Amber Archive Oct 2015: by subject

[AMBER-Developers] [AMBER] problem with randomizing velocities
- Ross Walker (Thu Oct 15 2015 - 10:00:41 PDT)
- David A Case (Sun Oct 04 2015 - 23:17:15 PDT)
[AMBER] "Vlimit exceeded for step..." error
- David A Case (Sat Oct 10 2015 - 06:56:32 PDT)
- Vu Truong (Fri Oct 09 2015 - 12:16:31 PDT)
- David A Case (Thu Oct 08 2015 - 14:37:33 PDT)
- Vu Truong (Thu Oct 08 2015 - 13:21:47 PDT)
[AMBER] &rst + distance + coordinate restraint
- Gerald Monard (Sat Oct 31 2015 - 10:21:50 PDT)
- Gerald Monard (Sat Oct 31 2015 - 10:02:00 PDT)
[AMBER] (too) high absolute values for charges using resp and gaussian
- Ye Mei (Tue Oct 27 2015 - 03:02:40 PDT)
- Karl Kirschner (Tue Oct 27 2015 - 02:36:36 PDT)
- Jérémie Knoops (Tue Oct 27 2015 - 01:38:47 PDT)
[AMBER] /share/apps/amber/amber14/bin/sander.MPI: error while loading shared libraries: libmpi_cxx.so.1: cannot open shared object file: No such file or directory
- Repic Matej (Thu Oct 01 2015 - 02:21:13 PDT)
- Atila Petrosian (Thu Oct 01 2015 - 01:34:23 PDT)
[AMBER] 1-4 nonbonded interactions does not cancel in MMPBSA calculation
- Jason Swails (Tue Oct 20 2015 - 06:42:19 PDT)
- Jérémie Knoops (Tue Oct 20 2015 - 00:48:32 PDT)
- Renato Freitas (Mon Oct 19 2015 - 14:22:51 PDT)
[AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II)
- Pengfei Li (Sat Oct 24 2015 - 07:23:41 PDT)
- Ross Walker (Fri Oct 23 2015 - 15:48:57 PDT)
- Marcelo Andrade Chagas (Fri Oct 23 2015 - 15:41:43 PDT)
- Pengfei Li (Thu Oct 22 2015 - 13:58:17 PDT)
- Marcelo Andrade Chagas (Thu Oct 22 2015 - 12:24:17 PDT)
- Marcelo Andrade Chagas (Thu Oct 22 2015 - 09:37:09 PDT)
- Marcelo Andrade Chagas (Thu Oct 22 2015 - 09:34:02 PDT)
- Marcelo Andrade Chagas (Thu Oct 22 2015 - 08:37:28 PDT)
- Pengfei Li (Thu Oct 22 2015 - 07:36:43 PDT)
- Marcelo Andrade Chagas (Thu Oct 22 2015 - 07:34:51 PDT)
[AMBER] [AMEBR] Amino acid side-chain carbonyl C=O(ASP, GLU) and side-cahin -HN (LYS, ARG) close proximity
- Carlos Simmerling (Fri Oct 30 2015 - 04:05:32 PDT)
- V. Kumar (Thu Oct 29 2015 - 05:05:20 PDT)
[AMBER] [cpptraj] Changes in RMSF functionality?
- Daniel Roe (Mon Oct 19 2015 - 10:10:36 PDT)
- Juan Eiros Zamora (Mon Oct 19 2015 - 09:30:48 PDT)
[AMBER] [SPAM] AMBER Digest, Vol 1365, Issue 1
- 崔克新 (Wed Oct 14 2015 - 02:10:05 PDT)
[AMBER] ^.^. as a new atom type when running DFTB with sander from Ambertools 15
- Jason Swails (Thu Oct 08 2015 - 04:48:45 PDT)
- Emilio Lence (Thu Oct 08 2015 - 01:07:06 PDT)
- Jonathan Sheehan (Wed Oct 07 2015 - 23:28:11 PDT)
- Daniel Roe (Wed Oct 07 2015 - 20:58:40 PDT)
- David A Case (Wed Oct 07 2015 - 20:06:33 PDT)
- Gustavo Seabra (Wed Oct 07 2015 - 19:16:13 PDT)
- Jonathan Sheehan (Wed Oct 07 2015 - 13:41:46 PDT)
- Emilio Lence (Tue Oct 06 2015 - 04:54:31 PDT)
- Gustavo Seabra (Mon Oct 05 2015 - 13:17:11 PDT)
- Jonathan Sheehan (Mon Oct 05 2015 - 12:02:24 PDT)
- Jonathan Sheehan (Mon Oct 05 2015 - 11:28:04 PDT)
- Gustavo Seabra (Mon Oct 05 2015 - 06:03:04 PDT)
- Emilio Lence (Mon Oct 05 2015 - 03:26:03 PDT)
- Gustavo Seabra (Fri Oct 02 2015 - 12:51:29 PDT)
- Emilio Lence (Fri Oct 02 2015 - 11:11:03 PDT)
[AMBER] A question about MMPBSA calculation
- Jason Swails (Mon Oct 12 2015 - 09:59:41 PDT)
- anu chandra (Mon Oct 12 2015 - 09:14:08 PDT)
[AMBER] AIB parameter
- Elisa Frezza (Fri Oct 09 2015 - 04:56:06 PDT)
[AMBER] ALA but must be GLY MM-PBSA
- Aleksandra Skoric (Sun Oct 25 2015 - 11:26:57 PDT)
- bharat lakhani (Sun Oct 25 2015 - 08:46:42 PDT)
[AMBER] AMBER Digest, Vol 1361, Issue 1
- Jason Swails (Sun Oct 04 2015 - 13:33:28 PDT)
- Chitrak Gupta (Sun Oct 04 2015 - 11:00:49 PDT)
[AMBER] AMBER Digest, Vol 1364, Issue 1
- Jason Swails (Fri Oct 09 2015 - 07:49:12 PDT)
- Arjun Sharma (Fri Oct 09 2015 - 07:02:14 PDT)
[AMBER] AMBER14 testing error
- Jason Swails (Sat Oct 31 2015 - 08:47:11 PDT)
- Mahmoud A. A. Ibrahim (Sat Oct 31 2015 - 00:25:22 PDT)
- Marcelo Andrade Chagas (Fri Oct 30 2015 - 12:06:18 PDT)
- Hai Nguyen (Fri Oct 30 2015 - 11:56:49 PDT)
- Mahmoud A. A. Ibrahim (Fri Oct 30 2015 - 11:40:41 PDT)
[AMBER] AmberTools 15, Mac El Captain and Fink
- Alan (Tue Oct 27 2015 - 03:29:15 PDT)
- Jason Swails (Mon Oct 26 2015 - 18:08:10 PDT)
- Jason Swails (Mon Oct 26 2015 - 18:02:23 PDT)
- Alan (Mon Oct 26 2015 - 16:24:48 PDT)
- Ross Walker (Mon Oct 26 2015 - 16:15:22 PDT)
- Alan (Mon Oct 26 2015 - 16:03:33 PDT)
[AMBER] AmberTools14 configuration problem
- Jason Swails (Sat Oct 17 2015 - 09:09:19 PDT)
- David A Case (Fri Oct 16 2015 - 11:00:32 PDT)
