Amber Archive Nov 2015: by subject

[AMBER] "Vlimit exceeded for step..." error
- Jason Swails (Wed Nov 18 2015 - 08:21:49 PST)
- Vishnudatt Pandey (Wed Nov 18 2015 - 01:35:39 PST)
[AMBER] &rst + distance + coordinate restraint
- Gerald Monard (Tue Nov 03 2015 - 07:27:50 PST)
- Jason Swails (Tue Nov 03 2015 - 06:56:57 PST)
- Gerald Monard (Tue Nov 03 2015 - 06:39:32 PST)
- Daniel Roe (Mon Nov 02 2015 - 09:09:06 PST)
- Jason Swails (Sun Nov 01 2015 - 02:52:20 PST)
[AMBER] (no subject)
- Facebook (Tue Nov 24 2015 - 07:09:44 PST)
- Facebook (Tue Nov 24 2015 - 05:13:14 PST)
- Facebook (Fri Nov 20 2015 - 11:32:07 PST)
- Facebook (Fri Nov 20 2015 - 10:06:55 PST)
- Facebook (Fri Nov 20 2015 - 03:58:07 PST)
- Facebook (Wed Nov 18 2015 - 22:30:12 PST)
[AMBER] (too) high absolute values for charges using resp and gaussian
- Karl Kirschner (Mon Nov 02 2015 - 07:53:31 PST)
- Jérémie Knoops (Mon Nov 02 2015 - 05:20:14 PST)
- Jérémie Knoops (Mon Nov 02 2015 - 01:06:55 PST)
[AMBER] 10 Lowest energy structures from GB ==>Explicit solvent refinement
- V. Kumar (Sun Nov 22 2015 - 04:19:37 PST)
- David A Case (Sat Nov 21 2015 - 17:34:08 PST)
- V. Kumar (Sat Nov 21 2015 - 07:25:37 PST)
[AMBER] A query about distance between periodic images
- anu chandra (Mon Nov 09 2015 - 08:20:03 PST)
[AMBER] add support 4 file format antechamber
- David A Case (Fri Nov 13 2015 - 04:54:15 PST)
- Sofia Vasilakaki (Thu Nov 12 2015 - 10:50:14 PST)
[AMBER] Adding parameters to the force field
- David A Case (Sun Nov 29 2015 - 17:34:30 PST)
- Timofey Tyugashev (Fri Nov 27 2015 - 04:07:04 PST)
[AMBER] AMBER14 cuda installation problem
- Sanjib Paul (Thu Nov 05 2015 - 02:27:52 PST)
- Charles Lin (Wed Nov 04 2015 - 22:38:03 PST)
- Charles Lin (Wed Nov 04 2015 - 22:35:53 PST)
- Sanjib Paul (Wed Nov 04 2015 - 22:20:32 PST)
[AMBER] Apologize
- Carlos Romero (Sat Nov 21 2015 - 17:59:14 PST)
[AMBER] At line 434 of file make_crd_hg.F (unit = 5, file = 'stdin') Fortran runtime error: Bad value during floating point read.
- Bill (Thu Nov 26 2015 - 14:38:32 PST)
- David A Case (Thu Nov 26 2015 - 14:07:46 PST)
- leila karami (Thu Nov 26 2015 - 11:50:16 PST)
- leila karami (Thu Nov 26 2015 - 08:14:12 PST)
[AMBER] Backbone
- mohammad r (Wed Nov 18 2015 - 12:40:28 PST)
- David A Case (Wed Nov 18 2015 - 12:34:41 PST)
- mohammad r (Wed Nov 18 2015 - 07:36:15 PST)
- Daniel Roe (Wed Nov 18 2015 - 07:15:34 PST)
- Jason Swails (Wed Nov 18 2015 - 06:12:57 PST)
- mohammad r (Wed Nov 18 2015 - 05:15:25 PST)
- Karl Kirschner (Wed Nov 18 2015 - 02:09:26 PST)
- mohammad r (Wed Nov 18 2015 - 01:50:30 PST)
- mohammad r (Wed Nov 18 2015 - 01:49:57 PST)
- mohammad roostaie (Wed Nov 18 2015 - 01:52:09 PST)
[AMBER] Can LEaP create peptides with D-amino acids?
- Carlos Simmerling (Mon Nov 23 2015 - 05:07:57 PST)
- Marion, Antoine (Mon Nov 23 2015 - 04:00:38 PST)
- Carlos Simmerling (Mon Nov 23 2015 - 03:10:23 PST)
- Yip Yew Mun (Mon Nov 23 2015 - 00:19:37 PST)
[AMBER] Can't install AMBER14: MissingProgram...Install patch from your package manager
- Jose Borreguero (Sun Nov 01 2015 - 07:54:55 PST)
[AMBER] can't install MMPBSA.py.MPI
- case (Mon Nov 09 2015 - 17:20:23 PST)
- Hai Nguyen (Mon Nov 09 2015 - 14:44:19 PST)
- 情生太郎 (Mon Nov 09 2015 - 14:31:37 PST)
[AMBER] Center of mass restraints with pmemd.cuda
- Jason Swails (Wed Nov 04 2015 - 07:29:54 PST)
- abdennour braka (Wed Nov 04 2015 - 07:26:28 PST)
- Kevin Hauser (Wed Nov 04 2015 - 07:00:24 PST)
- abdennour braka (Wed Nov 04 2015 - 06:57:12 PST)
[AMBER] Combined cartesian and NMR restraints
- Peter Podbevšek (Fri Nov 13 2015 - 05:32:46 PST)
[AMBER] Convert namd input file into sander input format?
