Amber Archive Mar 2017: by subject

[AMBER-Developers] web site inaccessible?
- Hai Nguyen (Mon Mar 27 2017 - 07:54:20 PDT)
- David Case (Mon Mar 27 2017 - 07:31:14 PDT)
[AMBER] 1-4 VDW and 1-4 EEL Energy Components in mm-gbsa
- Jason Swails (Fri Mar 03 2017 - 06:09:00 PST)
- Atila Petrosian (Fri Mar 03 2017 - 01:01:24 PST)
[AMBER] 2D rms plot doubt
- SHAILESH KUMAR (Mon Mar 20 2017 - 09:57:35 PDT)
- Daniel Roe (Mon Mar 20 2017 - 05:27:20 PDT)
- Daniel Roe (Mon Mar 20 2017 - 05:23:33 PDT)
- Mary Varughese (Sat Mar 18 2017 - 10:14:55 PDT)
- SHAILESH KUMAR (Sat Mar 18 2017 - 10:10:05 PDT)
- Daniel Roe (Sat Mar 18 2017 - 09:36:55 PDT)
- SHAILESH KUMAR (Sat Mar 18 2017 - 06:58:01 PDT)
- Elvis Martis (Sat Mar 18 2017 - 03:11:19 PDT)
- Mary Varughese (Sat Mar 18 2017 - 02:56:00 PDT)
[AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16
- Paul Westphaelinger (Thu Mar 30 2017 - 12:46:48 PDT)
- Charles Lin (Thu Mar 30 2017 - 12:26:04 PDT)
- Paul Westphälinger (Thu Mar 30 2017 - 07:57:04 PDT)
[AMBER] [MTKPP & pmemd error]: Installation of Amber 12 with Amber-too13 on Fedora25-64bit
- Vasantha Kumar (Mon Mar 20 2017 - 08:49:48 PDT)
- Hai Nguyen (Mon Mar 20 2017 - 08:46:30 PDT)
- Vasantha Kumar (Mon Mar 20 2017 - 08:38:01 PDT)
- Hai Nguyen (Sat Mar 18 2017 - 23:19:36 PDT)
- Bill Ross (Sat Mar 18 2017 - 22:46:07 PDT)
- Vasantha Kumar (Sat Mar 18 2017 - 19:19:19 PDT)
- Vasantha Kumar (Sat Mar 18 2017 - 19:12:19 PDT)
- David Case (Sat Mar 18 2017 - 08:22:33 PDT)
- Bill Ross (Fri Mar 17 2017 - 23:55:50 PDT)
- Vasantha Kumar (Fri Mar 17 2017 - 23:33:42 PDT)
[AMBER] A problem about the frcmod produced by ParmChk
- David Case (Mon Mar 13 2017 - 19:15:23 PDT)
- JinpengYang (Mon Mar 13 2017 - 18:07:16 PDT)
[AMBER] About PCA with cpptraj
- Elvis Martis (Wed Mar 15 2017 - 10:06:26 PDT)
- Daniel Roe (Wed Mar 15 2017 - 10:03:19 PDT)
- Elvis Martis (Wed Mar 15 2017 - 09:34:00 PDT)
[AMBER] Accelerated MD
- Daniel Roe (Thu Mar 09 2017 - 05:36:51 PST)
- Beale, John (Thu Mar 09 2017 - 04:49:36 PST)
- Beale, John (Thu Mar 09 2017 - 04:47:56 PST)
- Neha Gandhi (Thu Mar 09 2017 - 04:46:09 PST)
- Beale, John (Thu Mar 09 2017 - 02:51:12 PST)
[AMBER] Amber 16 MD simulation Problems
- David Case (Mon Mar 06 2017 - 18:39:03 PST)
- 杨满意 (Mon Mar 06 2017 - 03:38:14 PST)
- Elvis Martis (Mon Mar 06 2017 - 03:22:26 PST)
- 杨满意 (Mon Mar 06 2017 - 02:53:46 PST)
- David Case (Sun Mar 05 2017 - 10:21:47 PST)
- Elvis Martis (Sun Mar 05 2017 - 02:28:54 PST)
- 杨满意 (Sat Mar 04 2017 - 20:11:03 PST)
[AMBER] Amber Mailing List problem
- Marcos Serrou do Amaral (Thu Mar 30 2017 - 07:02:09 PDT)
- George Tzotzos (Thu Mar 30 2017 - 06:59:43 PDT)
[AMBER] AmberTools compilation
- Tom Dreyfus (Thu Mar 09 2017 - 07:54:24 PST)
- Hai Nguyen (Thu Mar 09 2017 - 07:40:25 PST)
- Tom Dreyfus (Thu Mar 09 2017 - 07:36:09 PST)
- Hai Nguyen (Thu Mar 09 2017 - 07:30:23 PST)
- Tom Dreyfus (Thu Mar 09 2017 - 07:22:47 PST)
- Hai Nguyen (Thu Mar 09 2017 - 07:23:15 PST)
- Tom Dreyfus (Thu Mar 09 2017 - 06:41:44 PST)
- David Case (Thu Mar 09 2017 - 06:16:50 PST)
- Daniel Roe (Thu Mar 09 2017 - 06:08:32 PST)
- Tom Dreyfus (Thu Mar 09 2017 - 05:56:15 PST)
- Nhai (Thu Mar 09 2017 - 05:51:03 PST)
- Daniel Roe (Thu Mar 09 2017 - 05:48:02 PST)
- Tom Dreyfus (Thu Mar 09 2017 - 05:45:18 PST)
- Daniel Roe (Thu Mar 09 2017 - 05:33:00 PST)
- Tom Dreyfus (Thu Mar 09 2017 - 05:04:44 PST)
[AMBER] anionic Ser ?
