniel Roe (Fri Apr 29 2016 - 09:16:03 PDT)
- Jason Swails (Fri Apr 29 2016 - 08:59:13 PDT)
- Daniel Roe (Fri Apr 29 2016 - 08:27:56 PDT)
- Arati Paudyal (Fri Apr 29 2016 - 08:25:42 PDT)
- Daniel Roe (Fri Apr 29 2016 - 07:21:44 PDT)
- Arati Paudyal (Fri Apr 29 2016 - 06:41:40 PDT)
[AMBER] aMD ruins membrane structure
- Dickson, Callum J (Mon Apr 04 2016 - 07:11:11 PDT)
- Michael Shokhen (Fri Apr 01 2016 - 01:03:06 PDT)
[AMBER] Antechamber Problem
- Bill Ross (Wed Apr 13 2016 - 01:15:47 PDT)
- Beale, John (Wed Apr 13 2016 - 00:47:28 PDT)
- Bill Ross (Wed Apr 13 2016 - 00:42:09 PDT)
- Beale, John (Wed Apr 13 2016 - 00:18:07 PDT)
[AMBER] Any issues if I make PMEMD understand bonds span imaging?
- David Cerutti (Wed Apr 06 2016 - 13:49:28 PDT)
[AMBER] Approach for transmembrane protein
- anu chandra (Tue Apr 19 2016 - 08:07:39 PDT)
- Elisa Pieri (Tue Apr 19 2016 - 05:03:53 PDT)
[AMBER] atom does not have a type
- jixiaofeng (Thu Apr 21 2016 - 19:31:45 PDT)
- jixiaofeng (Thu Apr 21 2016 - 19:23:53 PDT)
[AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj
- peter.schmidtke.discngine.servier.com (Wed Apr 20 2016 - 05:30:27 PDT)
- David A Case (Wed Apr 20 2016 - 05:09:30 PDT)
- peter.schmidtke.discngine.servier.com (Wed Apr 20 2016 - 01:27:25 PDT)
- David A Case (Tue Apr 19 2016 - 11:20:14 PDT)
- Daniel Roe (Tue Apr 19 2016 - 09:00:24 PDT)
- peter.schmidtke.discngine.servier.com (Tue Apr 19 2016 - 08:23:13 PDT)
- David A Case (Tue Apr 19 2016 - 06:20:00 PDT)
- peter.schmidtke.discngine.servier.com (Tue Apr 19 2016 - 05:41:14 PDT)
[AMBER] Both positional and distance restraints
- Damiano Spadoni (Mon Apr 18 2016 - 11:46:39 PDT)
- David A Case (Mon Apr 18 2016 - 04:31:18 PDT)
- Damiano Spadoni (Wed Apr 13 2016 - 06:59:06 PDT)
[AMBER] Box dimensions
- 達南杰 (Mon Apr 11 2016 - 20:18:20 PDT)
- Daniel Roe (Mon Apr 11 2016 - 19:44:09 PDT)
- 達南杰 (Mon Apr 11 2016 - 19:36:17 PDT)
- Daniel Roe (Mon Apr 11 2016 - 09:40:29 PDT)
- 達南杰 (Mon Apr 11 2016 - 04:28:21 PDT)
[AMBER] build a phosphorylated protein structure pdb file
- YanhuaOuyang (Tue Apr 05 2016 - 04:58:21 PDT)
- David A Case (Mon Apr 04 2016 - 18:50:05 PDT)
- Bill Ross (Mon Apr 04 2016 - 18:34:03 PDT)
- YanhuaOuyang (Mon Apr 04 2016 - 18:25:46 PDT)
- YanhuaOuyang (Mon Apr 04 2016 - 18:04:40 PDT)
- Carlos Simmerling (Mon Apr 04 2016 - 03:10:17 PDT)
- YanhuaOuyang (Mon Apr 04 2016 - 00:21:29 PDT)
[AMBER] Building Cyclic Peptide in xleap
- Maral Aminpour (Thu Apr 28 2016 - 08:15:02 PDT)
- David Cerutti (Fri Apr 22 2016 - 09:52:09 PDT)
- Kenneth McGuinness (Fri Apr 22 2016 - 09:43:36 PDT)
- Bill Ross (Thu Apr 21 2016 - 16:53:42 PDT)
- David A Case (Thu Apr 21 2016 - 16:35:06 PDT)
- Maral Aminpour (Thu Apr 21 2016 - 13:55:19 PDT)
[AMBER] building DNA with extruded base
- giulia palermo (Tue Apr 19 2016 - 13:50:12 PDT)
- Christina Bergonzo (Tue Apr 19 2016 - 11:56:54 PDT)
- David A Case (Tue Apr 19 2016 - 11:24:03 PDT)
- giulia palermo (Tue Apr 19 2016 - 10:17:46 PDT)
[AMBER] Calculate Percentage of Hydrogen Occurrence
- Daniel Roe (Fri Apr 29 2016 - 08:24:33 PDT)
- Jag Silwal (Fri Apr 29 2016 - 06:27:54 PDT)
[AMBER] CHAMBER and CMAP error using new c36 FF
- Jason Swails (Wed Apr 13 2016 - 03:33:11 PDT)
- Jun Feng (Tue Apr 12 2016 - 11:35:44 PDT)
- Hai Nguyen (Tue Apr 12 2016 - 07:34:02 PDT)
- Jason Swails (Tue Apr 12 2016 - 07:27:38 PDT)
- Jun Feng (Tue Apr 12 2016 - 07:22:49 PDT)
- Jun Feng (Mon Apr 11 2016 - 10:18:17 PDT)
[AMBER] CHAMBER error for the updated CHARMM36 force fields
- Hai Nguyen (Tue Apr 12 2016 - 09:23:37 PDT)
- Chitrak Gupta (Tue Apr 12 2016 - 08:23:46 PDT)
[AMBER] Change PBRadii after simulation
- Arati Paudyal (Mon Apr 18 2016 - 06:34:50 PDT)
- Carlos Simmerling (Mon Apr 18 2016 - 06:04:05 PDT)
- Jag Silwal (Mon Apr 18 2016 - 05:50:14 PDT)
- Jason Swails (Sun Apr 17 2016 - 08:00:52 PDT)
- Carlos Simmerling (Sun Apr 17 2016 - 04:53:37 PDT)
- Jag Silwal (Sat Apr 16 2016 - 21:20:37 PDT)
- Carlos Simmerling (Sat Apr 16 2016 - 20:33:43 PDT)
- Jag Silwal (Sat Apr 16 2016 - 20:30:27 PDT)
[AMBER] clustering
- waleed zalloum (Mon Apr 18 2016 - 11:14:33 PDT)
[AMBER] Convergence problem with the SCC-DFTB example.