- Jason Swails (Fri Nov 06 2015 - 08:50:44 PST)
- Xing (Fri Nov 06 2015 - 08:33:23 PST)
[AMBER] cpptraj density command
- Ignacio J. General (Sun Nov 22 2015 - 06:09:41 PST)
- Daniel Roe (Sat Nov 21 2015 - 09:59:26 PST)
- David A Case (Sat Nov 21 2015 - 05:54:39 PST)
- Ignacio J. General (Sat Nov 21 2015 - 05:10:17 PST)
[AMBER] cpptraj grid command
- Daniel Roe (Thu Nov 26 2015 - 05:51:08 PST)
- Thomas Fox (Wed Nov 25 2015 - 00:27:48 PST)
- Daniel Roe (Fri Nov 20 2015 - 15:02:10 PST)
- Thomas Fox (Thu Nov 19 2015 - 09:09:56 PST)
- Daniel Roe (Thu Nov 19 2015 - 08:44:30 PST)
- Thomas Fox (Thu Nov 19 2015 - 04:43:05 PST)
[AMBER] Cpptraj Tutorial B1
- Aishani Prem (Thu Nov 05 2015 - 14:20:53 PST)
- Aishani Prem (Thu Nov 05 2015 - 14:18:17 PST)
- Daniel Roe (Thu Nov 05 2015 - 14:17:03 PST)
- V. Kumar (Thu Nov 05 2015 - 14:11:19 PST)
- Aishani Prem (Thu Nov 05 2015 - 13:45:35 PST)
[AMBER] cpptraj uses huge memory space while doing molsurf calculation
- David A Case (Wed Nov 11 2015 - 07:31:47 PST)
- anu chandra (Wed Nov 11 2015 - 05:16:31 PST)
[AMBER] decomp bad atom type: fe
- Abelak, Kavin (Mon Nov 02 2015 - 06:44:49 PST)
[AMBER] decomposition energy
- Jason Swails (Thu Nov 19 2015 - 09:16:47 PST)
- Fabian gmail (Thu Nov 19 2015 - 08:32:29 PST)
[AMBER] Deformed structures
- Damiano Spadoni (Thu Nov 26 2015 - 03:44:38 PST)
- David A Case (Wed Nov 25 2015 - 16:27:29 PST)
- Damiano Spadoni (Wed Nov 25 2015 - 08:23:29 PST)
[AMBER] Distorted and Failed Phosphate Simulations
- Jason Swails (Tue Nov 24 2015 - 05:17:54 PST)
- Sigurd Friis Truelsen (Tue Nov 24 2015 - 02:08:00 PST)
- Karl Kirschner (Fri Nov 20 2015 - 01:36:16 PST)
- David A Case (Thu Nov 19 2015 - 05:26:20 PST)
- pavel.banas.upol.cz (Thu Nov 19 2015 - 05:23:03 PST)
- Karl Kirschner (Thu Nov 19 2015 - 03:14:22 PST)
- Sigurd Friis Truelsen (Thu Nov 19 2015 - 02:48:32 PST)
[AMBER] Entropy can be neglecected under which condition
- Marc Zhang (Tue Nov 03 2015 - 05:35:54 PST)
- Carlos Simmerling (Tue Nov 03 2015 - 02:50:16 PST)
- sunita gupta (Tue Nov 03 2015 - 01:22:22 PST)
- Marc Zhang (Tue Nov 03 2015 - 01:05:57 PST)
[AMBER] Equilibrium temperature is higher than the target temperature in Langevin dynamics
- David A Case (Fri Nov 27 2015 - 07:14:43 PST)
- jinfeng liu (Thu Nov 26 2015 - 22:16:33 PST)
- David A Case (Thu Nov 26 2015 - 10:37:00 PST)
- David A Case (Thu Nov 26 2015 - 10:26:11 PST)
- jinfeng liu (Wed Nov 25 2015 - 17:40:16 PST)
- Daniel Roe (Wed Nov 25 2015 - 08:38:54 PST)
- jinfeng liu (Wed Nov 25 2015 - 07:24:16 PST)
- David A Case (Wed Nov 25 2015 - 07:02:50 PST)
- jinfeng liu (Wed Nov 25 2015 - 00:23:40 PST)
[AMBER] Error compiling amber14 with CUDA-7.0 (CentOS 7)
- Elvis Martis (Sat Nov 21 2015 - 19:29:15 PST)
- Jason Swails (Sat Nov 21 2015 - 04:25:26 PST)
- Sofia Vasilakaki (Sat Nov 21 2015 - 02:39:50 PST)
- Elvis Martis (Fri Nov 20 2015 - 20:51:24 PST)
- Jason Swails (Fri Nov 20 2015 - 04:56:40 PST)
- Elvis Martis (Thu Nov 19 2015 - 23:36:04 PST)
[AMBER] Error message while running alanine dipeptide tutorial (minimization)
- David A Case (Mon Nov 30 2015 - 15:41:52 PST)
- Bill (Mon Nov 30 2015 - 14:49:41 PST)
- Carlos Simmerling (Mon Nov 30 2015 - 04:06:15 PST)
- Nikolay N. Kuzmich (Mon Nov 30 2015 - 03:39:41 PST)
- David A Case (Fri Nov 27 2015 - 07:17:24 PST)
- Bill (Fri Nov 27 2015 - 00:35:33 PST)
- Nikolay N. Kuzmich (Fri Nov 27 2015 - 00:28:39 PST)
[AMBER] error with NMA calculation
- David A Case (Thu Nov 19 2015 - 05:12:46 PST)
- Jason Swails (Wed Nov 18 2015 - 18:51:45 PST)
- Mohammad Salem (Wed Nov 18 2015 - 15:38:54 PST)
- David A Case (Tue Nov 17 2015 - 04:19:03 PST)
- Mohammad (Mon Nov 16 2015 - 21:36:34 PST)
- Jason Swails (Fri Nov 13 2015 - 19:05:41 PST)
- Mohammad Salem (Fri Nov 13 2015 - 15:33:33 PST)
[AMBER] Error: ptraj is needed for MMPBSA