- FyD (Fri Mar 10 2017 - 06:08:38 PST)
- Michael Shokhen (Thu Mar 09 2017 - 07:38:20 PST)
- David Case (Thu Mar 09 2017 - 06:21:12 PST)
- Michael Shokhen (Thu Mar 09 2017 - 05:23:25 PST)
[AMBER] Antechamber Error
- David Case (Sat Mar 25 2017 - 08:21:09 PDT)
- Andrew Schaub (Sat Mar 25 2017 - 00:30:38 PDT)
- Elvis Martis (Thu Mar 23 2017 - 02:59:26 PDT)
- luca maggi (Thu Mar 23 2017 - 02:28:17 PDT)
- Elvis Martis (Thu Mar 23 2017 - 01:58:53 PDT)
- luca maggi (Thu Mar 23 2017 - 00:09:58 PDT)
- Elvis Martis (Tue Mar 21 2017 - 00:15:27 PDT)
- luca maggi (Mon Mar 20 2017 - 23:56:51 PDT)
[AMBER] Application of external electric field with QM/MM in Amber
- Kshatresh Dutta Dubey (Tue Mar 07 2017 - 12:47:15 PST)
[AMBER] autoimage for a protein filament
- Baker, Joseph (Thu Mar 30 2017 - 10:44:22 PDT)
- Daniel Roe (Thu Mar 30 2017 - 05:20:20 PDT)
- Baker, Joseph (Wed Mar 29 2017 - 19:10:08 PDT)
[AMBER] AWS GPU node crashes with AMBER 16
- Arnoult, Eric [JRDUS] (Wed Mar 22 2017 - 10:35:11 PDT)
[AMBER] Boron's parameter
- David Case (Fri Mar 10 2017 - 07:27:07 PST)
- jinfeng liu (Fri Mar 10 2017 - 04:35:54 PST)
[AMBER] C/Fortran compilation
- Hai Nguyen (Fri Mar 17 2017 - 09:00:15 PDT)
- Kanin Wichapong (Fri Mar 17 2017 - 08:42:27 PDT)
[AMBER] Chamber error; No NONBONDED
- Jason Swails (Thu Mar 23 2017 - 20:22:38 PDT)
- Sadegh Faramarzi Ganjabad (Wed Mar 22 2017 - 11:34:47 PDT)
[AMBER] constraint residues while enhanced sampling simulation
- Kat G (Wed Mar 29 2017 - 13:40:43 PDT)
[AMBER] converting trajectory file from NAMD to AMBER
- Hai Nguyen (Thu Mar 16 2017 - 09:49:09 PDT)
- Elvis Martis (Thu Mar 16 2017 - 09:37:06 PDT)
- Oleksii Zdorevskyi (Thu Mar 16 2017 - 09:31:21 PDT)
- Oleksii Zdorevskyi (Thu Mar 16 2017 - 08:40:12 PDT)
- Daniel Roe (Thu Mar 16 2017 - 08:05:45 PDT)
- Elvis Martis (Thu Mar 16 2017 - 07:45:43 PDT)
- Oleksii Zdorevskyi (Thu Mar 16 2017 - 07:43:12 PDT)
[AMBER] coordinates in restraint mast
- Daniel Roe (Fri Mar 31 2017 - 09:24:20 PDT)
- Thomas Evangelidis (Fri Mar 31 2017 - 08:44:06 PDT)
- Daniel Roe (Fri Mar 31 2017 - 08:14:53 PDT)
- Thomas Evangelidis (Fri Mar 31 2017 - 07:54:22 PDT)
- Hannes Loeffler (Fri Mar 31 2017 - 06:35:34 PDT)
- Thomas Evangelidis (Fri Mar 31 2017 - 06:13:37 PDT)
[AMBER] Count number of water molecules in minor groove of DNA
- The Cromicus Productions (Wed Mar 22 2017 - 12:33:02 PDT)
[AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds
- Eric Lang (Wed Mar 15 2017 - 01:49:03 PDT)
- Jason Swails (Tue Mar 14 2017 - 10:53:25 PDT)
- Eric Lang (Tue Mar 14 2017 - 07:40:22 PDT)
- Adrian Roitberg (Fri Mar 03 2017 - 07:02:52 PST)
- Eric Lang (Fri Mar 03 2017 - 07:01:36 PST)
- Eric Lang (Fri Mar 03 2017 - 06:52:38 PST)
- Adrian Roitberg (Fri Mar 03 2017 - 06:51:50 PST)
- Jason Swails (Fri Mar 03 2017 - 06:47:53 PST)
- Eric Lang (Fri Mar 03 2017 - 06:33:24 PST)
[AMBER] CpHMD: how is the charged system treated?
- Adrian Roitberg (Wed Mar 22 2017 - 07:18:23 PDT)
- Elisa Pieri (Wed Mar 22 2017 - 06:33:30 PDT)
[AMBER] cpptraj distance between centroid of a ring and an atom
- Daniel Roe (Thu Mar 23 2017 - 05:11:36 PDT)
- Neha Gandhi (Thu Mar 23 2017 - 00:41:54 PDT)
[AMBER] Cpptraj problems
- Daniel Roe (Thu Mar 30 2017 - 05:03:10 PDT)
- 杨满意 (Tue Mar 28 2017 - 20:43:52 PDT)
[AMBER] cpptraj: dihcovar and projection need trajin to work properly?