- Gustavo Seabra (Wed Apr 06 2016 - 07:21:29 PDT)
[AMBER] Conversion of CHARMM-GUI generated file into Lipid14 readable file
- Shreeramesh (Fri Apr 15 2016 - 05:01:04 PDT)
[AMBER] Could not find angle parameter
- David A Case (Wed Apr 13 2016 - 05:34:49 PDT)
- Jesmita Dhar (Mon Apr 11 2016 - 22:34:13 PDT)
- Daniel Roe (Mon Apr 11 2016 - 09:35:43 PDT)
- Jesmita Dhar (Mon Apr 11 2016 - 02:32:32 PDT)
[AMBER] CpHMD
- Jason Swails (Fri Apr 08 2016 - 05:07:50 PDT)
- 赵聪 (Fri Apr 08 2016 - 01:17:00 PDT)
[AMBER] Cpptraj LipidOrder error: mask groups are not the same length
- Amy Rice (Thu Apr 28 2016 - 12:29:44 PDT)
- hannes.loeffler.stfc.ac.uk (Thu Apr 28 2016 - 12:10:55 PDT)
- hannes.loeffler.stfc.ac.uk (Thu Apr 28 2016 - 12:06:04 PDT)
- Chris Moth (Thu Apr 28 2016 - 11:53:45 PDT)
- Amy Rice (Thu Apr 28 2016 - 11:30:14 PDT)
[AMBER] cpptraj SolventAcc and ligand distance plotting
- Saman Yousuf ali (Thu Apr 21 2016 - 14:17:40 PDT)
- Daniel Roe (Wed Apr 20 2016 - 13:21:57 PDT)
- Daniel Roe (Tue Apr 19 2016 - 09:02:48 PDT)
- Daniel Roe (Mon Apr 18 2016 - 07:33:23 PDT)
- Saman Yousuf ali (Sat Apr 16 2016 - 23:59:11 PDT)
[AMBER] cpptraj: reading in previously created covariance matrix
- Vlad Cojocaru (Wed Apr 06 2016 - 01:09:16 PDT)
- Daniel Roe (Tue Apr 05 2016 - 13:12:42 PDT)
- Vlad Cojocaru (Tue Apr 05 2016 - 12:52:57 PDT)
[AMBER] CUDA and restraint
- Ross Walker (Fri Apr 29 2016 - 08:28:42 PDT)
- Domenico Marson (Fri Apr 29 2016 - 06:37:19 PDT)
- Charles Lin (Fri Apr 29 2016 - 04:52:35 PDT)
- Domenico Marson (Fri Apr 29 2016 - 02:35:06 PDT)
- Bill Ross (Fri Apr 29 2016 - 01:28:22 PDT)
- Bill Ross (Fri Apr 29 2016 - 01:25:32 PDT)
- Domenico Marson (Fri Apr 29 2016 - 01:19:41 PDT)
- Charles Lin (Thu Apr 28 2016 - 09:27:00 PDT)
- Domenico Marson (Thu Apr 28 2016 - 03:31:34 PDT)
- Domenico Marson (Fri Apr 22 2016 - 02:21:43 PDT)
[AMBER] debug issue
- Zhenyu Meng (Thu Apr 28 2016 - 02:46:49 PDT)
- Zhenyu Meng (Wed Apr 27 2016 - 20:32:44 PDT)
- David A Case (Wed Apr 27 2016 - 05:20:07 PDT)
- Zhenyu Meng (Tue Apr 26 2016 - 23:53:13 PDT)
[AMBER] Decomposition energy after mutation!
- Jason Swails (Sat Apr 23 2016 - 21:58:51 PDT)
- Jag Silwal (Fri Apr 22 2016 - 09:52:14 PDT)
[AMBER] Early bird extended! ISQBP2016 meeting - Bergen Norway
- Vlad Cojocaru (Mon Apr 18 2016 - 12:34:15 PDT)
[AMBER] Electrostatic Energies - MMPBSA
- Jason Swails (Wed Apr 20 2016 - 11:30:55 PDT)
- Cortopassi, Wilian (Wed Apr 20 2016 - 04:04:24 PDT)
- Jason Swails (Tue Apr 19 2016 - 18:36:24 PDT)
- Cortopassi, Wilian (Tue Apr 19 2016 - 13:55:24 PDT)
[AMBER] Energies in QM/MM MD
- Dr. Andreas W. Goetz (Tue Apr 26 2016 - 16:02:20 PDT)
- Brian Radak (Mon Apr 25 2016 - 16:50:45 PDT)
- 王美婷 (Mon Apr 25 2016 - 01:46:48 PDT)
[AMBER] Error -per residue Energy Decomposition
- Arati Paudyal (Sat Apr 09 2016 - 16:56:24 PDT)
- Jason Swails (Fri Apr 08 2016 - 18:39:45 PDT)
- Arati Paudyal (Fri Apr 08 2016 - 12:12:41 PDT)
[AMBER] Error in 3DRISM calculation
- Tyler Luchko (Lists) (Sun Apr 17 2016 - 22:51:08 PDT)
- ATUL KUMAR (Sun Apr 17 2016 - 22:46:49 PDT)
[AMBER] error in MCPB.py 3b
- jixiaofeng (Sun Apr 17 2016 - 19:43:18 PDT)
[AMBER] Error in the conversion of CHARMM-GUI generated file into lipid14 readable format
- Shreeramesh (Thu Apr 21 2016 - 00:52:48 PDT)
[AMBER] Error while converting CHARMM-GUI generated file
- Batuhan Kav (Mon Apr 25 2016 - 06:39:47 PDT)
- Shreeramesh (Mon Apr 25 2016 - 05:17:08 PDT)
[AMBER] error while putting the whole path into python script
- Bill Ross (Wed Apr 20 2016 - 01:00:09 PDT)
- Marc van der Kamp (Wed Apr 20 2016 - 00:51:13 PDT)
- Ayesha Kanwal (Wed Apr 20 2016 - 00:37:51 PDT)
[AMBER] error while running MMPBSA script
- Jason Swails (Tue Apr 12 2016 - 07:07:26 PDT)
- Harmeet Kaur (Mon Apr 11 2016 - 21:52:12 PDT)
[AMBER] facing problems simulating in implicit solvent
- Carlos Simmerling (Sat Apr 16 2016 - 10:42:37 PDT)
- Avik Bhattacharjee (Sat Apr 16 2016 - 10:20:02 PDT)
- Daniel Roe (Sat Apr 16 2016 - 09:50:43 PDT)
- Avik Bhattacharjee (Sat Apr 16 2016 - 09:43:42 PDT)
[AMBER] ff12SB force field
- David Cerutti (Mon Apr 11 2016 - 13:48:59 PDT)
- wjli (Mon Apr 11 2016 - 07:02:23 PDT)
- Carlos Simmerling (Mon Apr 11 2016 - 06:50:55 PDT)
- wjli (Mon Apr 11 2016 - 06:47:05 PDT)
[AMBER] Force field parameters for glycerophophate
- anu chandra (Wed Apr 20 2016 - 15:24:47 PDT)
[AMBER] fortran i/o on system shared memory
- Bill Ross (Thu Apr 28 2016 - 23:31:13 PDT)
- Bill Ross (Thu Apr 28 2016 - 23:20:53 PDT)
[AMBER] Fortran Modernisation Workshop - Numerical Algorithms Group NAG
- CHAMI F. (Fri Apr 15 2016 - 03:23:45 PDT)
[AMBER] GeForce GTX 960 ?