- Ayesha Kanwal (Fri Nov 13 2015 - 04:17:35 PST)
[AMBER] Few queries about simulation of protein - carbohydrate system
- anu chandra (Tue Nov 17 2015 - 05:32:12 PST)
- Lachele Foley (Mon Nov 16 2015 - 11:40:12 PST)
- aneesh cna (Fri Nov 13 2015 - 05:20:05 PST)
- David A Case (Fri Nov 13 2015 - 04:50:14 PST)
- anu chandra (Wed Nov 11 2015 - 04:59:07 PST)
[AMBER] ff14SB acetylated residues
- Carlos Simmerling (Tue Nov 03 2015 - 02:43:11 PST)
- Neha Gandhi (Tue Nov 03 2015 - 01:37:47 PST)
[AMBER] For atom: .R<Na+ 264>.A<Na+ 1> Could not find vdW (or other) parameters for type: IP
- Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Fri Nov 13 2015 - 23:01:31 PST)
- David A Case (Thu Nov 12 2015 - 04:42:49 PST)
- Bill (Thu Nov 12 2015 - 01:57:21 PST)
- Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Thu Nov 12 2015 - 00:44:55 PST)
[AMBER] free energy of solvation of small molecules
- Fabian gmail (Mon Nov 30 2015 - 01:12:16 PST)
- hannes.loeffler.stfc.ac.uk (Mon Nov 30 2015 - 00:57:33 PST)
- Fabian gmail (Sun Nov 29 2015 - 08:08:05 PST)
- Fabian gmail (Sun Nov 29 2015 - 02:52:22 PST)
- Fabian gmail (Wed Nov 25 2015 - 08:00:35 PST)
- Hannes Loeffler (Wed Nov 25 2015 - 07:38:18 PST)
- Fabian gmail (Wed Nov 25 2015 - 07:15:06 PST)
- hannes.loeffler.stfc.ac.uk (Wed Nov 25 2015 - 05:03:46 PST)
- Fabian gmail (Wed Nov 25 2015 - 04:26:31 PST)
- Hannes Loeffler (Wed Nov 25 2015 - 03:10:41 PST)
- Fabian gmail (Wed Nov 25 2015 - 02:39:59 PST)
- Hannes Loeffler (Wed Nov 25 2015 - 02:16:34 PST)
- Fabian gmail (Wed Nov 25 2015 - 01:43:36 PST)
- Fabian gmail (Mon Nov 23 2015 - 05:11:44 PST)
- Josh Berryman (Sun Nov 22 2015 - 23:24:54 PST)
- Hannes Loeffler (Thu Nov 19 2015 - 08:54:49 PST)
- Fabian gmail (Thu Nov 19 2015 - 08:40:19 PST)
- Fabian gmail (Tue Nov 17 2015 - 08:11:33 PST)
- Hannes Loeffler (Tue Nov 17 2015 - 08:06:45 PST)
- Fabian gmail (Tue Nov 17 2015 - 07:35:04 PST)
- Hannes Loeffler (Tue Nov 17 2015 - 06:17:16 PST)
- Fabian gmail (Tue Nov 17 2015 - 05:51:50 PST)
[AMBER] Fwd: Regarding QM/MM calculation in AMBER14
- David A Case (Mon Nov 02 2015 - 05:51:27 PST)
- Jason Swails (Mon Nov 02 2015 - 05:46:33 PST)
- Adrian Roitberg (Mon Nov 02 2015 - 05:45:10 PST)
- Sivanandam M (Mon Nov 02 2015 - 04:41:01 PST)
[AMBER] Fwd: Replica exchange problem in visualization and interpretation of the MD out files
- Carlos Simmerling (Fri Nov 27 2015 - 06:35:12 PST)
- maryam azimzadehirani (Fri Nov 27 2015 - 02:58:09 PST)
[AMBER] Gaussian Accelerated Molecular Dynamics
- Ross Walker (Wed Nov 04 2015 - 19:32:32 PST)
- Filip Fratev (Wed Nov 04 2015 - 18:28:35 PST)
- Jason Swails (Wed Nov 04 2015 - 12:14:11 PST)
- Albert (Wed Nov 04 2015 - 11:03:07 PST)
- Ross Walker (Wed Nov 04 2015 - 10:59:41 PST)
- Filip Fratev (Wed Nov 04 2015 - 10:31:40 PST)
[AMBER] GIST
- Yulian Gavrilov (Thu Nov 12 2015 - 01:00:13 PST)
- Steven Ramsey (Wed Nov 11 2015 - 08:33:00 PST)
- Yulian Gavrilov (Wed Nov 11 2015 - 04:21:39 PST)
- Jonathan Gough (Tue Nov 10 2015 - 07:28:46 PST)
- Steven Ramsey (Tue Nov 10 2015 - 07:04:56 PST)
- Yulian Gavrilov (Tue Nov 10 2015 - 00:24:42 PST)
[AMBER] Gpu info
- Carlos Romero (Thu Nov 12 2015 - 16:42:12 PST)
- Scott Le Grand (Thu Nov 12 2015 - 16:15:21 PST)
- Carlos Romero (Thu Nov 12 2015 - 10:43:00 PST)
- Ross Walker (Thu Nov 12 2015 - 09:41:07 PST)
- Carlos Romero (Thu Nov 12 2015 - 09:24:02 PST)
[AMBER] GPU run fails
- Fabian gmail (Sun Nov 15 2015 - 01:14:37 PST)
- Ross Walker (Thu Nov 12 2015 - 09:04:47 PST)
- Jason Swails (Thu Nov 12 2015 - 09:02:31 PST)
- Fabian gmail (Thu Nov 12 2015 - 08:47:59 PST)
[AMBER] High Positive Values of delta G in MMPBSA
- Jason Swails (Wed Nov 11 2015 - 05:13:33 PST)
- Hira Jabeen (Wed Nov 11 2015 - 03:16:34 PST)
- Hira Jabeen (Wed Nov 11 2015 - 03:11:01 PST)
[AMBER] How comment in mdin sander input file?