- Daniel Roe (Wed Mar 01 2017 - 10:01:44 PST)
- Thomas Fox (Wed Mar 01 2017 - 09:54:04 PST)
- Daniel Roe (Wed Mar 01 2017 - 08:26:10 PST)
[AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered
- David Case (Thu Mar 09 2017 - 05:07:12 PST)
- Andreas Tosstorff (Thu Mar 09 2017 - 02:29:59 PST)
- kungking Hanpaibool (Thu Mar 09 2017 - 01:59:04 PST)
[AMBER] Difficulty using noshakemask in Amber15
- Chase Zagorec-Marks (Wed Mar 22 2017 - 10:16:25 PDT)
- Bill Ross (Tue Mar 21 2017 - 16:49:00 PDT)
- Chase Zagorec-Marks (Tue Mar 21 2017 - 16:43:03 PDT)
[AMBER] Dimer trajectory analysis
- Daniel Roe (Thu Mar 30 2017 - 05:16:58 PDT)
- Bill Ross (Wed Mar 29 2017 - 09:41:22 PDT)
- Andreas Tosstorff (Wed Mar 29 2017 - 09:34:23 PDT)
[AMBER] Discrepancy between gaff.dat and leaprc.gaff hybridization
- Maral Aminpour (Mon Mar 13 2017 - 13:17:52 PDT)
[AMBER] Distance between benzene ring of one molecule and centre of mass of other molecule
- Nhai (Wed Mar 01 2017 - 17:38:36 PST)
- konda003 . (Wed Mar 01 2017 - 13:54:53 PST)
[AMBER] distance calculations - Protein-RNA
- Daniel Roe (Thu Mar 16 2017 - 05:41:05 PDT)
- Sidhu, Khushwant (Dr.) (Thu Mar 16 2017 - 03:36:26 PDT)
[AMBER] Distance constraint
- Thakur, Abhishek (Thu Mar 09 2017 - 07:53:35 PST)
[AMBER] DU issue with Antechamber
- Abhilash J (Thu Mar 30 2017 - 03:21:14 PDT)
- David Case (Tue Mar 28 2017 - 10:01:36 PDT)
- Abhilash J (Sat Mar 25 2017 - 00:16:26 PDT)
- David Case (Thu Mar 23 2017 - 06:32:47 PDT)
- Abhilash J (Wed Mar 22 2017 - 21:21:37 PDT)
[AMBER] dUMP parameters
- FyD (Mon Mar 06 2017 - 22:57:11 PST)
- David Case (Sun Mar 05 2017 - 10:17:09 PST)
- ABEL Stephane (Sun Mar 05 2017 - 09:03:19 PST)
- Mrinal Arandhara (Sun Mar 05 2017 - 08:06:14 PST)
- Elvis Martis (Sun Mar 05 2017 - 07:58:29 PST)
- Mrinal Arandhara (Sun Mar 05 2017 - 07:53:42 PST)
- Elvis Martis (Sun Mar 05 2017 - 07:37:07 PST)
- Elvis Martis (Sun Mar 05 2017 - 07:34:01 PST)
- Mrinal Arandhara (Sun Mar 05 2017 - 07:20:35 PST)
[AMBER] error explicit solvent CpHMD production run
- Adrian Roitberg (Wed Mar 08 2017 - 07:30:21 PST)
- EGIDEA PUTI DEVINA (Wed Mar 08 2017 - 01:41:11 PST)
- Adrian Roitberg (Tue Mar 07 2017 - 05:25:14 PST)
- EGIDEA PUTI DEVINA (Mon Mar 06 2017 - 22:05:05 PST)
[AMBER] Error for reading the amber rst file
- David Case (Mon Mar 13 2017 - 08:02:23 PDT)
[AMBER] Error Importing pytraj to Python 2.7 Program
- Nhai (Tue Mar 21 2017 - 15:31:31 PDT)
- Samuel Bowerman (Tue Mar 21 2017 - 15:05:00 PDT)
- Samuel Bowerman (Tue Mar 21 2017 - 15:02:21 PDT)
- Hai Nguyen (Tue Mar 21 2017 - 14:59:53 PDT)
- Hai Nguyen (Tue Mar 21 2017 - 14:35:38 PDT)
- Samuel Bowerman (Tue Mar 21 2017 - 14:20:40 PDT)
[AMBER] Error in Cobalt parameters in CO-METHYLCOBALAMIN with MCPB.py
- Abhilash J (Wed Mar 15 2017 - 04:42:47 PDT)
- Pengfei Li (Tue Mar 14 2017 - 14:19:26 PDT)
- Abhilash J (Wed Mar 08 2017 - 01:45:50 PST)
[AMBER] Error when running QM/MM MD for actinide and lanthanide system by amber
- Goetz, Andreas (Mon Mar 13 2017 - 20:30:27 PDT)
- 鲁俊波 (Mon Mar 13 2017 - 19:22:19 PDT)
[AMBER] Error: FATAL: Atom .R<ZN 2>.A<ZN 1> does not have a type.