- Ross Walker (Mon Apr 25 2016 - 08:20:44 PDT)
- Marek Maly (Thu Apr 21 2016 - 15:36:45 PDT)
- Ross Walker (Thu Apr 21 2016 - 10:18:30 PDT)
- Marek Maly (Thu Apr 21 2016 - 08:51:43 PDT)
[AMBER] General question
- Charles Lin (Tue Apr 05 2016 - 22:57:17 PDT)
- Sreemol G (Tue Apr 05 2016 - 22:42:48 PDT)
- Charles Lin (Tue Apr 05 2016 - 21:43:16 PDT)
- Sreemol G (Tue Apr 05 2016 - 21:31:13 PDT)
- David A Case (Mon Apr 04 2016 - 06:01:39 PDT)
- hannes.loeffler.stfc.ac.uk (Mon Apr 04 2016 - 05:27:05 PDT)
- Sreemol G (Mon Apr 04 2016 - 04:35:01 PDT)
- hannes.loeffler.stfc.ac.uk (Mon Apr 04 2016 - 03:57:40 PDT)
- Sreemol G (Mon Apr 04 2016 - 03:39:24 PDT)
- hannes.loeffler.stfc.ac.uk (Mon Apr 04 2016 - 03:17:38 PDT)
- Sreemol G (Mon Apr 04 2016 - 02:57:41 PDT)
- hannes.loeffler.stfc.ac.uk (Mon Apr 04 2016 - 00:08:57 PDT)
- Sreemol G (Sun Apr 03 2016 - 23:47:58 PDT)
- hannes.loeffler.stfc.ac.uk (Sun Apr 03 2016 - 23:21:12 PDT)
- David Cerutti (Sun Apr 03 2016 - 23:19:53 PDT)
- Sreemol G (Sun Apr 03 2016 - 23:04:28 PDT)
[AMBER] General Type Improper Dihedrals vs. Specifics
- David Cerutti (Wed Apr 06 2016 - 18:25:15 PDT)
- David A Case (Wed Apr 06 2016 - 17:46:43 PDT)
- David Cerutti (Wed Apr 06 2016 - 14:50:37 PDT)
- Robert Molt (Wed Apr 06 2016 - 14:20:15 PDT)
[AMBER] geometric center with cpptraj
- Hai Nguyen (Mon Apr 11 2016 - 07:01:05 PDT)
- Batuhan Kav (Mon Apr 11 2016 - 03:00:52 PDT)
[AMBER] glycam O-glycosylation at Ser
- Neha Gandhi (Tue Apr 19 2016 - 00:16:46 PDT)
- Lachele Foley (Mon Apr 18 2016 - 23:59:06 PDT)
- Neha Gandhi (Mon Apr 18 2016 - 22:17:43 PDT)
[AMBER] hbond analysis of phosphotyrosine
- Wu Xu (Sat Apr 16 2016 - 09:41:32 PDT)
- Daniel Roe (Sat Apr 16 2016 - 09:38:45 PDT)
- Wu Xu (Fri Apr 15 2016 - 10:09:41 PDT)
- Daniel Roe (Fri Apr 15 2016 - 08:35:34 PDT)
- Wu Xu (Fri Apr 15 2016 - 05:13:13 PDT)
- David A Case (Fri Apr 15 2016 - 04:59:26 PDT)
- Hai Nguyen (Thu Apr 14 2016 - 23:48:38 PDT)
- Wu Xu (Thu Apr 14 2016 - 19:55:56 PDT)
[AMBER] Hbond command use with non-hydrogen bonds
- Daniel Roe (Thu Apr 07 2016 - 08:39:34 PDT)
- Krantzman, Kristin D (Thu Apr 07 2016 - 07:49:56 PDT)
[AMBER] help identifying dihedral parameters for paracetemol using Antechamber
- Andrew Schaub (Sat Apr 30 2016 - 22:01:04 PDT)
[AMBER] HEME group in a protein
- David A Case (Tue Apr 19 2016 - 04:41:03 PDT)
- Anna Cebrian Prats (Tue Apr 19 2016 - 04:14:45 PDT)
[AMBER] hoogsteen base pair
- David A Case (Fri Apr 01 2016 - 09:32:47 PDT)
- Martina Devi (Fri Apr 01 2016 - 08:25:28 PDT)
- Martina Devi (Fri Apr 01 2016 - 08:23:48 PDT)
[AMBER] How can I extract PDB files from a molecular dynamics simulation
- Luis Esteban (Sat Apr 16 2016 - 17:29:07 PDT)
- Daniel Roe (Fri Apr 15 2016 - 08:42:17 PDT)
- Luis Esteban (Thu Apr 14 2016 - 19:39:01 PDT)
- Kenneth McGuinness (Thu Apr 14 2016 - 19:10:23 PDT)
- Luis Esteban (Thu Apr 14 2016 - 19:02:03 PDT)
[AMBER] How can I use FF14SB in DOCK6 calculation?