- Alan (Mon Nov 02 2015 - 05:07:54 PST)
- David A Case (Mon Nov 02 2015 - 04:39:15 PST)
- Eiros Zamora, Juan (Mon Nov 02 2015 - 04:22:15 PST)
- Alan (Mon Nov 02 2015 - 01:49:12 PST)
[AMBER] how to add lipid
- mohammad r (Mon Nov 23 2015 - 10:48:28 PST)
- Parker de Waal (Mon Nov 23 2015 - 10:41:51 PST)
- mohammad r (Mon Nov 23 2015 - 10:31:15 PST)
- Parker de Waal (Mon Nov 23 2015 - 10:17:13 PST)
- Brian Radak (Mon Nov 23 2015 - 09:57:25 PST)
- mohammad r (Mon Nov 23 2015 - 09:52:41 PST)
- Brian Radak (Mon Nov 23 2015 - 09:03:56 PST)
- mohammad r (Mon Nov 23 2015 - 09:01:46 PST)
- mohammad r (Mon Nov 23 2015 - 09:01:11 PST)
[AMBER] How to add restraints to a ligand correctly while decoupling it from complex?
- Jason Swails (Tue Nov 03 2015 - 06:14:57 PST)
- wliu (Mon Nov 02 2015 - 04:56:29 PST)
[AMBER] How to choose between implicit and explicit solvent
- Josh Berryman (Mon Nov 09 2015 - 23:09:09 PST)
- Ross Walker (Mon Nov 09 2015 - 13:09:37 PST)
- Josh Berryman (Mon Nov 09 2015 - 12:43:37 PST)
- Fabian gmail (Thu Nov 05 2015 - 04:45:45 PST)
- David A Case (Thu Nov 05 2015 - 04:27:28 PST)
- Jean-Patrick Francoia (Thu Nov 05 2015 - 01:39:23 PST)
- Fabian gmail (Thu Nov 05 2015 - 00:51:13 PST)
- David A Case (Wed Nov 04 2015 - 10:07:04 PST)
- Fabian gmail (Wed Nov 04 2015 - 08:21:40 PST)
- Carlos Simmerling (Wed Nov 04 2015 - 06:15:39 PST)
- Jason Swails (Wed Nov 04 2015 - 06:07:48 PST)
- Jean-Patrick Francoia (Wed Nov 04 2015 - 05:47:03 PST)
- Carlos Simmerling (Wed Nov 04 2015 - 05:27:08 PST)
- Jean-Patrick Francoia (Wed Nov 04 2015 - 05:18:07 PST)
- Carlos Simmerling (Wed Nov 04 2015 - 03:12:06 PST)
- Jean-Patrick Francoia (Wed Nov 04 2015 - 01:15:29 PST)
[AMBER] how to create a 20% or 30% acetone / water equilibrated solvent box
- Fabian gmail (Sun Nov 15 2015 - 01:51:03 PST)
- David A Case (Thu Nov 12 2015 - 10:39:41 PST)
- Fabian gmail (Thu Nov 12 2015 - 08:43:18 PST)
[AMBER] How to fix malloc error during MM-PBSA calculation on AMBER14 ... mmpbsa_py_energy: malloc.c:2372: sysmalloc:
- Mijiddorj Batsaikhan (Mon Nov 30 2015 - 06:15:44 PST)
[AMBER] How to fix the QM/MM region box size and visualize it
- Gustavo Seabra (Mon Nov 23 2015 - 06:12:12 PST)
- Sivanandam M (Mon Nov 23 2015 - 05:15:28 PST)
[AMBER] how to plot a graph for enthalpy
- Ayesha Kanwal (Sat Nov 14 2015 - 13:03:58 PST)
- psu4.uic.edu (Sat Nov 14 2015 - 12:55:27 PST)
- Jason Swails (Sat Nov 14 2015 - 09:29:15 PST)
- Jason Swails (Sat Nov 14 2015 - 08:16:41 PST)
- asma.msbi28.iiu.edu.pk (Sat Nov 14 2015 - 07:37:47 PST)
- Ayesha Kanwal (Sat Nov 14 2015 - 07:33:11 PST)
- Ayesha Kanwal (Sat Nov 14 2015 - 06:43:46 PST)
- Jason Swails (Sat Nov 14 2015 - 03:54:33 PST)
- ayesha afzaal (Sat Nov 14 2015 - 02:09:17 PST)
[AMBER] How to solve the unfilled valence problem in antechamber
- David A Case (Mon Nov 09 2015 - 05:15:53 PST)
- 张敏华 (Sun Nov 08 2015 - 19:12:35 PST)
[AMBER] Import error when running MMPBSA.py
- Cockroft, Nicholas T. (Wed Nov 25 2015 - 10:25:03 PST)
- Dwight McGee (Tue Nov 24 2015 - 17:16:48 PST)
- Hai Nguyen (Tue Nov 24 2015 - 16:59:55 PST)
- Nhai (Tue Nov 24 2015 - 16:57:53 PST)
- Cockroft, Nicholas T. (Tue Nov 24 2015 - 16:41:51 PST)