- Elvis Martis (Tue Mar 28 2017 - 21:28:23 PDT)
- Andrew Schaub (Tue Mar 28 2017 - 20:47:47 PDT)
- Aishani Prem (Tue Mar 28 2017 - 18:22:06 PDT)
[AMBER] FEW- issues generating parameter files for MD
- Sowmya Indrakumar (Wed Mar 29 2017 - 01:27:02 PDT)
- Andreas Tosstorff (Wed Mar 29 2017 - 00:50:05 PDT)
- Sowmya Indrakumar (Tue Mar 28 2017 - 08:59:19 PDT)
- Andreas Tosstorff (Tue Mar 28 2017 - 08:45:41 PDT)
- Sowmya Indrakumar (Tue Mar 28 2017 - 08:37:45 PDT)
- Andreas Tosstorff (Tue Mar 28 2017 - 07:24:31 PDT)
- Andreas Tosstorff (Mon Mar 27 2017 - 08:28:06 PDT)
- Sowmya Indrakumar (Mon Mar 27 2017 - 08:18:40 PDT)
- Andreas Tosstorff (Mon Mar 27 2017 - 07:20:53 PDT)
- Sowmya Indrakumar (Mon Mar 27 2017 - 06:57:49 PDT)
[AMBER] Force/Energy vs extension curve from Steered MD
- Ramin Salimi (Mon Mar 27 2017 - 11:13:07 PDT)
- Ramin Salimi (Sun Mar 26 2017 - 21:48:49 PDT)
- Jason Swails (Sun Mar 26 2017 - 17:27:26 PDT)
- Ramin Salimi (Sun Mar 26 2017 - 14:21:49 PDT)
- Ramin Salimi (Sat Mar 25 2017 - 12:05:03 PDT)
- Adrian Roitberg (Sat Mar 25 2017 - 11:31:03 PDT)
- Ramin Salimi (Sat Mar 25 2017 - 11:15:19 PDT)
- Adrian Roitberg (Sat Mar 25 2017 - 11:03:39 PDT)
- Ramin Salimi (Sat Mar 25 2017 - 10:50:05 PDT)
- Ramin Salimi (Sat Mar 25 2017 - 10:36:15 PDT)
[AMBER] Force/energy vs extension curve in steered MD
- Ramin Salimi (Sat Mar 25 2017 - 10:02:22 PDT)
[AMBER] Fwd: H-bonds matrix
- giulia palermo (Thu Mar 02 2017 - 11:59:33 PST)
[AMBER] Generate DNA sequence with a mismatch
- diego.soler.uam.es (Fri Mar 17 2017 - 04:39:43 PDT)
[AMBER] Generate psf file for chamber
- Amy Rice (Thu Mar 09 2017 - 09:04:04 PST)
- Shanghaitech University WuMeng (Thu Mar 09 2017 - 02:56:23 PST)
[AMBER] Generating topology from Gaussian 09
- Elvis Martis (Thu Mar 16 2017 - 07:25:26 PDT)
- Vijay Achari (Thu Mar 16 2017 - 05:08:25 PDT)
[AMBER] H-bonds matrix
- giulia palermo (Thu Mar 02 2017 - 09:26:11 PST)
[AMBER] help in RDF
- Daniel Roe (Tue Mar 21 2017 - 08:30:33 PDT)
- Robin Jain (Tue Mar 21 2017 - 08:19:44 PDT)
[AMBER] Help with reconstructing pH-based mdcrd (trajectory) files
- Ingvild Isaksen (Wed Mar 15 2017 - 07:26:26 PDT)
- Daniel Roe (Wed Mar 15 2017 - 07:17:10 PDT)
- Ingvild Isaksen (Wed Mar 15 2017 - 06:42:21 PDT)
- Daniel Roe (Wed Mar 15 2017 - 06:15:05 PDT)
- Ingvild Isaksen (Wed Mar 15 2017 - 05:13:32 PDT)
[AMBER] Holes/bubbles in water during NVT (fix atoms)
- Daniel Roe (Wed Mar 01 2017 - 08:17:51 PST)
- David Cerutti (Wed Mar 01 2017 - 02:33:00 PST)
- Neha Gandhi (Tue Feb 28 2017 - 23:35:53 PST)
[AMBER] How to generate inputfile
- 杨满意 (Wed Mar 22 2017 - 05:48:51 PDT)
- David Case (Fri Mar 17 2017 - 07:12:57 PDT)
- 杨满意 (Fri Mar 17 2017 - 05:34:59 PDT)
- David Case (Thu Mar 16 2017 - 05:54:26 PDT)
- 杨满意 (Wed Mar 15 2017 - 18:49:43 PDT)
- David Case (Wed Mar 15 2017 - 07:19:25 PDT)
- 杨满意 (Tue Mar 14 2017 - 20:37:08 PDT)
[AMBER] How to generate inputfile (???)
- 杨满意 (Fri Mar 17 2017 - 06:09:32 PDT)
- David Poole (Thu Mar 16 2017 - 12:08:50 PDT)
[AMBER] How to get parmed.py script?
- Hai Nguyen (Wed Mar 15 2017 - 06:11:40 PDT)
- Sowmya Indrakumar (Wed Mar 15 2017 - 03:30:37 PDT)
- Karl Kirschner (Wed Mar 15 2017 - 03:25:13 PDT)
- Sowmya Indrakumar (Wed Mar 15 2017 - 02:31:05 PDT)
[AMBER] How to make rst file by using ptraj
- Daniel Roe (Sun Mar 05 2017 - 04:40:32 PST)
- David Case (Sat Mar 04 2017 - 12:51:02 PST)
- Daniel Roe (Sat Mar 04 2017 - 12:19:13 PST)
- Vishal Nemaysh (Sat Mar 04 2017 - 07:24:09 PST)
[AMBER] How to perform Newton-Raphson minimization to protein
- David Case (Fri Mar 24 2017 - 07:20:28 PDT)
- 巩梦雪 (Fri Mar 24 2017 - 06:53:26 PDT)
- David Case (Thu Mar 23 2017 - 06:38:01 PDT)
- 巩梦雪 (Thu Mar 23 2017 - 05:22:59 PDT)
[AMBER] How to use MCPB.py to generate OH parameters
- Pengfei Li (Tue Mar 14 2017 - 14:09:38 PDT)
- Alice Zeng (Sun Mar 12 2017 - 21:25:36 PDT)
[AMBER] how to use TImerge to do TI simulations
- Sowmya Indrakumar (Tue Mar 07 2017 - 07:44:46 PST)