- Marc van der Kamp (Fri Apr 29 2016 - 01:09:37 PDT)
- Mijiddorj Batsaikhan (Thu Apr 28 2016 - 22:03:55 PDT)
- Dwight McGee (Thu Apr 28 2016 - 06:53:43 PDT)
- Mijiddorj Batsaikhan (Thu Apr 28 2016 - 03:20:40 PDT)
[AMBER] How to deal with monoatomic ion, such as ILs anion
- Takuya Uto (Mon Apr 25 2016 - 03:50:16 PDT)
- Bill Ross (Sat Apr 23 2016 - 11:50:33 PDT)
- Andrew Schaub (Sat Apr 23 2016 - 11:41:21 PDT)
- Bill Ross (Sat Apr 23 2016 - 11:30:51 PDT)
- Takuya Uto (Sat Apr 23 2016 - 02:49:22 PDT)
- kurisaki (Thu Apr 21 2016 - 18:57:39 PDT)
- Takuya Uto (Thu Apr 21 2016 - 18:45:45 PDT)
[AMBER] How to deal with monoatomic ion, such as ILs cation
- Bill Ross (Thu Apr 21 2016 - 18:39:21 PDT)
- Takuya Uto (Thu Apr 21 2016 - 18:29:56 PDT)
[AMBER] how to embed amber14
- David A Case (Mon Apr 18 2016 - 04:26:23 PDT)
- Jason Swails (Mon Apr 18 2016 - 03:54:09 PDT)
- Ayesha Kanwal (Mon Apr 18 2016 - 03:47:23 PDT)
- Jason Swails (Sun Apr 17 2016 - 09:27:03 PDT)
- Ayesha Kanwal (Thu Apr 14 2016 - 03:34:57 PDT)
[AMBER] how to prepare a pdb file of a protein being phosphorylated at specific residues
- YanhuaOuyang (Mon Apr 04 2016 - 00:06:29 PDT)
- Mijiddorj Batsaikhan (Sun Apr 03 2016 - 21:53:13 PDT)
- 欧阳艳华 (Sun Apr 03 2016 - 20:15:03 PDT)
[AMBER] How to prepare files cyclodextrin to use witch glycam04
- CRISTIAN ROSSI PERARO (Sat Apr 09 2016 - 10:49:56 PDT)
- FyD (Sat Apr 09 2016 - 01:10:52 PDT)
- Lachele Foley (Fri Apr 08 2016 - 21:29:02 PDT)
- CRISTIAN ROSSI PERARO (Fri Apr 08 2016 - 20:32:49 PDT)
- Lachele Foley (Fri Apr 08 2016 - 20:07:24 PDT)
- CRISTIAN ROSSI PERARO (Fri Apr 08 2016 - 19:35:28 PDT)
[AMBER] How to read mdinfo file without crashing the simulation?
- Dr. M. Shahid (Mon Apr 25 2016 - 05:31:51 PDT)
- Karolina Markowska (Mon Apr 25 2016 - 05:00:08 PDT)
- Bill Ross (Sun Apr 24 2016 - 15:46:55 PDT)
- Karolina Markowska (Sun Apr 24 2016 - 12:16:02 PDT)
- Bill Ross (Sat Apr 23 2016 - 11:55:45 PDT)
- Bill Ross (Sat Apr 23 2016 - 11:53:25 PDT)
- Karolina Markowska (Fri Apr 22 2016 - 02:24:26 PDT)
- Bill Ross (Thu Apr 21 2016 - 11:22:16 PDT)
- Bill Ross (Thu Apr 21 2016 - 11:10:07 PDT)
- Hannes Loeffler (Thu Apr 21 2016 - 05:46:24 PDT)
- David A Case (Thu Apr 21 2016 - 05:14:54 PDT)
- Karolina Markowska (Thu Apr 21 2016 - 03:43:18 PDT)
- Hannes Loeffler (Thu Apr 21 2016 - 03:13:49 PDT)
- Karolina Markowska (Thu Apr 21 2016 - 03:11:56 PDT)
- Dr. M. Shahid (Thu Apr 21 2016 - 02:29:41 PDT)
- Karolina Markowska (Thu Apr 21 2016 - 02:01:03 PDT)
[AMBER] How to rebuild pH-based trajectory files from CpHMD restarted simulations
- Jason Swails (Mon Apr 25 2016 - 03:16:18 PDT)
- Elisa Pieri (Mon Apr 25 2016 - 02:39:46 PDT)
[AMBER] how to run a MD of a phosphorylated protein using amber
- YanhuaOuyang (Sun Apr 03 2016 - 23:46:28 PDT)
- Mijiddorj Batsaikhan (Sun Apr 03 2016 - 21:30:28 PDT)
- 欧阳艳华 (Sun Apr 03 2016 - 20:21:43 PDT)
[AMBER] How to use tiMerge properly in pmemd TI calculation
- jfliu.itcs.ecnu.edu.cn (Sun Apr 03 2016 - 07:22:50 PDT)
- hannes.loeffler.stfc.ac.uk (Sun Apr 03 2016 - 07:03:23 PDT)
- jfliu.itcs.ecnu.edu.cn (Sun Apr 03 2016 - 06:55:48 PDT)
- hannes.loeffler.stfc.ac.uk (Sun Apr 03 2016 - 06:41:22 PDT)
- jfliu.itcs.ecnu.edu.cn (Sun Apr 03 2016 - 06:29:11 PDT)
[AMBER] Hydrophobic solution environment ???