- Ivanov, Maxim (Tue Oct 13 2015 - 14:25:14 PDT)
[AMBER] aMD: Bad data for namelist object ethreshp
- David A Case (Sat Oct 24 2015 - 05:28:39 PDT)
- Claire Coderch Boué (Fri Oct 23 2015 - 09:29:56 PDT)
[AMBER] ante-MMPBSA question
- Jason Swails (Tue Oct 27 2015 - 08:41:15 PDT)
- Daniel Roe (Tue Oct 27 2015 - 07:22:53 PDT)
- Mohammad Salem (Mon Oct 26 2015 - 15:49:23 PDT)
- Mohammad Salem (Mon Oct 26 2015 - 15:18:25 PDT)
[AMBER] applying restraints using tinker
- Jason Swails (Wed Oct 28 2015 - 13:04:01 PDT)
- Christina Berti (Wed Oct 28 2015 - 10:51:16 PDT)
[AMBER] Atom 1512 was assigned a lower molecule # than previous atom
- Daniel Roe (Mon Oct 05 2015 - 12:36:32 PDT)
- Osman, Roman (Mon Oct 05 2015 - 12:15:01 PDT)
- Daniel Roe (Mon Oct 05 2015 - 12:09:12 PDT)
- Osman, Roman (Mon Oct 05 2015 - 11:51:19 PDT)
[AMBER] Atom match error in MMPBSA calculation
- Progress Zhang (Thu Oct 22 2015 - 14:31:52 PDT)
[AMBER] atomiccorr
- Daniel Roe (Thu Oct 29 2015 - 07:49:16 PDT)
- Hadeer ELHabashy (Mon Oct 26 2015 - 04:43:47 PDT)
[AMBER] Best suitable 'igb' value for MMPBSA.py calculation
- psu4.uic.edu (Sat Oct 24 2015 - 13:10:48 PDT)
- Carlos Simmerling (Fri Oct 23 2015 - 12:02:16 PDT)
- Ray Luo, Ph.D. (Fri Oct 23 2015 - 11:23:29 PDT)
- Hai Nguyen (Fri Oct 23 2015 - 08:20:47 PDT)
- Jason Swails (Fri Oct 23 2015 - 07:16:29 PDT)
- anu chandra (Fri Oct 23 2015 - 07:02:25 PDT)
[AMBER] Building a structure of levansucrase (1PT2) with a fructosyl residue attached to Asp86
- Surasak Chunsrivirot (Mon Oct 05 2015 - 00:53:49 PDT)
- Lachele Foley (Sat Oct 03 2015 - 21:17:59 PDT)
- Surasak Chunsrivirot (Thu Oct 01 2015 - 21:28:12 PDT)
[AMBER] Can't install AMBER14: MissingProgram...Install patch from your package manager
- Daniel Roe (Sat Oct 31 2015 - 16:33:31 PDT)
- Jose Borreguero (Sat Oct 31 2015 - 15:54:06 PDT)
[AMBER] Charmm to Amber (where’s chamber?)
- Jason Swails (Fri Oct 30 2015 - 08:47:37 PDT)
- Alan (Fri Oct 30 2015 - 08:02:46 PDT)
- Jason Swails (Thu Oct 29 2015 - 18:40:39 PDT)
- Alan (Thu Oct 29 2015 - 16:21:51 PDT)
- Jason Swails (Wed Oct 28 2015 - 07:08:05 PDT)
- David A Case (Wed Oct 28 2015 - 05:25:16 PDT)
- Alan (Wed Oct 28 2015 - 04:27:37 PDT)
- Alan (Wed Oct 28 2015 - 02:32:32 PDT)
[AMBER] compare two trajectories
- Xing (Thu Oct 15 2015 - 19:29:08 PDT)
[AMBER] compatibility of targeted MD with GPU amber vs. sander
- Charles Lin (Fri Oct 23 2015 - 15:18:16 PDT)
- Naomi Rose Latorraca (Fri Oct 23 2015 - 15:13:46 PDT)
[AMBER] Constant pH MD
- Hadeer ELHabashy (Mon Oct 26 2015 - 01:11:40 PDT)
- Hadeer ELHabashy (Mon Oct 26 2015 - 01:07:05 PDT)
[AMBER] Controlling size of the box
- Daniel Roe (Fri Oct 09 2015 - 02:51:39 PDT)
- Nicholus Bhattacharjee (Fri Oct 09 2015 - 01:49:01 PDT)
- Jason Swails (Thu Oct 08 2015 - 09:50:01 PDT)
- David A Case (Thu Oct 08 2015 - 09:41:00 PDT)
- Jason Swails (Thu Oct 08 2015 - 08:51:57 PDT)
- Nicholus Bhattacharjee (Thu Oct 08 2015 - 08:48:31 PDT)
[AMBER] coordination number
- Hadeer ELHabashy (Tue Oct 27 2015 - 03:57:02 PDT)
[AMBER] Correctly deriving force constants for Amber
- Nash, Anthony (Thu Oct 15 2015 - 11:58:30 PDT)
- Adrian Roitberg (Thu Oct 15 2015 - 11:53:02 PDT)
- Nash, Anthony (Thu Oct 15 2015 - 11:47:19 PDT)
- David A Case (Thu Oct 15 2015 - 09:35:33 PDT)
- Nash, Anthony (Thu Oct 15 2015 - 05:07:22 PDT)
[AMBER] CpHMD for non protein residues
- Rahul Ramesh (Sun Oct 18 2015 - 15:22:15 PDT)
- Jason Swails (Fri Oct 16 2015 - 12:58:09 PDT)
- Rahul Ramesh (Fri Oct 16 2015 - 10:57:57 PDT)
- Jason Swails (Fri Oct 16 2015 - 04:57:55 PDT)
- Rahul Ramesh (Thu Oct 15 2015 - 20:43:18 PDT)
- Brian Radak (Mon Oct 05 2015 - 06:57:03 PDT)
- Jason Swails (Sun Oct 04 2015 - 19:01:24 PDT)
- Rahul Ramesh (Sun Oct 04 2015 - 17:30:25 PDT)
- Adrian Roitberg (Sun Oct 04 2015 - 16:34:35 PDT)
- Rahul Ramesh (Sun Oct 04 2015 - 14:42:42 PDT)
[AMBER] cpin file
- Jason Swails (Tue Oct 06 2015 - 09:14:09 PDT)
- Arjun Sharma (Tue Oct 06 2015 - 07:16:33 PDT)
[AMBER] CPPTRAJ
- Thomas Cheatham (Sun Oct 18 2015 - 21:41:09 PDT)
- Nhai (Sun Oct 18 2015 - 21:16:37 PDT)
- Wong Li Zhe (Sun Oct 18 2015 - 21:06:48 PDT)
[AMBER] cpptraj - bridging water
- Lara rajam (Tue Oct 27 2015 - 08:54:52 PDT)
- Daniel Roe (Tue Oct 27 2015 - 07:25:12 PDT)
- Lara rajam (Mon Oct 26 2015 - 11:56:39 PDT)
[AMBER] CPPTRAJ : different RMSD calculation in a single run
- Jason Swails (Fri Oct 16 2015 - 08:49:19 PDT)
- anu chandra (Fri Oct 16 2015 - 06:29:25 PDT)
- Jason Swails (Fri Oct 16 2015 - 05:19:01 PDT)
- anu chandra (Fri Oct 16 2015 - 05:02:10 PDT)