- Hannes Loeffler (Tue Mar 07 2017 - 07:25:51 PST)
- Sowmya Indrakumar (Tue Mar 07 2017 - 07:01:07 PST)
- Sowmya Indrakumar (Tue Mar 07 2017 - 06:55:53 PST)
[AMBER] hydophobic
- Thakur, Abhishek (Thu Mar 09 2017 - 12:28:58 PST)
[AMBER] install AMBER16 GTX480
- Ross Walker (Tue Mar 21 2017 - 17:09:38 PDT)
- Jason Swails (Mon Mar 20 2017 - 11:29:30 PDT)
- Kanin Wichapong (Mon Mar 20 2017 - 06:46:54 PDT)
[AMBER] Installation issue
- Daniel Roe (Sat Mar 25 2017 - 05:59:51 PDT)
- George Tzotzos (Sat Mar 25 2017 - 05:37:03 PDT)
[AMBER] Installing Amber14 and AmberTools15 Error
- Scott Brozell (Thu Mar 30 2017 - 00:00:27 PDT)
- Erma Fatiha Muhammad (Wed Mar 29 2017 - 19:59:11 PDT)
[AMBER] Installing AmberTools16 - ld library issue
- Giannis Gl (Mon Mar 13 2017 - 11:14:52 PDT)
- Hai Nguyen (Mon Mar 13 2017 - 11:03:14 PDT)
- Daniel Roe (Mon Mar 13 2017 - 10:37:58 PDT)
- Giannis Gl (Mon Mar 13 2017 - 10:32:43 PDT)
[AMBER] Installing AmberTools16 - Sierra MacOs
- Bill Ross (Mon Mar 13 2017 - 14:30:10 PDT)
- Hai Nguyen (Mon Mar 13 2017 - 14:23:25 PDT)
- Hai Nguyen (Mon Mar 13 2017 - 14:11:56 PDT)
- Giannis Gl (Mon Mar 13 2017 - 14:08:14 PDT)
- Bill Ross (Mon Mar 13 2017 - 14:02:44 PDT)
- Giannis Gl (Mon Mar 13 2017 - 14:01:56 PDT)
- Giannis Gl (Mon Mar 13 2017 - 14:00:24 PDT)
- Hai Nguyen (Mon Mar 13 2017 - 13:57:06 PDT)
- Hai Nguyen (Mon Mar 13 2017 - 13:51:56 PDT)
- Giannis Gl (Mon Mar 13 2017 - 13:46:28 PDT)
- Hai Nguyen (Mon Mar 13 2017 - 13:37:37 PDT)
- Giannis Gl (Mon Mar 13 2017 - 13:32:11 PDT)
- Hai Nguyen (Mon Mar 13 2017 - 13:27:50 PDT)
- Hai Nguyen (Mon Mar 13 2017 - 13:27:09 PDT)
- Giannis Gl (Mon Mar 13 2017 - 12:10:49 PDT)
[AMBER] Intel Xeon Phi 7120P
- Elvis Martis (Wed Mar 15 2017 - 00:03:44 PDT)
- Sofia Vasilakaki (Tue Mar 14 2017 - 07:26:43 PDT)
[AMBER] Is it possible to create a bugreport.ambermd.org mailinglist?
- Daniel Roe (Wed Mar 22 2017 - 06:04:30 PDT)
- Paul Westphälinger (Wed Mar 22 2017 - 00:39:01 PDT)
- Hai Nguyen (Tue Mar 21 2017 - 13:23:07 PDT)
- Paul Westphälinger (Tue Mar 21 2017 - 11:56:41 PDT)
[AMBER] Issue generating parameter files - FEW
- Sowmya Indrakumar (Tue Mar 21 2017 - 08:06:10 PDT)
[AMBER] Issue regarding ligand parameterization
- Bruno Falcone (Mon Mar 20 2017 - 07:21:22 PDT)
- David Case (Mon Mar 20 2017 - 05:06:17 PDT)
- Nirupma Singh (Sun Mar 19 2017 - 22:55:18 PDT)
[AMBER] issues generating parameter files for the ligands- FEW
- Sowmya Indrakumar (Fri Mar 17 2017 - 08:13:03 PDT)
[AMBER] Issues Regaring the PDB files from Trajectory frames
- Ramin Salimi (Fri Mar 31 2017 - 16:03:33 PDT)
- Hai Nguyen (Fri Mar 31 2017 - 14:37:45 PDT)
- Ramin Salimi (Fri Mar 31 2017 - 14:30:29 PDT)
- Hai Nguyen (Fri Mar 31 2017 - 14:27:14 PDT)
- Ramin Salimi (Fri Mar 31 2017 - 14:23:52 PDT)
[AMBER] Issues running TI simulations
- Sowmya Indrakumar (Thu Mar 16 2017 - 05:21:07 PDT)
- Bill Ross (Thu Mar 16 2017 - 02:36:50 PDT)
- Sowmya Indrakumar (Thu Mar 16 2017 - 02:30:37 PDT)
- Bill Ross (Thu Mar 16 2017 - 02:24:42 PDT)
- Sowmya Indrakumar (Thu Mar 16 2017 - 02:10:04 PDT)
[AMBER] Linkage problem in branched oligosaccharide
- Lachele Foley (Thu Mar 30 2017 - 05:39:52 PDT)
- Manju Sah (Wed Mar 29 2017 - 05:32:14 PDT)
- David Case (Wed Mar 29 2017 - 04:57:40 PDT)
- Sangeetha B (Wed Mar 29 2017 - 02:09:13 PDT)
- Daniel Roe (Tue Mar 28 2017 - 06:22:22 PDT)
- Manju Sah (Tue Mar 28 2017 - 05:36:34 PDT)
[AMBER] maximum distance for protein-ligand interactions in MM/GBSA
- Thomas Evangelidis (Sat Mar 11 2017 - 07:34:05 PST)
[AMBER] Memory footprint goes on increasing: pytraj traj.iterchunk used, distances between bonds calculation
- Hai Nguyen (Sun Mar 12 2017 - 14:34:49 PDT)
- Hai Nguyen (Sun Mar 12 2017 - 14:30:15 PDT)
- SHAILESH KUMAR (Sun Mar 12 2017 - 14:13:51 PDT)
- Nhai (Sun Mar 12 2017 - 13:41:00 PDT)
- SHAILESH KUMAR (Sun Mar 12 2017 - 13:17:30 PDT)
[AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16?