- Dwight McGee (Tue Nov 24 2015 - 16:30:41 PST)
- Cockroft, Nicholas T. (Tue Nov 24 2015 - 14:00:11 PST)
[AMBER] ions cannot be viewed in gaussview
- Jason Swails (Mon Nov 02 2015 - 09:40:13 PST)
- Martina Devi (Mon Nov 02 2015 - 09:24:17 PST)
- Jason Swails (Mon Nov 02 2015 - 08:16:44 PST)
- Martina Devi (Mon Nov 02 2015 - 08:14:30 PST)
- Daniel Roe (Mon Nov 02 2015 - 07:47:10 PST)
- Aleksandra Skoric (Mon Nov 02 2015 - 05:54:44 PST)
- David A Case (Mon Nov 02 2015 - 05:54:36 PST)
- Jason Swails (Mon Nov 02 2015 - 05:41:43 PST)
- Martina Devi (Mon Nov 02 2015 - 05:20:34 PST)
- MOHD HOMAIDUR RAHMAN (Sun Nov 01 2015 - 21:44:06 PST)
- Gustavo Seabra (Sun Nov 01 2015 - 14:37:21 PST)
- Jason Swails (Sun Nov 01 2015 - 10:43:48 PST)
- Martina Devi (Sun Nov 01 2015 - 10:34:26 PST)
- Gustavo Seabra (Sun Nov 01 2015 - 09:04:04 PST)
- Robert Molt (Sun Nov 01 2015 - 07:28:17 PST)
- Martina Devi (Sun Nov 01 2015 - 07:12:43 PST)
- Martina Devi (Sat Oct 31 2015 - 12:12:20 PDT)
[AMBER] iwrap=1 "can mess up diffusion and other calculations"
- Jason Swails (Tue Nov 24 2015 - 20:57:26 PST)
- Robert Molt (Tue Nov 24 2015 - 19:02:49 PST)
- Jason Swails (Tue Nov 24 2015 - 18:57:12 PST)
- Charles Lin (Tue Nov 24 2015 - 18:56:52 PST)
- Robert Molt (Tue Nov 24 2015 - 17:45:57 PST)
[AMBER] Lipid14 simulation :MC Barostat vs Berendsen Barostat and NTR=1
- Jason Swails (Fri Nov 13 2015 - 13:17:32 PST)
- Himanshu Joshi (Fri Nov 13 2015 - 12:03:56 PST)
- Ross Walker (Fri Nov 13 2015 - 09:11:49 PST)
- Himanshu Joshi (Fri Nov 13 2015 - 03:47:37 PST)
- Himanshu Joshi (Fri Nov 13 2015 - 03:42:49 PST)
[AMBER] mac hangs when compile ambertools15 on El capitan
- Hai Nguyen (Mon Nov 30 2015 - 20:38:54 PST)
[AMBER] make complex
- David A Case (Mon Nov 09 2015 - 05:21:09 PST)
- Jason Swails (Mon Nov 09 2015 - 04:56:23 PST)
- Fatemeh Sadat Alavi (Mon Nov 09 2015 - 00:03:47 PST)
- case (Sun Nov 08 2015 - 09:50:42 PST)
- Fatemeh Sadat Alavi (Sun Nov 08 2015 - 02:24:58 PST)
[AMBER] Making .mdl files for 1DRISM calculations
- David A Case (Wed Nov 18 2015 - 12:27:02 PST)
- Tyler Luchko (Lists) (Wed Nov 18 2015 - 09:51:52 PST)
- Ella Gale (Wed Nov 18 2015 - 04:51:40 PST)
- Tyler Luchko (Lists) (Tue Nov 17 2015 - 12:56:27 PST)
- Ella Gale (Tue Nov 17 2015 - 07:22:53 PST)
[AMBER] MD simulation for multiple ligands
- Jason Swails (Mon Nov 23 2015 - 14:28:50 PST)
- Balajee Ramachandran (Mon Nov 23 2015 - 07:57:47 PST)
[AMBER] MM-PBSA quasi harmonic
- Jason Swails (Sun Nov 01 2015 - 03:04:07 PST)
- Debodyuti Dutta (Sat Oct 31 2015 - 20:32:33 PDT)
[AMBER] MMGBSA Decomp on Heme Systems
- Vivek Bharadwaj (Wed Nov 25 2015 - 09:20:02 PST)
- Jason Swails (Tue Nov 24 2015 - 09:24:38 PST)
- Vivek Bharadwaj (Tue Nov 24 2015 - 08:46:43 PST)
[AMBER] MMPBSA
- David A Case (Sun Nov 29 2015 - 17:29:31 PST)
- Balajee Ramachandran (Sun Nov 29 2015 - 11:06:45 PST)
[AMBER] MMPBSA Electrostatic energy
- asma.msbi28.iiu.edu.pk (Wed Nov 11 2015 - 17:44:38 PST)
- Jason Swails (Wed Nov 11 2015 - 10:24:53 PST)
- Asma Abro 28-FBAS/MSBI/F09 (Wed Nov 11 2015 - 08:58:09 PST)
- Jason Swails (Wed Nov 11 2015 - 08:52:28 PST)
- Asma Abro 28-FBAS/MSBI/F09 (Wed Nov 11 2015 - 08:49:35 PST)
- Jason Swails (Wed Nov 11 2015 - 08:33:12 PST)