[AMBER] cpptraj density
- Björn Karlsson (Tue Oct 13 2015 - 11:10:54 PDT)
[AMBER] cpptraj uses huge memory space while doing molsurf calculation
- Daniel Roe (Thu Oct 29 2015 - 11:46:58 PDT)
- anu chandra (Wed Oct 28 2015 - 05:48:40 PDT)
[AMBER] cutoff problem with a periodic crystal box
- David A Case (Thu Oct 15 2015 - 05:33:22 PDT)
- Hadeer ELHabashy (Thu Oct 15 2015 - 05:08:53 PDT)
- Jason Swails (Thu Oct 15 2015 - 04:59:56 PDT)
- Hadeer ELHabashy (Thu Oct 15 2015 - 00:26:43 PDT)
[AMBER] Cytochrome P450 with heme simulation
- Jason Swails (Fri Oct 09 2015 - 06:18:31 PDT)
- Abelak, Kavin (Fri Oct 09 2015 - 03:47:47 PDT)
[AMBER] Differences on MMPBSA calculation results
- Ray Luo, Ph.D. (Tue Oct 20 2015 - 12:13:54 PDT)
- Jason Swails (Tue Oct 20 2015 - 06:46:28 PDT)
- MarcZhang (Tue Oct 20 2015 - 03:01:03 PDT)
- Jason Swails (Mon Oct 19 2015 - 08:25:46 PDT)
- MarcZhang (Mon Oct 19 2015 - 08:00:18 PDT)
- MarcZhang (Mon Oct 19 2015 - 07:58:57 PDT)
[AMBER] Different Parameters for Nonbonded Interactions
- Jason Swails (Wed Oct 28 2015 - 18:49:09 PDT)
- Batuhan Kav (Wed Oct 28 2015 - 08:02:08 PDT)
[AMBER] difficulties in generate .prmtop and .inpcrd file
- Emilio Lence (Sat Oct 17 2015 - 07:40:27 PDT)
- MarcZhang (Thu Oct 15 2015 - 13:07:10 PDT)
[AMBER] difficulties in generate .prmtop and .inpcrd file for complex using Guassian calculated ligand charges
- David A Case (Thu Oct 15 2015 - 05:35:46 PDT)
- Emilio Lence (Thu Oct 15 2015 - 02:02:20 PDT)
- MarcZhang (Thu Oct 15 2015 - 01:23:01 PDT)
- Emilio Lence (Wed Oct 14 2015 - 03:31:53 PDT)
- Jin Zhang (Wed Oct 14 2015 - 02:20:36 PDT)
[AMBER] Dihedral/improper coefficient in AMBER + rmin vs sigma for lennard jones
- Jason Swails (Thu Oct 08 2015 - 05:14:15 PDT)
- conor parks (Wed Oct 07 2015 - 21:33:05 PDT)
[AMBER] Documentation on Prepin File Format
- David A Case (Fri Oct 16 2015 - 10:50:53 PDT)
- Robert Molt (Fri Oct 16 2015 - 05:19:32 PDT)
- Jason Swails (Fri Oct 16 2015 - 05:13:55 PDT)
- Robert Molt (Fri Oct 16 2015 - 05:00:19 PDT)
[AMBER] donor and acceptor masks
- Daniel Roe (Sat Oct 17 2015 - 11:39:58 PDT)
- Hadeer ELHabashy (Sat Oct 17 2015 - 10:57:16 PDT)
- Daniel Roe (Sat Oct 17 2015 - 10:43:58 PDT)
- Hadeer ELHabashy (Sat Oct 17 2015 - 09:56:21 PDT)
- Thomas Cheatham (Sat Oct 17 2015 - 09:41:47 PDT)
- Hadeer ELHabashy (Sat Oct 17 2015 - 09:34:54 PDT)
- Hadeer ELHabashy (Sat Oct 17 2015 - 09:09:43 PDT)
- Daniel Roe (Sat Oct 17 2015 - 08:22:57 PDT)
- Hadeer ELHabashy (Sat Oct 17 2015 - 08:22:18 PDT)
- Hadeer ELHabashy (Sat Oct 17 2015 - 08:20:36 PDT)
- Jason Swails (Sat Oct 17 2015 - 08:16:37 PDT)
- Hadeer ELHabashy (Sat Oct 17 2015 - 08:14:27 PDT)
- Jason Swails (Sat Oct 17 2015 - 08:09:30 PDT)
- Hadeer ELHabashy (Sat Oct 17 2015 - 08:05:49 PDT)
- Emilio Lence (Sat Oct 17 2015 - 07:43:57 PDT)
- Daniel Roe (Sat Oct 17 2015 - 07:42:44 PDT)
- Emilio Lence (Sat Oct 17 2015 - 07:23:24 PDT)
- Hadeer ELHabashy (Sat Oct 17 2015 - 07:06:27 PDT)
[AMBER] Elementary VMD Problem with Amber Trajectory
- Robert Molt (Fri Oct 30 2015 - 16:25:06 PDT)
- Jason Swails (Fri Oct 30 2015 - 14:45:54 PDT)
- Robert Molt (Fri Oct 30 2015 - 14:24:31 PDT)
[AMBER] error with line 165 of cpinutil.py
- Hadeer ELHabashy (Wed Oct 14 2015 - 07:07:09 PDT)
- Jason Swails (Wed Oct 14 2015 - 07:04:22 PDT)
- Juan Eiros Zamora (Wed Oct 14 2015 - 07:01:23 PDT)
- Hadeer ELHabashy (Wed Oct 14 2015 - 06:41:36 PDT)
- Jason Swails (Wed Oct 14 2015 - 05:47:33 PDT)
- Hadeer ELHabashy (Wed Oct 14 2015 - 03:34:04 PDT)
[AMBER] Error: ptraj is needed for MMPBSA
- Ayesha Kanwal (Wed Oct 14 2015 - 11:35:47 PDT)
- Jason Swails (Wed Oct 14 2015 - 05:44:19 PDT)
- Ayesha Kanwal (Wed Oct 14 2015 - 02:12:48 PDT)
- Jason Swails (Tue Oct 13 2015 - 14:06:10 PDT)
- Ayesha Kanwal (Tue Oct 13 2015 - 13:04:28 PDT)
- Jason Swails (Tue Oct 13 2015 - 04:47:53 PDT)
- Ayesha Kanwal (Mon Oct 12 2015 - 20:59:56 PDT)
- Jason Swails (Mon Oct 12 2015 - 08:12:35 PDT)
- Kenneth Huang (Mon Oct 12 2015 - 08:08:12 PDT)
- Ayesha Kanwal (Mon Oct 12 2015 - 07:55:35 PDT)
- Daniel Roe (Mon Oct 12 2015 - 07:34:21 PDT)
- Ayesha Kanwal (Mon Oct 12 2015 - 06:48:32 PDT)
- Jason Swails (Sun Oct 11 2015 - 08:28:47 PDT)
- Jason Swails (Sun Oct 11 2015 - 08:26:18 PDT)
- Ayesha Kanwal (Sun Oct 11 2015 - 07:30:18 PDT)
- Ayesha Kanwal (Sun Oct 11 2015 - 07:23:49 PDT)
[AMBER] EVB related query
- David A Case (Thu Oct 15 2015 - 05:13:18 PDT)
- bijyalaxmi athokpam (Wed Oct 14 2015 - 01:54:26 PDT)
[AMBER] ff12SB vs ff14SB for protein-ligand MD simulations?