- David A Case (Sat Apr 02 2016 - 07:59:20 PDT)
- Mijiddorj Batsaikhan (Sat Apr 02 2016 - 01:50:43 PDT)
[AMBER] Hydroxyproline
- David A Case (Sat Apr 23 2016 - 05:38:51 PDT)
- Carlos Simmerling (Sat Apr 23 2016 - 05:36:26 PDT)
- Mijiddorj Batsaikhan (Sat Apr 23 2016 - 05:00:41 PDT)
[AMBER] Implicit Solvent simulation - membrane proteins
- Ray Luo (Mon Apr 11 2016 - 11:21:47 PDT)
- Hai Nguyen (Mon Apr 11 2016 - 10:58:51 PDT)
- Balaji Selvam (Mon Apr 11 2016 - 10:51:35 PDT)
[AMBER] interactive MD applied to AI
- Bill Ross (Thu Apr 21 2016 - 20:16:19 PDT)
- Hai Nguyen (Thu Apr 21 2016 - 19:59:10 PDT)
- Bill Ross (Thu Apr 21 2016 - 18:37:27 PDT)
- Hai Nguyen (Thu Apr 21 2016 - 18:17:39 PDT)
- Bill Ross (Thu Apr 21 2016 - 17:25:58 PDT)
- Bill Ross (Tue Apr 19 2016 - 12:19:05 PDT)
[AMBER] Introducing the exciting next step in MD software development
- Adrian Roitberg (Fri Apr 01 2016 - 06:36:36 PDT)
- Bill Ross (Fri Apr 01 2016 - 06:34:19 PDT)
- Chris Moth (Fri Apr 01 2016 - 06:20:34 PDT)
- Thomas Pochapsky (Fri Apr 01 2016 - 05:48:59 PDT)
- Adrian Roitberg (Fri Apr 01 2016 - 04:31:02 PDT)
- Brent Krueger (Fri Apr 01 2016 - 04:05:04 PDT)
- ABEL Stephane 175950 (Fri Apr 01 2016 - 03:55:00 PDT)
- Jason Swails (Fri Apr 01 2016 - 03:32:51 PDT)
[AMBER] Is it possible to run TI with pmemd using the AMOEBA force field?
- David Cerutti (Sun Apr 10 2016 - 19:36:29 PDT)
- Jason Swails (Sun Apr 10 2016 - 17:13:27 PDT)
- Sumsamber Lee (Sun Apr 10 2016 - 15:07:03 PDT)
[AMBER] LEAP RUN FAILED
- Bill Ross (Thu Apr 14 2016 - 04:10:10 PDT)
- Neal Broomhead (Thu Apr 14 2016 - 02:38:06 PDT)
[AMBER] MD of 1:1 mixture compound
- Saman Yousuf ali (Tue Apr 26 2016 - 22:10:56 PDT)
[AMBER] MD simulations of deprotonated tyrosine residue with AMBER
- Jason Swails (Mon Apr 04 2016 - 09:03:17 PDT)
- ABEL Stephane 175950 (Mon Apr 04 2016 - 06:55:55 PDT)
- Adrian Roitberg (Mon Apr 04 2016 - 06:31:22 PDT)
- ABEL Stephane 175950 (Mon Apr 04 2016 - 06:22:41 PDT)
[AMBER] MD tutorial workflows
- James Starlight (Mon Apr 11 2016 - 01:36:35 PDT)
[AMBER] Metal geometry
- Pengfei Li (Mon Apr 11 2016 - 20:11:44 PDT)
- Vasantha Kumar (Sun Apr 10 2016 - 06:40:34 PDT)
- Pengfei Li (Sat Apr 09 2016 - 19:42:44 PDT)
- Pengfei Li (Sat Apr 09 2016 - 07:29:15 PDT)
- Vasantha Kumar (Sat Apr 09 2016 - 04:20:27 PDT)
- FyD (Sat Apr 09 2016 - 01:19:01 PDT)
- Vasantha Kumar (Fri Apr 08 2016 - 16:42:04 PDT)
- Vasantha Kumar (Fri Apr 08 2016 - 16:29:14 PDT)
- David Cerutti (Fri Apr 08 2016 - 08:01:26 PDT)
- Carlos Simmerling (Fri Apr 08 2016 - 07:32:51 PDT)
- Vasantha Kumar (Fri Apr 08 2016 - 06:13:15 PDT)
[AMBER] mm_pbsa.pl ERROR
- yhzahsc (Thu Apr 14 2016 - 19:26:46 PDT)
- yhzahsc (Thu Apr 14 2016 - 19:25:59 PDT)
- David A Case (Thu Apr 14 2016 - 04:45:32 PDT)
- Bill Ross (Thu Apr 14 2016 - 01:44:49 PDT)
- yhzahsc (Thu Apr 14 2016 - 00:42:02 PDT)
[AMBER] mm_pbsa.pl, that I'm doing this right?
- CRISTIAN ROSSI PERARO (Mon Apr 11 2016 - 12:07:42 PDT)
- Ray Luo (Mon Apr 11 2016 - 08:25:21 PDT)
- CRISTIAN ROSSI PERARO (Sun Apr 10 2016 - 11:17:32 PDT)
[AMBER] MMGBSA and dielectric constants
- Jason Swails (Wed Apr 13 2016 - 09:49:58 PDT)
- Cortopassi, Wilian (Wed Apr 13 2016 - 09:37:34 PDT)
[AMBER] MMPBSA : Calculation when keeping explicit water molecules
- Alessandro Contini (Fri Apr 08 2016 - 05:38:24 PDT)
- Jason Swails (Fri Apr 08 2016 - 05:11:17 PDT)
- 楊承翰 (Thu Apr 07 2016 - 21:14:59 PDT)
[AMBER] mmpbsa complex
- Jason Swails (Fri Apr 29 2016 - 18:46:45 PDT)
- McElheny, Dan (Fri Apr 29 2016 - 13:57:42 PDT)
- Jason Swails (Thu Apr 21 2016 - 19:12:53 PDT)
- McElheny, Dan (Thu Apr 21 2016 - 12:42:52 PDT)
[AMBER] mmpbsa_py_energy failed with prmtop lig_tleap.prm
- Jason Swails (Mon Apr 04 2016 - 06:47:34 PDT)
- sunita gupta (Mon Apr 04 2016 - 05:17:32 PDT)
- Bill Miller III (Fri Apr 01 2016 - 05:22:32 PDT)
- sunita gupta (Thu Mar 31 2016 - 23:22:59 PDT)
[AMBER] Modelling of proteins
- Bill Ross (Fri Apr 22 2016 - 12:03:07 PDT)
- Aishani Prem (Fri Apr 22 2016 - 11:56:18 PDT)
- David Cerutti (Thu Apr 14 2016 - 14:42:52 PDT)
- Aishani Prem (Thu Apr 14 2016 - 14:30:00 PDT)
[AMBER] mpi problems
- Marcelo Andrade Chagas (Mon Apr 18 2016 - 12:16:22 PDT)
- Gard Nelson (Mon Apr 18 2016 - 11:46:06 PDT)
[AMBER] Multiple restraints for minimization
- Stevens, David Ryan (Mon Apr 11 2016 - 14:25:07 PDT)
- Daniel Roe (Mon Apr 11 2016 - 12:34:55 PDT)
- Stevens, David Ryan (Mon Apr 11 2016 - 11:56:29 PDT)
- Bill Ross (Mon Apr 11 2016 - 11:53:15 PDT)