- Asma Abro 28-FBAS/MSBI/F09 (Wed Nov 11 2015 - 08:22:33 PST)
[AMBER] MMPBSA.py QM entropy calculation error
- Daniel Roe (Thu Nov 05 2015 - 14:58:12 PST)
- Jason Swails (Thu Nov 05 2015 - 14:44:07 PST)
- Nic Steussy (Thu Nov 05 2015 - 11:35:28 PST)
[AMBER] mono methylated lysine
- Sourav Purohit (Mon Nov 16 2015 - 22:01:50 PST)
- Bala subramanian (Mon Nov 16 2015 - 01:16:36 PST)
[AMBER] N- and C- terminals constant PH simulation
- Jason Swails (Wed Nov 11 2015 - 05:23:58 PST)
- Carlos Simmerling (Wed Nov 11 2015 - 04:31:19 PST)
- Hadeer ELHabashy (Wed Nov 11 2015 - 01:16:56 PST)
[AMBER] NAB nmode() output Clarification
- Guqin Shi (Wed Nov 25 2015 - 07:20:39 PST)
- David A Case (Wed Nov 25 2015 - 06:59:56 PST)
- Guqin Shi (Tue Nov 24 2015 - 14:57:19 PST)
[AMBER] ncorr in rotdif command seems redundant to me. Please help.
- David A Case (Wed Nov 04 2015 - 04:16:37 PST)
- Jose Borreguero (Wed Nov 04 2015 - 03:28:43 PST)
- Daniel Roe (Tue Nov 03 2015 - 19:38:15 PST)
- case (Tue Nov 03 2015 - 17:49:28 PST)
- Jose Borreguero (Tue Nov 03 2015 - 14:39:41 PST)
[AMBER] neighbouring protons
- Jason Swails (Tue Nov 10 2015 - 04:32:34 PST)
- Neha Gandhi (Tue Nov 10 2015 - 01:59:41 PST)
[AMBER] net charge issue during constant pH simulation with explicit solvent model
- Jason Swails (Wed Nov 18 2015 - 08:40:32 PST)
- zhonghe xu (Tue Nov 17 2015 - 23:19:34 PST)
[AMBER] NMR restraints + minimization+Could not find cntrl namelist
- V. Kumar (Thu Nov 05 2015 - 12:57:17 PST)
- David A Case (Thu Nov 05 2015 - 11:49:47 PST)
- V. Kumar (Thu Nov 05 2015 - 09:29:56 PST)
- Carlos Simmerling (Thu Nov 05 2015 - 09:25:14 PST)
- V. Kumar (Thu Nov 05 2015 - 09:21:42 PST)
[AMBER] NOE calculation cpptraj
- Neha Gandhi (Mon Nov 09 2015 - 20:00:03 PST)
- David A Case (Mon Nov 09 2015 - 05:13:25 PST)
- Jason Swails (Mon Nov 09 2015 - 05:00:50 PST)
- Neha Gandhi (Sun Nov 08 2015 - 18:49:22 PST)
[AMBER] Not matching test AMBER14 with CUDA
- Ross Walker (Sun Nov 29 2015 - 21:52:27 PST)
- Mijiddorj Batsaikhan (Sun Nov 29 2015 - 21:22:56 PST)
[AMBER] Number of water molecule to solvate 2.5KDa peptide in TIP3PBOX
- V. Kumar (Wed Nov 18 2015 - 06:39:49 PST)
- David A Case (Wed Nov 18 2015 - 06:22:17 PST)
- V. Kumar (Wed Nov 18 2015 - 01:32:30 PST)
[AMBER] orientational restraints in MD simulation
- Naomi Rose Latorraca (Thu Nov 05 2015 - 00:34:12 PST)
[AMBER] PLUMED patching with AMBER
- Sanjib Paul (Sun Nov 15 2015 - 22:02:25 PST)
- Giovanni Bussi (Sat Nov 14 2015 - 08:48:59 PST)
- Sanjib Paul (Sat Nov 14 2015 - 04:57:51 PST)
- Giovanni Bussi (Fri Nov 13 2015 - 07:18:13 PST)
- Sanjib Paul (Fri Nov 13 2015 - 04:06:56 PST)
- Jason Swails (Thu Nov 12 2015 - 08:45:35 PST)
- Giovanni Bussi (Thu Nov 12 2015 - 08:35:06 PST)
- Jason Swails (Thu Nov 12 2015 - 04:55:53 PST)
- Giovanni Bussi (Thu Nov 12 2015 - 04:09:53 PST)
- Sanjib Paul (Thu Nov 12 2015 - 02:40:49 PST)
- Giovanni Bussi (Sun Nov 08 2015 - 23:14:35 PST)
- Sanjib Paul (Sun Nov 08 2015 - 21:24:45 PST)
[AMBER] Polardecomp in 3D-RISM fails
- Jason Swails (Thu Nov 12 2015 - 05:19:05 PST)
- Josep Maria Campanera Alsina (Thu Nov 12 2015 - 04:31:54 PST)
[AMBER] Positive delta G in MM-PBSA
- Jason Swails (Sat Nov 14 2015 - 10:14:41 PST)