- koushik kasavajhala (Wed Oct 21 2015 - 18:39:23 PDT)
- yunshi11 . (Wed Oct 21 2015 - 18:28:34 PDT)
- Carlos Simmerling (Wed Oct 21 2015 - 18:16:48 PDT)
- yunshi11 . (Wed Oct 21 2015 - 18:10:07 PDT)
[AMBER] Fwd: donor and acceptor masks
- Emilio Lence (Sat Oct 17 2015 - 07:51:36 PDT)
[AMBER] Fwd: EVB related query
- bijyalaxmi athokpam (Thu Oct 15 2015 - 04:39:50 PDT)
[AMBER] Glycam force field parameters for derivatives?
- Lachele Foley (Fri Oct 30 2015 - 18:40:35 PDT)
- yunshi11 . (Thu Oct 29 2015 - 21:51:36 PDT)
[AMBER] gromacs to amber file format
- Jason Swails (Tue Oct 20 2015 - 06:52:23 PDT)
- Hai Nguyen (Tue Oct 20 2015 - 06:31:40 PDT)
- neha chaudhary (Tue Oct 20 2015 - 05:07:03 PDT)
[AMBER] Guanine base pair planarity in G-guadruplex
- V. Kumar (Thu Oct 29 2015 - 04:26:47 PDT)
- V. Kumar (Wed Oct 28 2015 - 09:02:10 PDT)
[AMBER] h-bond calculation - tokenise error
- Daniel Roe (Fri Oct 09 2015 - 08:14:01 PDT)
- Sidhu, Khushwant (Dr.) (Fri Oct 09 2015 - 07:57:40 PDT)
[AMBER] Halogen bond force field in AMBER
- psu4.uic.edu (Wed Oct 28 2015 - 23:03:39 PDT)
[AMBER] Help
- Carlos Simmerling (Fri Oct 16 2015 - 13:01:53 PDT)
- Jason Swails (Fri Oct 16 2015 - 13:01:49 PDT)
- Balajee Ramachandran (Fri Oct 16 2015 - 12:55:26 PDT)
[AMBER] Help - buy the Amber software
- Adam Winiarski (Tue Oct 27 2015 - 04:01:13 PDT)
[AMBER] Ho Atom Inclusion in PDB from Leap
- Robert Molt (Wed Oct 14 2015 - 15:20:09 PDT)
- David A Case (Wed Oct 14 2015 - 13:26:27 PDT)
- Robert Molt (Wed Oct 14 2015 - 11:31:00 PDT)
[AMBER] How can amber differentiate between terminal Oxygens
- Hadeer ELHabashy (Tue Oct 27 2015 - 03:58:55 PDT)
- Jason Swails (Mon Oct 26 2015 - 09:19:20 PDT)
- Hadeer ELHabashy (Mon Oct 26 2015 - 07:29:04 PDT)
- Jason Swails (Mon Oct 26 2015 - 07:21:35 PDT)
- Hadeer ELHabashy (Mon Oct 26 2015 - 07:01:37 PDT)
- Jason Swails (Mon Oct 26 2015 - 06:59:49 PDT)
- Hadeer ELHabashy (Mon Oct 26 2015 - 06:37:50 PDT)
- Jason Swails (Mon Oct 26 2015 - 06:09:50 PDT)
- Hadeer ELHabashy (Mon Oct 26 2015 - 05:58:23 PDT)
- Jason Swails (Mon Oct 26 2015 - 05:37:20 PDT)
- Hadeer ELHabashy (Mon Oct 26 2015 - 04:41:10 PDT)
- David A Case (Thu Oct 22 2015 - 15:21:08 PDT)
- Hadeer ELHabashy (Thu Oct 22 2015 - 07:00:59 PDT)
[AMBER] How do you place two molecules in one water box?
- David Eugene Jones (Mon Oct 12 2015 - 12:22:44 PDT)
- Ben Roberts (Mon Oct 12 2015 - 12:13:53 PDT)
- David Eugene Jones (Mon Oct 12 2015 - 12:02:17 PDT)
- Lachele Foley (Mon Oct 12 2015 - 12:01:39 PDT)
- Ben Roberts (Mon Oct 12 2015 - 11:45:22 PDT)
- David Eugene Jones (Mon Oct 12 2015 - 11:28:54 PDT)
[AMBER] how to convert mdcrd to NetCDF trajectory file?
- Daniel Roe (Thu Oct 29 2015 - 07:52:50 PDT)
- V. Kumar (Mon Oct 26 2015 - 02:14:26 PDT)
- Soumendranath Bhakat (Sun Oct 25 2015 - 13:47:58 PDT)
- Nhai (Sun Oct 25 2015 - 12:51:56 PDT)
- shahab shariati (Sun Oct 25 2015 - 10:39:17 PDT)
- shahab shariati (Sun Oct 25 2015 - 10:19:19 PDT)
- shahab shariati (Sun Oct 25 2015 - 10:16:42 PDT)
[AMBER] How to do a QMMM calculation with a dynamic QM region
- Hector A. Baldoni (Wed Oct 07 2015 - 04:05:53 PDT)
- Emilio Lence (Wed Oct 07 2015 - 02:55:20 PDT)
- 崔克新 (Wed Oct 07 2015 - 02:18:00 PDT)
[AMBER] how to generate a model beta-sheet structure
- Daniel Roe (Thu Oct 29 2015 - 07:34:25 PDT)
- Hai Nguyen (Wed Oct 28 2015 - 10:22:14 PDT)
- Jagannath Mondal (Wed Oct 28 2015 - 10:13:18 PDT)
[AMBER] How to prevent the water molecules entering into the binding pocket during the MD simulation ?
- Vitaly V. Chaban (Fri Oct 30 2015 - 03:48:54 PDT)
- fjliu (Thu Oct 29 2015 - 23:20:57 PDT)
[AMBER] http://q4md-forcefieldtools.org/ unavailable
- Emilio Lence (Mon Oct 12 2015 - 01:06:07 PDT)
- Jérémie Knoops (Fri Oct 09 2015 - 04:59:54 PDT)
[AMBER] hydrogen bond cpptraj
- Lara rajam (Wed Oct 07 2015 - 18:18:51 PDT)
[AMBER] If it's possible to add restraint on the steered MD ?
- 崔克新 (Fri Oct 23 2015 - 02:06:55 PDT)
[AMBER] Info: Bond types are assigned for valence state 5 with penalty of 1
- David A Case (Mon Oct 05 2015 - 19:44:39 PDT)
- Atila Petrosian (Mon Oct 05 2015 - 13:57:53 PDT)
[AMBER] ions cannot be viewed in gaussview
- Gustavo Seabra (Sat Oct 31 2015 - 10:53:32 PDT)
- Jason Swails (Sat Oct 31 2015 - 09:23:58 PDT)
- Martina Devi (Sat Oct 31 2015 - 09:08:25 PDT)
- Jason Swails (Fri Oct 30 2015 - 08:50:02 PDT)
- Martina Devi (Fri Oct 30 2015 - 07:18:37 PDT)
[AMBER] Is it possible to simulate a periodic crystal ?