- Paul Westphaelinger (Tue Mar 28 2017 - 08:29:14 PDT)
- Paul Westphaelinger (Fri Mar 24 2017 - 01:53:43 PDT)
- Paul Westphälinger (Thu Mar 23 2017 - 03:38:38 PDT)
- Paul Westphälinger (Wed Mar 22 2017 - 09:17:27 PDT)
- David Case (Wed Mar 22 2017 - 08:24:20 PDT)
- Paul Westphälinger (Wed Mar 22 2017 - 00:42:22 PDT)
- paul (Tue Mar 21 2017 - 04:35:39 PDT)
- Jason Swails (Mon Mar 20 2017 - 11:24:28 PDT)
- paul (Mon Mar 20 2017 - 09:01:53 PDT)
- David Case (Mon Mar 20 2017 - 07:44:01 PDT)
- paul (Mon Mar 20 2017 - 07:12:48 PDT)
- paul (Mon Mar 20 2017 - 07:02:10 PDT)
[AMBER] Methods to count the different species
- Liyang Zhu (Wed Mar 01 2017 - 18:24:39 PST)
- Daniel Roe (Wed Mar 01 2017 - 08:13:56 PST)
[AMBER] MM energy contributions of atoms in a molecule
- Bruno Falcone (Wed Mar 01 2017 - 06:43:33 PST)
[AMBER] MM/GBSA residual decomposition issue
- nagakumarb.ccamp.res.in (Fri Mar 17 2017 - 08:13:20 PDT)
- Bharatham, Nagakumar (Fri Mar 17 2017 - 05:29:57 PDT)
[AMBER] multinode pmemd.cuda.MPI jac9999 behavior
- Ross Walker (Thu Mar 23 2017 - 16:18:41 PDT)
- Scott Brozell (Thu Mar 23 2017 - 15:58:52 PDT)
- Niel Henriksen (Tue Mar 21 2017 - 13:50:00 PDT)
- Scott Brozell (Tue Mar 21 2017 - 12:52:34 PDT)
[AMBER] NMODE ERROR MESSAGE
- konda003 . (Fri Mar 17 2017 - 09:02:46 PDT)
[AMBER] Nmode using MMPBSA.py
- Dwight McGee (Wed Mar 22 2017 - 09:29:52 PDT)
- David Case (Wed Mar 22 2017 - 08:12:42 PDT)
- konda003 . (Tue Mar 21 2017 - 14:06:36 PDT)
[AMBER] Oligosaccharide linkage breaking problem during Solvent minimization
- Manju Sah (Wed Mar 29 2017 - 02:53:19 PDT)
[AMBER] OPEN SHELL MOLECULES
- David Case (Wed Mar 08 2017 - 18:57:47 PST)
- Hai Nguyen (Wed Mar 08 2017 - 14:38:30 PST)
- Stellamaris Sotomayor Burneo (Wed Mar 08 2017 - 14:19:29 PST)
[AMBER] pmemd.cuda and taskset on K80
- Ross Walker (Wed Mar 01 2017 - 17:22:05 PST)
- Diego Gomes (Wed Mar 01 2017 - 08:10:24 PST)
[AMBER] pmemd.MPI error on lonestar5 super comp.
- Daniel Roe (Mon Mar 20 2017 - 05:30:49 PDT)
- Miguel Rivera (Sun Mar 19 2017 - 15:48:00 PDT)
[AMBER] Potential on QM atoms - details about cutoff
- Elisa Pieri (Fri Mar 10 2017 - 07:13:19 PST)
[AMBER] Preparation of ligand enantiomers
- George Tzotzos (Tue Mar 28 2017 - 10:14:45 PDT)
[AMBER] prepare prepin file from MCPB results
- Abhilash J (Wed Mar 08 2017 - 01:31:34 PST)
- Pengfei Li (Mon Mar 06 2017 - 20:00:18 PST)
- Elvis Martis (Mon Mar 06 2017 - 02:38:50 PST)
- Abhilash J (Mon Mar 06 2017 - 00:34:14 PST)
[AMBER] prepc vs prepi
- David Case (Tue Mar 14 2017 - 14:43:28 PDT)
- Yong Duan (Tue Mar 14 2017 - 12:55:51 PDT)
- Yong Duan (Tue Mar 14 2017 - 12:36:07 PDT)
[AMBER] Problem in configuring+compiling cpptraj development version with Sander compiled with AmberTools16
- SHAILESH KUMAR (Fri Mar 10 2017 - 07:51:54 PST)
- Hai Nguyen (Fri Mar 10 2017 - 07:26:32 PST)
- SHAILESH KUMAR (Fri Mar 10 2017 - 06:25:56 PST)
- Daniel Roe (Fri Mar 10 2017 - 05:38:59 PST)
- SHAILESH KUMAR (Fri Mar 10 2017 - 05:35:04 PST)
- Daniel Roe (Fri Mar 10 2017 - 05:05:24 PST)
- SHAILESH KUMAR (Fri Mar 10 2017 - 02:50:34 PST)
[AMBER] Problem with keyboard in xleap
- David Case (Wed Mar 22 2017 - 08:40:36 PDT)
- Miguel Garavís (Wed Mar 22 2017 - 05:59:59 PDT)
- Daniel Roe (Wed Mar 22 2017 - 05:38:21 PDT)
- Elvis Martis (Wed Mar 22 2017 - 05:23:41 PDT)
- Miguel Garavís (Wed Mar 22 2017 - 05:07:33 PDT)
- Andreas Tosstorff (Wed Mar 22 2017 - 04:33:18 PDT)
- Miguel Garavís (Wed Mar 22 2017 - 03:59:30 PDT)
[AMBER] problem with solvation
- David Case (Tue Mar 14 2017 - 07:27:52 PDT)
- Maryam Hamzehee (Tue Mar 14 2017 - 00:21:18 PDT)
[AMBER] Problems in using Parmchk2
- David Case (Tue Mar 21 2017 - 07:15:51 PDT)
- 杨满意 (Thu Mar 16 2017 - 07:13:06 PDT)
- David Case (Thu Mar 16 2017 - 05:50:56 PDT)
- 杨满意 (Wed Mar 15 2017 - 19:09:35 PDT)
- David Case (Wed Mar 15 2017 - 15:10:50 PDT)
- 杨满意 (Wed Mar 15 2017 - 07:08:58 PDT)
[AMBER] problems with heating
- David Case (Tue Mar 07 2017 - 05:04:43 PST)
- Alicia Merlino (Mon Mar 06 2017 - 20:44:37 PST)
[AMBER] Query regarding extension of Molecular dynamics simulation from 50ns to 100ns
- Bill Ross (Mon Mar 06 2017 - 21:09:10 PST)
- Elvis Martis (Mon Mar 06 2017 - 21:07:32 PST)
- Elvis Martis (Mon Mar 06 2017 - 21:04:21 PST)
- Lovika Mittal (Mon Mar 06 2017 - 20:59:15 PST)
- Elvis Martis (Mon Mar 06 2017 - 20:35:14 PST)
- Lovika Mittal (Mon Mar 06 2017 - 20:26:12 PST)
[AMBER] Question about the implementation of the Steered MD
- Feng Pan (Fri Mar 10 2017 - 08:45:31 PST)
- abdennour braka (Thu Mar 09 2017 - 23:26:36 PST)
[AMBER] Question about the propagation of error in MM/PBSA binding free energy calculation.