[AMBER] power failure + resume
- Jason Swails (Sun Nov 08 2015 - 08:25:31 PST)
- Bill (Sun Nov 08 2015 - 04:14:37 PST)
- Bill (Sun Nov 08 2015 - 03:57:00 PST)
- shahab shariati (Sun Nov 08 2015 - 03:40:49 PST)
- shahab shariati (Sun Nov 08 2015 - 03:32:29 PST)
- Jason Swails (Fri Nov 06 2015 - 09:00:00 PST)
- shahab shariati (Fri Nov 06 2015 - 08:29:38 PST)
- Daniel Roe (Fri Nov 06 2015 - 07:53:09 PST)
- shahab shariati (Fri Nov 06 2015 - 05:59:19 PST)
[AMBER] Problem with MMPBSA
- psu4.uic.edu (Sat Nov 14 2015 - 13:08:16 PST)
- Soong Jiaxin (Wed Nov 11 2015 - 06:12:20 PST)
- Jason Swails (Wed Nov 11 2015 - 05:27:42 PST)
- Soong Jiaxin (Wed Nov 11 2015 - 05:18:06 PST)
- Jason Swails (Wed Nov 11 2015 - 04:59:21 PST)
- Soong Jiaxin (Wed Nov 11 2015 - 02:23:16 PST)
- Bill (Wed Nov 11 2015 - 01:49:26 PST)
- Soong Jiaxin (Wed Nov 11 2015 - 01:26:30 PST)
[AMBER] Protein-Drug complex MD simulation issues
- Bill (Tue Nov 24 2015 - 03:58:24 PST)
- Vahid Kshani (Tue Nov 24 2015 - 03:28:12 PST)
[AMBER] ptraj and cpptraj
- Jason Swails (Thu Nov 05 2015 - 08:11:20 PST)
- 袁浩亮 (Thu Nov 05 2015 - 08:10:13 PST)
[AMBER] Putting a harmonic constraint between atoms
- Jason Swails (Thu Nov 19 2015 - 06:26:28 PST)
- Debodyuti Dutta (Thu Nov 19 2015 - 05:52:16 PST)
[AMBER] QM/MM Umbrella
- Adrian Roitberg (Mon Nov 09 2015 - 08:00:32 PST)
- Mahmood Jasim (Mon Nov 09 2015 - 07:05:31 PST)
[AMBER] QMMM: ERROR!
- David A Case (Mon Nov 23 2015 - 05:26:42 PST)
- Jason Swails (Mon Nov 23 2015 - 04:12:14 PST)
- Ayesha Kanwal (Mon Nov 23 2015 - 04:05:14 PST)
- Ayesha Kanwal (Mon Nov 23 2015 - 02:36:48 PST)
- Ross Walker (Sun Nov 22 2015 - 21:42:20 PST)
- Ayesha Kanwal (Sun Nov 22 2015 - 21:32:02 PST)
[AMBER] query about Br
- David A Case (Tue Nov 24 2015 - 08:32:00 PST)
- Ayesha Kanwal (Tue Nov 24 2015 - 05:03:02 PST)
- Ayesha Kanwal (Tue Nov 24 2015 - 00:20:00 PST)
[AMBER] query for plotting enthalpy graph
- David A Case (Fri Nov 20 2015 - 04:46:16 PST)
- Ayesha Kanwal (Thu Nov 19 2015 - 23:56:50 PST)
- Jason Swails (Sat Nov 14 2015 - 05:58:23 PST)
- Ayesha Kanwal (Sat Nov 14 2015 - 05:53:18 PST)
[AMBER] Questions about TI
- hannes.loeffler.stfc.ac.uk (Wed Nov 18 2015 - 01:35:58 PST)
- psu4.uic.edu (Wed Nov 18 2015 - 00:17:43 PST)
- lipengfei_mail (Thu Nov 12 2015 - 06:45:41 PST)
[AMBER] relaxation time CphMD
- Jason Swails (Fri Nov 13 2015 - 07:59:08 PST)
- Brian Radak (Fri Nov 13 2015 - 07:41:20 PST)
- Arjun Sharma (Fri Nov 13 2015 - 07:03:55 PST)
[AMBER] rMD || Distance-Restrained Molecular Dynamics Refinement in Explicit Solvent (AMBER) -- SCRIPT
- V. Kumar (Mon Nov 02 2015 - 09:28:37 PST)
- Jason Swails (Mon Nov 02 2015 - 08:49:27 PST)
- V. Kumar (Mon Nov 02 2015 - 07:12:13 PST)
- Carlos Simmerling (Mon Nov 02 2015 - 04:38:37 PST)
- V. Kumar (Mon Nov 02 2015 - 04:29:08 PST)
[AMBER] Role of VDWAALS and EEL in minimization
- Carlos Simmerling (Tue Nov 10 2015 - 03:18:50 PST)
- muhammad tahir ayub (Mon Nov 09 2015 - 22:22:13 PST)
[AMBER] Running simulations in a cluster
- Jason Swails (Mon Nov 23 2015 - 14:26:20 PST)
- Aishani Prem (Mon Nov 23 2015 - 14:22:47 PST)
[AMBER] Sampling of membrane-protein system
- Brian Radak (Wed Nov 11 2015 - 07:43:44 PST)