- David A Case (Thu Oct 15 2015 - 10:20:38 PDT)
- Hadeer ELHabashy (Wed Oct 14 2015 - 11:38:17 PDT)
- Hadeer ELHabashy (Wed Oct 14 2015 - 11:23:29 PDT)
- Jason Swails (Wed Oct 14 2015 - 07:05:45 PDT)
- Hadeer ELHabashy (Wed Oct 14 2015 - 06:51:37 PDT)
[AMBER] Leap : problem with copying and combining DNA items
- David A Case (Mon Oct 05 2015 - 14:01:29 PDT)
- Jérémie Knoops (Mon Oct 05 2015 - 05:34:14 PDT)
[AMBER] Leap PDB Input Error
- case (Fri Oct 16 2015 - 18:18:23 PDT)
- Robert Molt (Fri Oct 16 2015 - 16:13:31 PDT)
[AMBER] Lennard-Jones parameter for Sp, Sp2 and Sp3 Nitrogen
- Ebert Maximilian (Mon Oct 19 2015 - 14:37:43 PDT)
[AMBER] Making Parameter and Topology Files for Protein-Ligand Complex
- David A Case (Sat Oct 10 2015 - 07:04:12 PDT)
- Emilio Lence (Sat Oct 10 2015 - 04:09:04 PDT)
- Jim Wu (Fri Oct 09 2015 - 16:14:09 PDT)
[AMBER] many atoms, same name
- case (Tue Oct 13 2015 - 18:29:33 PDT)
- Jason Swails (Tue Oct 13 2015 - 11:34:17 PDT)
- Hadeer ELHabashy (Tue Oct 13 2015 - 11:08:08 PDT)
[AMBER] Measuring distance between protein and graphene surface
- Hai Nguyen (Tue Oct 20 2015 - 11:09:41 PDT)
- Krantzman, Kristin D (Tue Oct 20 2015 - 11:01:37 PDT)
[AMBER] Measuring minimum distance between protein and graphene surface
- Krantzman, Kristin D (Tue Oct 20 2015 - 15:07:38 PDT)
- Christina Bergonzo (Tue Oct 20 2015 - 12:26:54 PDT)
- Krantzman, Kristin D (Tue Oct 20 2015 - 11:20:15 PDT)
[AMBER] Membrane protein imagining problems
- Romero, Raquel (Tue Oct 20 2015 - 04:51:20 PDT)
- Hai Nguyen (Mon Oct 19 2015 - 12:59:07 PDT)
- Daniel Roe (Mon Oct 19 2015 - 12:43:01 PDT)
- Romero, Raquel (Sun Oct 18 2015 - 15:33:09 PDT)
[AMBER] Metal Ion Model
- Pengfei Li (Fri Oct 30 2015 - 12:57:07 PDT)
- Carlos Modenutti (Fri Oct 30 2015 - 12:06:42 PDT)
- Pengfei Li (Fri Oct 23 2015 - 12:28:42 PDT)
- Carlos Modenutti (Thu Oct 22 2015 - 15:42:05 PDT)
[AMBER] Minimization
- Emilio Lence (Wed Oct 14 2015 - 03:38:06 PDT)
- Wong Li Zhe (Wed Oct 14 2015 - 02:17:34 PDT)
[AMBER] missingdisulfide
- Jason Swails (Tue Oct 27 2015 - 12:54:56 PDT)
- Abelak, Kavin (Tue Oct 27 2015 - 11:51:43 PDT)
[AMBER] mixing rules for various water models in AMBER
- Jason Swails (Sun Oct 04 2015 - 10:38:18 PDT)
- Conor Parks (Sun Oct 04 2015 - 09:30:31 PDT)
- Jason Swails (Sun Oct 04 2015 - 07:31:45 PDT)
- conor parks (Sat Oct 03 2015 - 23:32:58 PDT)
- Jason Swails (Sat Oct 03 2015 - 22:27:28 PDT)
- conor parks (Sat Oct 03 2015 - 21:14:26 PDT)
[AMBER] MMPBSA for multiple mutants
- Fabian gmail (Thu Oct 29 2015 - 08:35:18 PDT)
- Jason Swails (Thu Oct 29 2015 - 08:32:24 PDT)
- Fabian gmail (Thu Oct 29 2015 - 08:27:58 PDT)
[AMBER] MMPBSA for peptides interaction
- Fabian gmail (Thu Oct 22 2015 - 06:16:22 PDT)
[AMBER] MMPBSA tutorial A3.2
- Fabian gmail (Thu Oct 22 2015 - 06:17:19 PDT)
- Jason Swails (Thu Oct 22 2015 - 06:14:20 PDT)
- Fabian gmail (Thu Oct 22 2015 - 03:51:06 PDT)
- Fabian gmail (Thu Oct 22 2015 - 03:38:16 PDT)
- Fabian gmail (Thu Oct 22 2015 - 03:11:06 PDT)
- Jason Swails (Tue Oct 20 2015 - 10:59:05 PDT)
- Fabian gmail (Tue Oct 20 2015 - 07:08:16 PDT)
- Jason Swails (Tue Oct 20 2015 - 06:59:06 PDT)
- Fabian gmail (Tue Oct 20 2015 - 05:41:24 PDT)
- Fabian gmail (Tue Oct 20 2015 - 05:20:00 PDT)
- Vlad Cojocaru (Tue Oct 20 2015 - 04:50:42 PDT)
- Fabian gmail (Tue Oct 20 2015 - 03:19:47 PDT)
- Fabian gmail (Mon Oct 19 2015 - 08:34:35 PDT)
- Jason Swails (Mon Oct 19 2015 - 08:24:11 PDT)
- Fabian gmail (Mon Oct 19 2015 - 07:26:33 PDT)
- Fabian gmail (Mon Oct 19 2015 - 07:17:02 PDT)
[AMBER] mmpbsa.py error
- Jason Swails (Sat Oct 31 2015 - 11:57:26 PDT)
- Mohammad Salem (Sat Oct 31 2015 - 10:24:24 PDT)
- Jason Swails (Fri Oct 30 2015 - 17:18:33 PDT)
- Mohammad Salem (Fri Oct 30 2015 - 17:08:21 PDT)
[AMBER] MMPBSA: multiple trajectory approach usage
- George Tzotzos (Wed Oct 21 2015 - 09:38:01 PDT)
- Dwight McGee (Wed Oct 21 2015 - 09:31:49 PDT)
- George Tzotzos (Wed Oct 21 2015 - 09:10:54 PDT)
- Dwight McGee (Wed Oct 21 2015 - 08:53:41 PDT)
- George Tzotzos (Wed Oct 21 2015 - 08:19:44 PDT)
[AMBER] N- and C- terminals constant PH simulation
- Dr. Anselm Horn (Fri Oct 30 2015 - 05:10:46 PDT)
- Hadeer ELHabashy (Fri Oct 30 2015 - 04:22:02 PDT)
- Jason Swails (Tue Oct 27 2015 - 08:34:02 PDT)
- Hadeer ELHabashy (Tue Oct 27 2015 - 06:32:56 PDT)
[AMBER] No Internet Access
- Ross Walker (Thu Oct 15 2015 - 07:59:22 PDT)
- Shahryar Alavi (Thu Oct 15 2015 - 01:27:00 PDT)
[AMBER] non-standard residue (DNA-protein crosslink)
- Carlos Simmerling (Fri Oct 09 2015 - 09:41:17 PDT)
- Jackle, Chasen (Fri Oct 09 2015 - 09:35:14 PDT)
[AMBER] Not atom type for Bromine atom in amber GAFF
- MarcZhang (Thu Oct 15 2015 - 13:29:07 PDT)
[AMBER] Not atom type for Bromine atom in amber GAFF force field?