- Daniel Roe (Mon Apr 11 2016 - 10:08:54 PDT)
- Stevens, David Ryan (Mon Apr 11 2016 - 09:03:08 PDT)
[AMBER] Natural bond orbital analysis
- Kenneth McGuinness (Thu Apr 14 2016 - 13:06:53 PDT)
- David A Case (Wed Apr 13 2016 - 17:59:49 PDT)
- Kenneth McGuinness (Wed Apr 13 2016 - 07:31:40 PDT)
[AMBER] No torsion terms for CB-N*-CR-H5
- Bill Ross (Thu Apr 28 2016 - 01:14:05 PDT)
- Prayagraj Fandilolu (Wed Apr 27 2016 - 23:29:11 PDT)
- David A Case (Sun Apr 24 2016 - 17:33:16 PDT)
- Prayagraj Fandilolu (Sun Apr 24 2016 - 00:12:13 PDT)
[AMBER] on antechamber
- David A Case (Sat Apr 30 2016 - 05:16:06 PDT)
- Brett (Sat Apr 30 2016 - 02:00:14 PDT)
- Daniel Roe (Mon Apr 18 2016 - 07:24:29 PDT)
- David A Case (Mon Apr 18 2016 - 04:24:15 PDT)
- Brett (Mon Apr 18 2016 - 02:28:10 PDT)
- hannes.loeffler.stfc.ac.uk (Sun Apr 17 2016 - 23:49:59 PDT)
- Brett (Sun Apr 17 2016 - 23:38:26 PDT)
[AMBER] on the MD of protein-ligand
- David Cerutti (Thu Apr 07 2016 - 23:08:13 PDT)
- Brett (Thu Apr 07 2016 - 22:48:53 PDT)
[AMBER] parmed.py
- Daniel Roe (Tue Apr 26 2016 - 08:14:35 PDT)
- Sanjib Paul (Tue Apr 26 2016 - 07:44:15 PDT)
[AMBER] PCA
- Daniel Roe (Fri Apr 08 2016 - 09:34:11 PDT)
- Sofia Vasilakaki (Thu Apr 07 2016 - 11:59:38 PDT)
[AMBER] Periodicity box
- Eiros Zamora, Juan (Fri Apr 01 2016 - 02:21:15 PDT)
[AMBER] PMF calculation via tunnel (SMD)
- wjli (Sun Apr 10 2016 - 05:03:23 PDT)
[AMBER] problem in 3DRISM convergence
- David A Case (Wed Apr 20 2016 - 05:17:23 PDT)
- ATUL KUMAR (Wed Apr 20 2016 - 03:29:41 PDT)
[AMBER] Problem in calculating auto time correlation function with ptraj
- David A Case (Wed Apr 27 2016 - 18:20:55 PDT)
- Daniel Roe (Wed Apr 27 2016 - 09:26:16 PDT)
- Saheb Dutta (Wed Apr 27 2016 - 08:32:55 PDT)
[AMBER] Problem Running MMPBSA.py
- Jason Swails (Tue Apr 26 2016 - 05:45:06 PDT)
- Dwight McGee (Mon Apr 25 2016 - 21:41:20 PDT)
- Martin Floor (Mon Apr 25 2016 - 15:29:23 PDT)
[AMBER] Problem with MCPB.py
- FyD (Sat Apr 09 2016 - 01:28:41 PDT)
- Surya Prakash Tiwari (Fri Apr 08 2016 - 11:09:32 PDT)
[AMBER] Problems running MD simulation using residual dipolar couplings as restraints
- Francisco Corzana López (Fri Apr 01 2016 - 08:13:01 PDT)
- David A Case (Fri Apr 01 2016 - 06:20:15 PDT)
- Francisco Corzana López (Thu Mar 31 2016 - 23:31:35 PDT)
[AMBER] Problems with periodic boundaries
- David A Case (Sat Apr 02 2016 - 07:53:51 PDT)
- Carlos Simmerling (Fri Apr 01 2016 - 13:38:42 PDT)
- Luke Presson (Fri Apr 01 2016 - 13:27:53 PDT)
- Carlos Simmerling (Fri Apr 01 2016 - 12:40:51 PDT)
- Luke Presson (Fri Apr 01 2016 - 12:37:01 PDT)
- Daniel Roe (Fri Apr 01 2016 - 10:51:38 PDT)
- Luke Presson (Fri Apr 01 2016 - 06:24:53 PDT)
[AMBER] protein complex dissociation during md
- Dr. Anselm Horn (Fri Apr 29 2016 - 01:56:27 PDT)
- Brett (Mon Apr 25 2016 - 06:54:34 PDT)
[AMBER] Protein-DNA docking
- Lara rajam (Tue Apr 12 2016 - 13:56:02 PDT)
- Carlos Simmerling (Tue Apr 12 2016 - 13:50:46 PDT)
- Hai Nguyen (Tue Apr 12 2016 - 13:51:07 PDT)
- Lara rajam (Tue Apr 12 2016 - 13:38:40 PDT)
[AMBER] QM calculation
- mohammad r (Fri Apr 08 2016 - 02:12:24 PDT)
- Marc van der Kamp (Tue Apr 05 2016 - 14:31:24 PDT)
- Gustavo Seabra (Tue Apr 05 2016 - 13:06:51 PDT)
- mohammad r (Mon Apr 04 2016 - 12:06:04 PDT)
- David A Case (Mon Apr 04 2016 - 05:54:03 PDT)
- mohammad r (Sun Apr 03 2016 - 11:20:49 PDT)
- David A Case (Sun Apr 03 2016 - 06:05:25 PDT)
- mohammad r (Sun Apr 03 2016 - 03:48:04 PDT)
- David A Case (Sat Apr 02 2016 - 07:56:39 PDT)
- mohammad r (Fri Apr 01 2016 - 22:54:34 PDT)
[AMBER] qmmm mmpbsa spin multiplicity problem
- Ayesha Fatima (Thu Apr 21 2016 - 19:18:16 PDT)
- Jason Swails (Thu Apr 21 2016 - 10:02:04 PDT)
- Ayesha Fatima (Thu Apr 21 2016 - 08:32:28 PDT)
[AMBER] Quasi-harmonic calculation
- David A Case (Mon Apr 18 2016 - 04:35:41 PDT)
- Amika Sood (Wed Apr 13 2016 - 06:15:06 PDT)
[AMBER] query about .mdcrd file
- Ayesha Kanwal (Tue Apr 19 2016 - 23:12:36 PDT)
- Christina Bergonzo (Tue Apr 19 2016 - 10:27:08 PDT)
- Ayesha Kanwal (Tue Apr 19 2016 - 10:12:36 PDT)
- Dr. M. Shahid (Tue Apr 19 2016 - 05:48:20 PDT)
- Ayesha Kanwal (Tue Apr 19 2016 - 04:23:44 PDT)
[AMBER] query regarding -refc
- David Cerutti (Mon Apr 11 2016 - 05:58:12 PDT)
- ABHIJEET CHOWDHURY (Sun Apr 10 2016 - 23:02:59 PDT)
- David Cerutti (Sun Apr 10 2016 - 21:29:53 PDT)
- ABHIJEET CHOWDHURY (Sun Apr 10 2016 - 21:11:07 PDT)
[AMBER] query regarding dssp plot cpptraj.