- Ofir Tal (Wed Nov 11 2015 - 06:02:11 PST)
- Jason Swails (Wed Nov 11 2015 - 05:10:42 PST)
- Ofir Tal (Wed Nov 11 2015 - 03:13:21 PST)
[AMBER] Saving trajectories with ntwprt
- Jason Swails (Fri Nov 13 2015 - 05:29:57 PST)
- Batuhan Kav (Fri Nov 13 2015 - 05:25:02 PST)
[AMBER] Simulating Inifinite DNA molecules
- Jason Swails (Thu Nov 12 2015 - 10:28:34 PST)
- Ilyas Yildirim (Thu Nov 12 2015 - 08:59:34 PST)
- Balaji Selvam (Thu Nov 12 2015 - 08:56:31 PST)
[AMBER] Stability calculations from MMGB/PBSA
- Andrea Spitaleri (Thu Nov 12 2015 - 01:20:41 PST)
- Rajeswari A. (Wed Nov 11 2015 - 23:55:25 PST)
- Jason Swails (Wed Nov 11 2015 - 05:33:32 PST)
- David A Case (Wed Nov 11 2015 - 04:59:37 PST)
- Carlos Simmerling (Wed Nov 11 2015 - 04:35:56 PST)
- Rajeswari A. (Wed Nov 11 2015 - 00:54:14 PST)
[AMBER] temperature control issue during constant pH simulation with explicit solvent model
- Jason Swails (Tue Nov 17 2015 - 05:26:05 PST)
- Carlos Simmerling (Tue Nov 17 2015 - 05:19:25 PST)
- zhonghe xu (Tue Nov 17 2015 - 05:14:13 PST)
[AMBER] trajout or mask pdb with connection records (title is wrong, see this one)
- Daniel Roe (Thu Nov 05 2015 - 08:00:24 PST)
- windy (Wed Nov 04 2015 - 22:21:45 PST)
- Jason Swails (Tue Nov 03 2015 - 05:06:44 PST)
- windy (Mon Nov 02 2015 - 18:55:53 PST)
[AMBER] trajout our mask pdb with connection records
- windy (Mon Nov 02 2015 - 18:53:29 PST)
[AMBER] Tutorial 22 - aMD - how long should it last on Titan Black?
- Karolina Markowska (Mon Nov 02 2015 - 05:23:23 PST)
[AMBER] Tutorial A26: error in reading nameless control
- Ruth Helena Tichauer (Mon Nov 02 2015 - 06:22:39 PST)
- Jason Swails (Mon Nov 02 2015 - 06:17:45 PST)
- Ruth Helena Tichauer (Mon Nov 02 2015 - 06:13:05 PST)
- David A Case (Mon Nov 02 2015 - 04:37:48 PST)
- Ruth Helena Tichauer (Mon Nov 02 2015 - 01:28:19 PST)
[AMBER] Typo or My Confusion
- Ross Walker (Thu Nov 19 2015 - 08:16:45 PST)
- Jason Swails (Wed Nov 18 2015 - 08:20:49 PST)
- Robert Molt (Wed Nov 18 2015 - 07:25:10 PST)
- David A Case (Wed Nov 18 2015 - 06:11:31 PST)
- Robert Molt (Tue Nov 17 2015 - 19:57:02 PST)
- Robert Molt (Tue Nov 17 2015 - 19:56:42 PST)
[AMBER] units of charge density
- Ignacio J. General (Fri Nov 20 2015 - 06:24:45 PST)
[AMBER] urea force field
- Carlos Romero (Fri Nov 20 2015 - 13:23:12 PST)
- Jason Swails (Thu Nov 19 2015 - 07:29:30 PST)
- Carlos Romero (Thu Nov 19 2015 - 06:47:01 PST)
- Karl Kirschner (Wed Nov 18 2015 - 23:24:23 PST)
- Carlos Romero (Wed Nov 18 2015 - 16:39:34 PST)
[AMBER] What to expect when MD a peptide and a small organic molecule ?
- Jean-Patrick Francoia (Fri Nov 06 2015 - 02:06:35 PST)
- Carlos Simmerling (Thu Nov 05 2015 - 03:38:06 PST)
- Jean-Patrick Francoia (Thu Nov 05 2015 - 01:37:59 PST)
- Jason Swails (Wed Nov 04 2015 - 06:01:04 PST)
- Jean-Patrick Francoia (Wed Nov 04 2015 - 05:42:22 PST)
[AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond
- Carlos Simmerling (Mon Nov 30 2015 - 13:58:51 PST)
- Pengfei Li (Mon Nov 30 2015 - 13:51:13 PST)
- V. Kumar (Mon Nov 30 2015 - 12:38:10 PST)
- Carlos Simmerling (Mon Nov 30 2015 - 09:02:45 PST)
- V. Kumar (Mon Nov 30 2015 - 09:00:21 PST)

Amber Archive Nov 2015 by subject