- Jason Swails (Thu Oct 15 2015 - 10:14:13 PDT)
- MarcZhang (Thu Oct 15 2015 - 09:42:08 PDT)
[AMBER] Oxygen parameters for AMBER99SB-ILDN
- Ebert Maximilian (Mon Oct 26 2015 - 07:05:52 PDT)
[AMBER] Pairwise energy decomposition
- Carlos Simmerling (Tue Oct 06 2015 - 03:39:08 PDT)
- Sara Omar (Mon Oct 05 2015 - 22:28:09 PDT)
[AMBER] parameters for Boron
- jixiaofeng (Tue Oct 27 2015 - 00:36:09 PDT)
[AMBER] Parameters for trigonal bi-pyramid and square bi-pyramid Fe(II)
- Francesco Pietra (Thu Oct 01 2015 - 08:17:33 PDT)
[AMBER] paramfit multiple dihedral commbination
- Carlos Simmerling (Mon Oct 26 2015 - 12:32:35 PDT)
- Adrian Roitberg (Mon Oct 26 2015 - 11:50:02 PDT)
- CHAMI F. (Mon Oct 26 2015 - 11:47:17 PDT)
[AMBER] paramfit multiple dihedrals combination
- CHAMI F. (Mon Oct 26 2015 - 10:53:57 PDT)
[AMBER] pmemd.cuda.MPI on Comet- MPI dying
- Kenneth Huang (Wed Oct 28 2015 - 19:48:31 PDT)
- Ross Walker (Tue Oct 27 2015 - 10:01:54 PDT)
- Kenneth Huang (Tue Oct 27 2015 - 09:56:56 PDT)
- Ross Walker (Thu Oct 22 2015 - 21:37:32 PDT)
- Kenneth Huang (Thu Oct 22 2015 - 20:39:47 PDT)
- Ross Walker (Thu Oct 22 2015 - 09:16:53 PDT)
- Kenneth Huang (Thu Oct 22 2015 - 07:08:11 PDT)
- Ross Walker (Wed Oct 21 2015 - 14:14:28 PDT)
- Kenneth Huang (Wed Oct 21 2015 - 09:30:41 PDT)
[AMBER] Polardecomp in 3D-RISM fails
- Josep Maria Campanera Alsina (Tue Oct 27 2015 - 05:29:47 PDT)
- Jason Swails (Thu Oct 22 2015 - 13:20:06 PDT)
- Tyler Luchko (Lists) (Thu Oct 22 2015 - 12:47:53 PDT)
- Josep Maria Campanera Alsina (Thu Oct 22 2015 - 12:33:43 PDT)
[AMBER] Prepgen difficulty
- Marion, Antoine (Mon Oct 12 2015 - 07:22:32 PDT)
- David A Case (Mon Oct 12 2015 - 05:45:52 PDT)
- Robert Molt (Sun Oct 11 2015 - 08:41:48 PDT)
[AMBER] Problem configuring amber14
- Jason Swails (Fri Oct 23 2015 - 07:08:13 PDT)
- Mochena, Mogus D. (Fri Oct 23 2015 - 06:41:48 PDT)
- Fabian gmail (Thu Oct 22 2015 - 03:18:43 PDT)
- David A Case (Wed Oct 21 2015 - 12:58:05 PDT)
- Jason Swails (Wed Oct 21 2015 - 12:38:34 PDT)
- Mochena, Mogus D. (Wed Oct 21 2015 - 11:11:21 PDT)
[AMBER] problem with randomizing velocities
- David A Case (Thu Oct 15 2015 - 09:30:54 PDT)
- Kalenkiewicz, Andrew (NIH/NICHD) [F] (Thu Oct 15 2015 - 08:41:28 PDT)
- Hector A. Baldoni (Fri Oct 02 2015 - 21:14:09 PDT)
- Bill Ross (Fri Oct 02 2015 - 14:12:11 PDT)
- Bill Ross (Fri Oct 02 2015 - 14:05:39 PDT)
- Kalenkiewicz, Andrew (NIH/NICHD) [F] (Fri Oct 02 2015 - 13:58:55 PDT)
[AMBER] Problem with VDW energy
- Brent Krueger (Fri Oct 02 2015 - 11:33:14 PDT)
- David A Case (Fri Oct 02 2015 - 11:30:42 PDT)
- Ross Walker (Fri Oct 02 2015 - 11:04:45 PDT)
- Brent Krueger (Fri Oct 02 2015 - 10:54:07 PDT)
[AMBER] Problems with the installation of ambertools15.
- David A Case (Tue Oct 20 2015 - 04:51:49 PDT)
- Jinfeng Huang (Mon Oct 19 2015 - 20:33:15 PDT)
[AMBER] QM/MM performance
- David A Case (Sun Oct 04 2015 - 11:13:28 PDT)
- Sofia Vasilakaki (Sun Oct 04 2015 - 04:23:02 PDT)
[AMBER] QM/MM Umbrella
- Emilio Lence (Tue Oct 27 2015 - 09:11:39 PDT)
- Brian Radak (Tue Oct 27 2015 - 07:00:58 PDT)
- Adrian Roitberg (Tue Oct 27 2015 - 05:30:54 PDT)
- Mahmood Jasim (Tue Oct 27 2015 - 05:05:38 PDT)
- Adrian Roitberg (Fri Oct 23 2015 - 06:39:38 PDT)
- Mahmood Jasim (Fri Oct 23 2015 - 04:56:31 PDT)
[AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE in AMBER 12 using the new set 3ob-3-1
- Emilio Lence (Thu Oct 01 2015 - 07:22:46 PDT)
- Gustavo Seabra (Thu Oct 01 2015 - 06:43:22 PDT)
- Emilio Lence (Thu Oct 01 2015 - 05:47:07 PDT)
[AMBER] QMMM with inorganic molecules
- Robert Arbon (Thu Oct 29 2015 - 02:27:14 PDT)
- Brian Radak (Tue Oct 27 2015 - 10:31:45 PDT)
- Robert Arbon (Tue Oct 27 2015 - 10:09:42 PDT)
[AMBER] Query about adding hydrogens
- David Case (Sat Oct 24 2015 - 07:31:03 PDT)
[AMBER] query about Bromide ion forcefield parameter
- Brent Krueger (Fri Oct 16 2015 - 05:59:04 PDT)
- Jason Swails (Fri Oct 16 2015 - 05:12:00 PDT)
- jagannath mondal (Thu Oct 15 2015 - 21:56:30 PDT)
- David A Case (Mon Oct 12 2015 - 05:47:36 PDT)
- jagannath mondal (Mon Oct 12 2015 - 04:01:09 PDT)
[AMBER] Question about mask in cpptraj
- Mohd Farid Ismail (Mon Oct 05 2015 - 22:12:19 PDT)
- Daniel Roe (Mon Oct 05 2015 - 06:02:09 PDT)
- Mohd Farid Ismail (Sun Oct 04 2015 - 21:19:05 PDT)
- Daniel Roe (Sun Oct 04 2015 - 20:53:52 PDT)
- Mohd Farid Ismail (Sun Oct 04 2015 - 20:42:58 PDT)
[AMBER] R.E.D. server down or out?