- Adrian Roitberg (Tue Mar 28 2017 - 10:11:17 PDT)
[AMBER] Questions about Amber TI tutorial
- Hannes Loeffler (Wed Mar 22 2017 - 01:19:25 PDT)
- Hannes Loeffler (Tue Mar 21 2017 - 13:56:48 PDT)
- Sadegh Faramarzi Ganjabad (Tue Mar 21 2017 - 12:50:28 PDT)
[AMBER] Questions about MCPB.py
- Mingyuan_xu (Wed Mar 29 2017 - 18:57:03 PDT)
[AMBER] RDF plot
- Sowmya Indrakumar (Tue Mar 28 2017 - 11:17:06 PDT)
- Daniel Roe (Tue Mar 28 2017 - 10:49:46 PDT)
- Sowmya Indrakumar (Tue Mar 28 2017 - 10:28:18 PDT)
- Daniel Roe (Tue Mar 28 2017 - 10:16:47 PDT)
- Sowmya Indrakumar (Tue Mar 28 2017 - 10:04:57 PDT)
- Daniel Roe (Tue Mar 28 2017 - 09:55:37 PDT)
- Sowmya Indrakumar (Tue Mar 28 2017 - 09:18:32 PDT)
- Daniel Roe (Tue Mar 28 2017 - 06:59:32 PDT)
- Sowmya Indrakumar (Tue Mar 28 2017 - 06:03:19 PDT)
- Gustavo Seabra (Tue Mar 28 2017 - 05:55:07 PDT)
- Sowmya Indrakumar (Tue Mar 28 2017 - 05:49:36 PDT)
- Gustavo Seabra (Tue Mar 28 2017 - 04:26:15 PDT)
- Sowmya Indrakumar (Tue Mar 28 2017 - 03:51:28 PDT)
- Ming Tang (Tue Mar 28 2017 - 03:41:17 PDT)
- Sowmya Indrakumar (Tue Mar 28 2017 - 03:35:39 PDT)
[AMBER] rdf_with_center_in_cpptraj_16
- Daniel Roe (Mon Mar 06 2017 - 05:21:05 PST)
[AMBER] RE : suitable basis sets for QM/MM
- Vaibhav Dixit (Thu Mar 16 2017 - 22:01:28 PDT)
- Budhathoki, Dipesh (Thu Mar 16 2017 - 13:51:04 PDT)
- Goetz, Andreas (Thu Mar 16 2017 - 12:25:00 PDT)
- Budhathoki, Dipesh (Thu Mar 16 2017 - 10:49:00 PDT)
[AMBER] reg "rel delta G binding computation using TIMD"
- Smriti Sharma (Mon Mar 06 2017 - 19:37:43 PST)
- Hannes Loeffler (Mon Mar 06 2017 - 03:43:40 PST)
- Smriti Sharma (Mon Mar 06 2017 - 02:12:32 PST)
[AMBER] REMD processor number
- Andreas Tosstorff (Thu Mar 02 2017 - 09:04:47 PST)
[AMBER] renumber residues
- David Case (Fri Mar 24 2017 - 11:05:59 PDT)
- Daniel Roe (Fri Mar 24 2017 - 08:01:16 PDT)
- Thakur, Abhishek (Fri Mar 24 2017 - 07:15:15 PDT)
[AMBER] residue contribution for covalent inhibitor
- nagakumarb.ccamp.res.in (Fri Mar 24 2017 - 06:54:34 PDT)
[AMBER] restarting Amber calculations gives abnormal structures
- David Case (Fri Mar 31 2017 - 11:18:31 PDT)
- Chris Neale (Fri Mar 31 2017 - 10:01:10 PDT)
- Daniel Roe (Fri Mar 31 2017 - 09:57:01 PDT)
- Marc van der Kamp (Fri Mar 31 2017 - 09:37:53 PDT)
- Chris Neale (Fri Mar 31 2017 - 09:30:34 PDT)
- Marc van der Kamp (Thu Mar 30 2017 - 23:58:25 PDT)
- Sadegh Faramarzi Ganjabad (Thu Mar 30 2017 - 22:17:15 PDT)
- Chris Neale (Wed Mar 29 2017 - 12:36:15 PDT)
- Sadegh Faramarzi Ganjabad (Wed Mar 29 2017 - 12:26:56 PDT)
- David Case (Wed Mar 29 2017 - 04:50:28 PDT)
- Sadegh Faramarzi Ganjabad (Tue Mar 28 2017 - 13:29:49 PDT)
- David Case (Tue Mar 28 2017 - 09:47:13 PDT)
- Sadegh Faramarzi Ganjabad (Sat Mar 25 2017 - 20:53:09 PDT)
[AMBER] Restraint on Z-projection of a distance
- Feng Pan (Fri Mar 24 2017 - 12:15:50 PDT)
- Chitrak Gupta (Fri Mar 24 2017 - 11:44:53 PDT)
[AMBER] Segmentation fault when starting parmchk2 for a modified aminoacid residue
- Junmei Wang (Thu Mar 02 2017 - 08:13:04 PST)
[AMBER] Select specific frames within cpptraj?