- Daniel Roe (Sun Apr 10 2016 - 08:04:29 PDT)
- Saman Yousuf ali (Sat Apr 09 2016 - 08:20:18 PDT)
[AMBER] Question about RESP with iodine
- Lorenzo Gontrani (Wed Apr 27 2016 - 06:50:53 PDT)
- Pengfei Li (Wed Apr 27 2016 - 06:39:37 PDT)
- David A Case (Wed Apr 27 2016 - 05:26:19 PDT)
- Lorenzo Gontrani (Wed Apr 27 2016 - 03:55:29 PDT)
[AMBER] questions about energy terms of amber MD
- David A Case (Thu Apr 21 2016 - 05:05:40 PDT)
- yuandandan (Wed Apr 20 2016 - 06:57:38 PDT)
[AMBER] Read/visualize volmap output (opendx)
- Jean-Patrick Francoia (Mon Apr 25 2016 - 13:46:47 PDT)
- Daniel Roe (Mon Apr 25 2016 - 12:41:02 PDT)
- Jean-Patrick Francoia (Mon Apr 25 2016 - 12:26:08 PDT)
- Daniel Roe (Mon Apr 25 2016 - 07:41:47 PDT)
- Jean-Patrick Francoia (Mon Apr 25 2016 - 06:12:45 PDT)
- Jason Swails (Mon Apr 25 2016 - 05:53:40 PDT)
- Jean-Patrick Francoia (Mon Apr 25 2016 - 03:54:13 PDT)
- Jason Swails (Mon Apr 25 2016 - 03:14:01 PDT)
- Jean-Patrick Francoia (Mon Apr 25 2016 - 01:44:54 PDT)
[AMBER] Refinement in explicit solvent
- Vasantha Kumar (Mon Apr 11 2016 - 16:30:22 PDT)
- David A Case (Mon Apr 11 2016 - 05:23:05 PDT)
- Vasantha Kumar (Mon Apr 11 2016 - 01:13:19 PDT)
[AMBER] Regarding atom types
- Elvis Martis (Fri Apr 22 2016 - 07:08:00 PDT)
- Daniel Roe (Thu Apr 21 2016 - 10:16:48 PDT)
- Elvis Martis (Tue Apr 19 2016 - 21:56:47 PDT)
[AMBER] Regarding Input file preparation in AMBER
- Bill Ross (Thu Apr 14 2016 - 00:40:20 PDT)
- Sivanandam M (Thu Apr 14 2016 - 00:01:41 PDT)
[AMBER] Regarding MM-PBSA calculation
- Jason Swails (Fri Apr 08 2016 - 05:12:32 PDT)
- Sivanandam M (Fri Apr 08 2016 - 03:44:33 PDT)
[AMBER] Regarding MM-PBSA free energy calculation
- Jason Swails (Fri Apr 08 2016 - 05:13:57 PDT)
- Sivanandam M (Fri Apr 08 2016 - 03:51:05 PDT)
[AMBER] Relation between binding affinity and free enegy
- Carlos Simmerling (Fri Apr 01 2016 - 07:15:45 PDT)
[AMBER] Release of Amber16 and AmberTools16
- David A Case (Sat Apr 30 2016 - 09:27:51 PDT)
[AMBER] RMSD graph for protein-RNA complex
- David A Case (Wed Apr 13 2016 - 05:23:55 PDT)
- Daniel Roe (Wed Apr 13 2016 - 05:01:25 PDT)
- Sreemol G (Tue Apr 12 2016 - 22:16:10 PDT)
- Andy Watkins (Tue Apr 12 2016 - 22:12:30 PDT)
- Sreemol G (Tue Apr 12 2016 - 22:06:57 PDT)
- Daniel Roe (Tue Apr 12 2016 - 12:50:46 PDT)
- Sreemol G (Tue Apr 12 2016 - 05:13:42 PDT)
- David A Case (Tue Apr 12 2016 - 04:45:25 PDT)
- Sreemol G (Mon Apr 11 2016 - 22:07:55 PDT)
- Daniel Roe (Fri Apr 08 2016 - 09:14:32 PDT)
- David A Case (Fri Apr 08 2016 - 04:31:53 PDT)
- Sreemol G (Fri Apr 08 2016 - 04:04:35 PDT)
- Dr. Anselm Horn (Fri Apr 08 2016 - 02:30:14 PDT)
- Sreemol G (Fri Apr 08 2016 - 01:15:07 PDT)
[AMBER] rotation angle around an axes
- Daniel Roe (Mon Apr 25 2016 - 10:59:24 PDT)
- giulia palermo (Mon Apr 25 2016 - 10:55:54 PDT)
[AMBER] Run Stage 2 of the RESP fit
- FyD (Wed Apr 06 2016 - 06:50:27 PDT)
- yhzahsc (Sun Apr 03 2016 - 17:35:20 PDT)
- Brent Krueger (Sun Apr 03 2016 - 06:49:40 PDT)
- yhzahsc (Sun Apr 03 2016 - 00:17:13 PDT)
[AMBER] running charmm force field in amber
- Neha Gandhi (Wed Apr 06 2016 - 18:40:52 PDT)
- Jason Swails (Wed Apr 06 2016 - 18:05:18 PDT)
- Ross Walker (Wed Apr 06 2016 - 17:50:23 PDT)
- Hai Nguyen (Wed Apr 06 2016 - 17:47:55 PDT)
- Neha Gandhi (Wed Apr 06 2016 - 17:37:56 PDT)
[AMBER] sander number of atoms limit
- David A Case (Tue Apr 05 2016 - 09:13:11 PDT)
- Jason Swails (Tue Apr 05 2016 - 05:07:23 PDT)
- Gould, Ian R (Tue Apr 05 2016 - 02:30:44 PDT)
- Gould, Ian R (Tue Apr 05 2016 - 02:27:26 PDT)
- Bill Ross (Tue Apr 05 2016 - 02:26:13 PDT)
- TERREUX RAPHAEL (Tue Apr 05 2016 - 02:16:04 PDT)
- Gould, Ian R (Tue Apr 05 2016 - 02:12:54 PDT)
- TERREUX RAPHAEL (Tue Apr 05 2016 - 01:59:59 PDT)
[AMBER] spherical restraint flatwell potentials
- Kenneth McGuinness (Mon Apr 04 2016 - 14:35:55 PDT)
- David Cerutti (Mon Apr 04 2016 - 12:33:29 PDT)
- Kenneth McGuinness (Mon Apr 04 2016 - 11:52:26 PDT)
- David Cerutti (Mon Apr 04 2016 - 11:32:18 PDT)
- Kenneth McGuinness (Mon Apr 04 2016 - 11:03:05 PDT)
[AMBER] System size limitations for Amber 14 pmemd.cuda?