- Tan Yaw Sing (Sun Oct 18 2015 - 19:43:19 PDT)
[AMBER] Random Number Generator Flag Ig
- Guqin Shi (Fri Oct 16 2015 - 12:34:09 PDT)
- Jason Swails (Fri Oct 16 2015 - 09:55:46 PDT)
- Jason Swails (Fri Oct 16 2015 - 09:49:57 PDT)
- Guqin Shi (Fri Oct 16 2015 - 09:48:37 PDT)
- Ross Walker (Fri Oct 16 2015 - 09:25:03 PDT)
- Guqin Shi (Fri Oct 16 2015 - 09:17:34 PDT)
- Guqin Shi (Fri Oct 16 2015 - 09:13:35 PDT)
[AMBER] Real-time hydrogen bond formation using VMD
- amin.imtech.res.in (Wed Oct 14 2015 - 01:47:38 PDT)
- Abhipriya K (Wed Oct 14 2015 - 00:55:56 PDT)
- Repic Matej (Wed Oct 14 2015 - 00:06:37 PDT)
- Abhipriya K (Tue Oct 13 2015 - 23:21:52 PDT)
[AMBER] RED-tools
- Hector A. Baldoni (Sun Oct 25 2015 - 19:33:37 PDT)
- Steven M. Graham (Sun Oct 25 2015 - 15:33:13 PDT)
- Hector A. Baldoni (Fri Oct 23 2015 - 10:12:20 PDT)
- Hector A. Baldoni (Thu Oct 22 2015 - 15:29:09 PDT)
- Nash, Anthony (Thu Oct 22 2015 - 13:27:27 PDT)
- Jason Swails (Thu Oct 22 2015 - 13:17:14 PDT)
- Nash, Anthony (Thu Oct 22 2015 - 12:36:40 PDT)
- Repic Matej (Mon Oct 19 2015 - 00:21:41 PDT)
[AMBER] Replica exchange temperature distribution
- maryam azimzadehirani (Tue Oct 27 2015 - 23:49:39 PDT)
- Jason Swails (Tue Oct 27 2015 - 20:07:53 PDT)
- maryam azimzadehirani (Tue Oct 27 2015 - 18:54:33 PDT)
[AMBER] RESP charge calculation
- Luciano Costa (Fri Oct 16 2015 - 19:47:42 PDT)
- li he (Thu Oct 15 2015 - 18:46:19 PDT)
- David A Case (Thu Oct 15 2015 - 13:10:03 PDT)
- li he (Thu Oct 15 2015 - 09:12:48 PDT)
- li he (Wed Oct 14 2015 - 11:22:37 PDT)
- li he (Wed Oct 14 2015 - 11:17:45 PDT)
[AMBER] RESP charge fitting
- li he (Wed Oct 14 2015 - 10:58:30 PDT)
- Xing (Wed Oct 14 2015 - 08:03:40 PDT)
[AMBER] resp input format 16I5
- stecue.gmail.com (Fri Oct 09 2015 - 09:08:58 PDT)
- Jason Swails (Fri Oct 09 2015 - 08:22:31 PDT)
- stecue.gmail.com (Fri Oct 09 2015 - 07:30:54 PDT)
[AMBER] Restraints
- Wong Li Zhe (Fri Oct 09 2015 - 06:50:03 PDT)
- Jason Swails (Fri Oct 09 2015 - 06:41:37 PDT)
- Wong Li Zhe (Fri Oct 09 2015 - 06:31:47 PDT)
- Wong Li Zhe (Fri Oct 09 2015 - 06:27:28 PDT)
- Jason Swails (Fri Oct 09 2015 - 06:23:09 PDT)
- Jason Swails (Fri Oct 09 2015 - 06:20:37 PDT)
- Wong Li Zhe (Fri Oct 09 2015 - 06:20:02 PDT)
- David A Case (Fri Oct 09 2015 - 06:03:49 PDT)
- Wong Li Zhe (Fri Oct 09 2015 - 05:48:41 PDT)
- Emilio Lence (Fri Oct 09 2015 - 05:41:08 PDT)
- Wong Li Zhe (Fri Oct 09 2015 - 05:23:53 PDT)
[AMBER] Resulting cutoff is too small for your lower limit
- case (Tue Oct 27 2015 - 10:27:30 PDT)
- Carlos Simmerling (Tue Oct 27 2015 - 06:18:18 PDT)
- jfliu (Tue Oct 27 2015 - 05:58:22 PDT)
[AMBER] sander missing from AmberTools15?
- Novosielski, Ryan (Fri Oct 16 2015 - 14:26:52 PDT)
- Jason Swails (Fri Oct 16 2015 - 14:20:29 PDT)
- Daniel Roe (Fri Oct 16 2015 - 14:13:46 PDT)
- Novosielski, Ryan (Fri Oct 16 2015 - 13:51:09 PDT)
- Daniel Roe (Fri Oct 16 2015 - 13:34:28 PDT)
- Novosielski, Ryan (Fri Oct 16 2015 - 13:14:56 PDT)
- Jason Swails (Fri Oct 16 2015 - 13:03:21 PDT)
- Novosielski, Ryan (Fri Oct 16 2015 - 12:55:59 PDT)
- Jason Swails (Fri Oct 16 2015 - 12:56:58 PDT)
- David A Case (Fri Oct 16 2015 - 12:55:03 PDT)
- Novosielski, Ryan (Fri Oct 16 2015 - 12:44:38 PDT)
[AMBER] SC15 Call for abstracts - "Producing High-Performance and Sustainable Software for Molecular Simulation"
- Ross Walker (Mon Oct 05 2015 - 11:10:41 PDT)
[AMBER] SGLDg
- Wu, Xiongwu (NIH/NHLBI) [E] (Wed Oct 21 2015 - 08:54:18 PDT)
- Jérémie Knoops (Tue Oct 20 2015 - 22:45:23 PDT)
[AMBER] SIGSEGV: Segmentation Fault
- Scott Brozell (Wed Oct 07 2015 - 17:53:42 PDT)
- Steven Cole Mercer (Wed Oct 07 2015 - 16:46:12 PDT)
[AMBER] small energy jump when restoring a simulation production
- Jason Swails (Tue Oct 27 2015 - 12:48:29 PDT)
- Fabian Glaser (Tue Oct 27 2015 - 11:35:53 PDT)
- Jason Swails (Tue Oct 27 2015 - 10:26:25 PDT)
- Jason Swails (Tue Oct 27 2015 - 10:23:15 PDT)
- Carlos Simmerling (Tue Oct 27 2015 - 10:04:47 PDT)
- Fabian gmail (Tue Oct 27 2015 - 10:02:08 PDT)
- Fabian gmail (Tue Oct 27 2015 - 09:42:13 PDT)
- Jason Swails (Tue Oct 27 2015 - 09:39:49 PDT)
- Fabian gmail (Tue Oct 27 2015 - 09:10:44 PDT)
- Adrian Roitberg (Tue Oct 27 2015 - 09:02:32 PDT)
- Jason Swails (Tue Oct 27 2015 - 08:46:05 PDT)
- Fabian gmail (Tue Oct 27 2015 - 07:03:19 PDT)
- Carlos Simmerling (Tue Oct 27 2015 - 06:56:44 PDT)
- Fabian gmail (Tue Oct 27 2015 - 06:36:05 PDT)
[AMBER] Steps after: AMBER annealing with restraints in vacuum.? towards improving the quality of structure with out RDC, Dihedrals
- V. Kumar (Fri Oct 23 2015 - 02:41:36 PDT)
- V. Kumar (Fri Oct 23 2015 - 02:22:05 PDT)
[AMBER] Steps after: AMBER annealing with restriaints in vocuum.? towards improving the quality of structure with out RDC, Dihedrals
- V. Kumar (Sat Oct 24 2015 - 16:39:37 PDT)
- David A Case (Sat Oct 24 2015 - 05:34:53 PDT)
- Kumar cerm (Thu Oct 22 2015 - 08:15:17 PDT)
[AMBER] Stopping sander in production phase. Why?