- Daniel Roe (Tue Mar 21 2017 - 13:17:37 PDT)
- Kenneth Huang (Tue Mar 21 2017 - 13:03:03 PDT)
[AMBER] Simulating a protein with modified amino acid residue, the saga continues. Atom ... does not have a type.
- David Case (Fri Mar 10 2017 - 11:13:03 PST)
- FyD (Fri Mar 10 2017 - 09:30:22 PST)
- Nikolay N. Kuzmich (Fri Mar 10 2017 - 08:35:09 PST)
- FyD (Tue Mar 07 2017 - 01:30:34 PST)
- David Case (Mon Mar 06 2017 - 18:36:03 PST)
- Thakur, Abhishek (Mon Mar 06 2017 - 11:32:51 PST)
- Nikolay N. Kuzmich (Mon Mar 06 2017 - 09:16:33 PST)
[AMBER] Split a Large trajectory into smaller trajectory
- Andreas Tosstorff (Wed Mar 29 2017 - 00:38:14 PDT)
- Vishal Nemaysh (Tue Mar 28 2017 - 21:30:33 PDT)
[AMBER] surf cpptraj non-standard residue
- Daniel Roe (Mon Mar 27 2017 - 08:02:25 PDT)
- Andreas Tosstorff (Mon Mar 27 2017 - 07:56:27 PDT)
- Elvis Martis (Mon Mar 27 2017 - 06:24:50 PDT)
- Andreas Tosstorff (Mon Mar 27 2017 - 05:50:18 PDT)
- Elvis Martis (Mon Mar 27 2017 - 05:38:39 PDT)
- Andreas Tosstorff (Mon Mar 27 2017 - 05:29:01 PDT)
[AMBER] Thermodynamic integration simulations issues
- Hannes Loeffler (Tue Mar 28 2017 - 06:21:26 PDT)
- Szymon Żaczek (Sun Mar 26 2017 - 13:02:04 PDT)
[AMBER] timerge question
- Jason Swails (Sat Mar 18 2017 - 11:33:10 PDT)
- Hannes Loeffler (Fri Mar 17 2017 - 02:38:06 PDT)
- Daniel Mermelstein (Thu Mar 16 2017 - 15:47:31 PDT)
- Adrian Roitberg (Thu Mar 16 2017 - 07:48:09 PDT)
[AMBER] unable to solvate a polymer
- Nhai (Wed Mar 22 2017 - 09:00:13 PDT)
- David Case (Wed Mar 22 2017 - 08:18:00 PDT)
- Bill Ross (Tue Mar 21 2017 - 16:12:29 PDT)
- Jon Mujika (Tue Mar 21 2017 - 16:00:19 PDT)
[AMBER] Unperturbed charge of the unit is not zero
- David Case (Mon Mar 13 2017 - 19:03:40 PDT)
- Eugene Cha (Mon Mar 13 2017 - 07:09:29 PDT)
[AMBER] water bridge
- Daniel Roe (Tue Mar 28 2017 - 06:20:22 PDT)
- Ming Tang (Tue Mar 28 2017 - 02:24:20 PDT)
[AMBER] Water molecules show three bonds in VMD
- MOHD HOMAIDUR RAHMAN (Thu Mar 30 2017 - 21:03:46 PDT)
- Daniel Roe (Thu Mar 30 2017 - 05:23:00 PDT)
- Andreas Tosstorff (Thu Mar 30 2017 - 04:20:20 PDT)
- 吴萌 (Thu Mar 30 2017 - 04:04:57 PDT)
[AMBER] what hardware is required for gou peer-ro-peer an how imporant is gpu-to-gpu nvlink
- Chris Neale (Tue Mar 28 2017 - 22:07:13 PDT)
- Jason Swails (Tue Mar 28 2017 - 21:27:13 PDT)
- Jason Swails (Tue Mar 28 2017 - 21:19:54 PDT)
- Chris Neale (Tue Mar 28 2017 - 19:27:43 PDT)
- Jason Swails (Tue Mar 28 2017 - 19:09:22 PDT)
- Chris Neale (Tue Mar 28 2017 - 17:38:22 PDT)
[AMBER] When does cpptraj use information from the original pdb file?
- Markowska (Fri Mar 03 2017 - 09:57:56 PST)
- Daniel Roe (Fri Mar 03 2017 - 07:02:11 PST)
[AMBER] Why molecular dynamics simulation was stopped without giving any error
- David Case (Thu Mar 23 2017 - 06:36:02 PDT)
- Bill Ross (Thu Mar 23 2017 - 00:42:16 PDT)
- Garima Singh (Wed Mar 22 2017 - 23:36:01 PDT)
[AMBER] 发自刘兰茹的邮件
- Vlad Cojocaru (Fri Mar 24 2017 - 06:50:38 PDT)
- David Case (Fri Mar 24 2017 - 05:19:58 PDT)
- Vlad Cojocaru (Fri Mar 24 2017 - 03:14:26 PDT)
- liulr13.mails.jlu.edu.cn (Fri Mar 24 2017 - 02:30:36 PDT)
- Vlad Cojocaru (Fri Mar 24 2017 - 01:53:00 PDT)
- 刘兰茹 (Fri Mar 24 2017 - 01:42:12 PDT)
[AMBER] 来自zengxitao的邮件
- Adrian Roitberg (Wed Mar 22 2017 - 10:30:23 PDT)
- zengxitao (Wed Mar 22 2017 - 10:28:16 PDT)
MM/GBSA residual decomposition issue
- Hai Nguyen (Fri Mar 17 2017 - 08:13:18 PDT)
- Bharatham, Nagakumar (Fri Mar 17 2017 - 07:50:48 PDT)

Amber Archive Mar 2017 by subject