- Kasprzak, Wojciech (NIH/NCI) [C] (Fri Apr 22 2016 - 05:48:38 PDT)
[AMBER] Targeted MD error
- Carlos Simmerling (Thu Apr 28 2016 - 10:03:03 PDT)
- Charles Lin (Thu Apr 28 2016 - 09:56:57 PDT)
- Shukla, Saurabh (Thu Apr 28 2016 - 09:46:03 PDT)
[AMBER] test: not getting emails from the list
- Jason Swails (Thu Apr 07 2016 - 09:31:35 PDT)
- Vlad Cojocaru (Thu Apr 07 2016 - 01:24:04 PDT)
[AMBER] The question about SMD
- Adrian Roitberg (Tue Apr 05 2016 - 07:23:47 PDT)
- wjli (Tue Apr 05 2016 - 06:56:05 PDT)
[AMBER] TI Calculation doubt
- Hannes Loeffler (Sat Apr 16 2016 - 01:18:23 PDT)
- Mary Varughese (Fri Apr 15 2016 - 23:34:02 PDT)
[AMBER] tleap - protein + ligand + heme group
- David A Case (Fri Apr 29 2016 - 09:27:28 PDT)
- Anna Cebrian Prats (Fri Apr 29 2016 - 08:16:21 PDT)
- Scott Brozell (Thu Apr 28 2016 - 10:35:26 PDT)
- David A Case (Thu Apr 28 2016 - 10:28:36 PDT)
- Anna Cebrian Prats (Thu Apr 28 2016 - 08:52:13 PDT)
[AMBER] tleap parametrization of metalo-binding proteins
- Pengfei Li (Thu Apr 28 2016 - 07:51:29 PDT)
- James Starlight (Wed Apr 27 2016 - 07:01:05 PDT)
- Pengfei Li (Wed Apr 27 2016 - 06:53:03 PDT)
- James Starlight (Wed Apr 27 2016 - 05:54:55 PDT)
- Yigal Lahav (Wed Apr 27 2016 - 04:07:26 PDT)
- James Starlight (Wed Apr 27 2016 - 02:25:23 PDT)
[AMBER] To convert the CHARMM-GUI formatted .pdb file into Lipid14 formatted .pdb file
- Jason Swails (Fri Apr 15 2016 - 13:07:54 PDT)
- Batuhan Kav (Fri Apr 15 2016 - 05:28:29 PDT)
- Shreeramesh (Fri Apr 15 2016 - 05:16:18 PDT)
- David A Case (Fri Apr 15 2016 - 05:03:10 PDT)
- Shreeramesh (Fri Apr 15 2016 - 04:27:48 PDT)
[AMBER] turning of non-bonded interactions with addExclusions
- Jason Swails (Mon Apr 04 2016 - 09:10:09 PDT)
- Batuhan Kav (Mon Apr 04 2016 - 02:42:30 PDT)
[AMBER] Using PBSA to Calculate Solvation Free Energy
- Ray Luo (Mon Apr 25 2016 - 15:56:49 PDT)
- Jiaqi Jin (Mon Apr 25 2016 - 15:31:48 PDT)
[AMBER] want to ask you about MMPBSA.py .mdcrd file
- Ayesha Kanwal (Tue Apr 19 2016 - 03:38:58 PDT)
- Ayesha Kanwal (Tue Apr 19 2016 - 03:32:31 PDT)
- Ayesha Kanwal (Tue Apr 19 2016 - 03:16:13 PDT)
- Dr. M. Shahid (Tue Apr 19 2016 - 03:04:39 PDT)
- Ayesha Kanwal (Tue Apr 19 2016 - 03:01:53 PDT)
- Ayesha Kanwal (Tue Apr 19 2016 - 02:59:01 PDT)
- Dr. M. Shahid (Tue Apr 19 2016 - 02:47:02 PDT)
- Ayesha Kanwal (Tue Apr 19 2016 - 02:21:44 PDT)
- Dr. M. Shahid (Tue Apr 19 2016 - 01:12:40 PDT)
- Ayesha Kanwal (Tue Apr 19 2016 - 00:55:36 PDT)
[AMBER] warning message for antechamber by acpype
- David A Case (Thu Apr 21 2016 - 12:26:40 PDT)
- Brett (Wed Apr 20 2016 - 07:41:28 PDT)
[AMBER] was the MCPB.py compiled correctly？
- jixiaofeng (Sun Apr 17 2016 - 19:59:35 PDT)
[AMBER] XLeap didn't save the parameter file
- David A Case (Fri Apr 22 2016 - 10:38:45 PDT)
- Bill Ross (Fri Apr 22 2016 - 09:28:56 PDT)
- Nikolay N. Kuzmich (Fri Apr 22 2016 - 05:39:11 PDT)
- David A Case (Wed Apr 20 2016 - 05:04:54 PDT)
- Bill Ross (Wed Apr 20 2016 - 01:33:09 PDT)
- Nikolay N. Kuzmich (Wed Apr 20 2016 - 01:27:17 PDT)
[AMBER] 回复： The question about SMD
- wjli (Tue Apr 05 2016 - 18:08:36 PDT)
- wjli (Tue Apr 05 2016 - 18:01:39 PDT)

Amber Archive Apr 2016 by subject