- Jason Swails (Fri Oct 23 2015 - 09:01:26 PDT)
- Atila Petrosian (Fri Oct 23 2015 - 08:48:54 PDT)
- Jason Swails (Fri Oct 23 2015 - 08:24:06 PDT)
- Atila Petrosian (Fri Oct 23 2015 - 08:12:31 PDT)
- Adrian Roitberg (Fri Oct 23 2015 - 07:13:24 PDT)
- Atila Petrosian (Fri Oct 23 2015 - 07:10:24 PDT)
- Atila Petrosian (Fri Oct 23 2015 - 06:40:41 PDT)
[AMBER] System gets unwrap while iwrap=1 in ti
- Khabiri, Morteza (Fri Oct 16 2015 - 06:52:41 PDT)
- Jason Swails (Thu Oct 15 2015 - 07:14:58 PDT)
- Khabiri, Morteza (Thu Oct 15 2015 - 07:02:37 PDT)
- Jason Swails (Thu Oct 15 2015 - 06:32:54 PDT)
- Khabiri, Morteza (Thu Oct 15 2015 - 06:18:17 PDT)
[AMBER] Temperature fluctuations in stage heating
- Repic Matej (Tue Oct 13 2015 - 02:19:49 PDT)
- Anitha Jagadesh (Mon Oct 12 2015 - 22:06:26 PDT)
[AMBER] The formulas of per-residue and pairwise-residue free energy decomposition in mm_pbsa
- wliu (Tue Oct 27 2015 - 23:14:27 PDT)
- Jason Swails (Tue Oct 20 2015 - 06:40:15 PDT)
- wliu (Mon Oct 19 2015 - 23:33:20 PDT)
[AMBER] The magnitude and the direction of the electric field
- Hadeer ELHabashy (Wed Oct 21 2015 - 05:54:48 PDT)
[AMBER] Time correlation function of an atom
- David A Case (Thu Oct 22 2015 - 15:30:19 PDT)
- Hadeer ELHabashy (Thu Oct 22 2015 - 09:06:07 PDT)
- Adrian Roitberg (Thu Oct 22 2015 - 08:56:00 PDT)
- Hadeer ELHabashy (Thu Oct 22 2015 - 08:54:24 PDT)
[AMBER] tinker_to_amber does not work
- David A Case (Fri Oct 16 2015 - 08:49:31 PDT)
- Jason Swails (Thu Oct 15 2015 - 07:54:04 PDT)
- Sun (Thu Oct 15 2015 - 07:21:26 PDT)
- Jason Swails (Wed Oct 14 2015 - 18:09:23 PDT)
- Sun (Wed Oct 14 2015 - 14:52:10 PDT)
[AMBER] TIP3 water not recognized
- Bill Ross (Fri Oct 02 2015 - 18:04:57 PDT)
- Chitrak Gupta (Fri Oct 02 2015 - 16:03:35 PDT)
[AMBER] Tutorial 22 - aMD - how long should it last on Titan Black?
- Karolina Markowska (Thu Oct 29 2015 - 08:32:17 PDT)
- Ross Walker (Thu Oct 29 2015 - 08:08:31 PDT)
- case (Thu Oct 29 2015 - 04:40:17 PDT)
- Karolina Markowska (Thu Oct 29 2015 - 02:35:40 PDT)
[AMBER] Tutorial 3 section 1
- Vlad Cojocaru (Tue Oct 20 2015 - 05:03:15 PDT)
- Abelak, Kavin (Tue Oct 20 2015 - 04:54:58 PDT)
[AMBER] Units of the dipole moment?
- Daniel Roe (Thu Oct 01 2015 - 11:51:06 PDT)
- Ucisik, Melek Nihan (Thu Oct 01 2015 - 10:02:23 PDT)
[AMBER] unusual structure_after equilibration
- Carlos Simmerling (Tue Oct 27 2015 - 06:19:18 PDT)
- Andrew Bostick (Tue Oct 27 2015 - 05:44:43 PDT)
[AMBER] Updates for PBSA energy calculations
- Jason Swails (Thu Oct 01 2015 - 13:13:28 PDT)
- Christina Berti (Thu Oct 01 2015 - 12:29:03 PDT)
[AMBER] What is the formula for calculating EPtot?
- conor parks (Thu Oct 15 2015 - 10:05:53 PDT)
- Jason Swails (Thu Oct 15 2015 - 08:58:19 PDT)
- conor parks (Thu Oct 15 2015 - 08:15:16 PDT)
- Jason Swails (Thu Oct 15 2015 - 07:56:20 PDT)
- Daniel Roe (Thu Oct 15 2015 - 07:31:05 PDT)
- Conor Parks (Thu Oct 15 2015 - 07:17:30 PDT)
- David A Case (Thu Oct 15 2015 - 05:42:08 PDT)
- Jason Swails (Thu Oct 15 2015 - 04:52:58 PDT)
- Yip Yew Mun (Thu Oct 15 2015 - 02:26:29 PDT)
[AMBER] Why is water box getting bigger?
- Karolina Markowska (Mon Oct 26 2015 - 05:51:00 PDT)
- Jason Swails (Mon Oct 26 2015 - 05:45:23 PDT)
- Karolina Markowska (Mon Oct 26 2015 - 05:34:42 PDT)
- Karolina Markowska (Fri Oct 23 2015 - 07:26:11 PDT)
- Jason Swails (Thu Oct 22 2015 - 07:05:38 PDT)
- Karolina Markowska (Thu Oct 22 2015 - 06:41:53 PDT)
- Jason Swails (Wed Oct 21 2015 - 05:10:18 PDT)
- Karolina Markowska (Wed Oct 21 2015 - 02:13:49 PDT)
- David A Case (Mon Oct 19 2015 - 06:16:16 PDT)
- Karolina Markowska (Mon Oct 19 2015 - 04:57:20 PDT)
[AMBER] Why PBSA decomposition takes so long time?
- Jason Swails (Fri Oct 30 2015 - 07:10:01 PDT)
- MarcZhang (Fri Oct 30 2015 - 03:52:40 PDT)
System gets unwrap while iwrap=1 in ti
- Jason Swails (Fri Oct 16 2015 - 04:54:43 PDT)
- case (Thu Oct 15 2015 - 18:55:57 PDT)
- Khabiri, Morteza (Thu Oct 15 2015 - 11:46:48 PDT)

Amber Archive Oct 2015 by subject