Amber Archive Jan 2020: by subject

[AMBER] [ Error with MD ] Energetics of the system
- David Case (Fri Jan 10 2020 - 05:43:39 PST)
- 조준범 (Thu Jan 09 2020 - 23:35:38 PST)
[AMBER] [ inpcrd file ]
- Gustaf Olsson (Thu Jan 09 2020 - 03:40:35 PST)
- 조준범 (Thu Jan 09 2020 - 03:09:29 PST)
[AMBER] [ Lone pair electron & Polymer ]
- 조준범 (Mon Jan 06 2020 - 22:06:13 PST)
[AMBER] [ MD Failure ]
- David Case (Mon Jan 13 2020 - 06:27:42 PST)
- 조준범 (Sun Jan 12 2020 - 08:19:33 PST)
[AMBER] [ Polymer ] Parameter Modification
- David Cerutti (Wed Jan 08 2020 - 21:56:12 PST)
- 조준범 (Wed Jan 08 2020 - 21:17:32 PST)
[AMBER] [ Polymer with Extra Points ]
- 조준범 (Thu Jan 09 2020 - 21:29:10 PST)
- David Cerutti (Thu Jan 09 2020 - 00:02:47 PST)
- 조준범 (Tue Jan 07 2020 - 01:04:40 PST)
- David Cerutti (Mon Jan 06 2020 - 23:56:54 PST)
- 조준범 (Mon Jan 06 2020 - 22:40:38 PST)
[AMBER] [ prmtop ] SOLVENT_POINTERS
- Carlos Simmerling (Fri Jan 10 2020 - 03:31:25 PST)
- 조준범 (Thu Jan 09 2020 - 21:15:18 PST)
[AMBER] About ferrocene
- MENDOZA Cesar (Mon Jan 27 2020 - 08:54:45 PST)
[AMBER] About ions coordinated to Zinc
- MENDOZA Cesar (Fri Jan 24 2020 - 15:18:38 PST)
- MENDOZA Cesar (Thu Jan 23 2020 - 07:23:05 PST)
- MENDOZA Cesar (Mon Jan 20 2020 - 06:45:22 PST)
[AMBER] About utilities to convert Amber input files for MD into the Tinker, NAMD, Genesis, or Desmond input files
- Elvis Martis (Tue Jan 28 2020 - 20:17:49 PST)
- Vlad (Tue Jan 28 2020 - 20:00:19 PST)
[AMBER] Adjacent cell molecules appear in the trajectory after autoimaging in cpptraj [ DOPC lipid bilayer simulation with lipid14 force field]
- Bhat Zahoor (Wed Jan 08 2020 - 01:46:26 PST)
[AMBER] AMBER 18 cuda installation
- David Case (Tue Jan 07 2020 - 18:47:26 PST)
[AMBER] Amber 18 installation error
- Billiot, Eugene (Tue Jan 07 2020 - 09:19:04 PST)
- David Case (Tue Jan 07 2020 - 06:09:08 PST)
- Billiot, Eugene (Mon Jan 06 2020 - 14:29:11 PST)
[AMBER] Amber on windows 10
- Elvis Martis (Tue Jan 28 2020 - 07:22:22 PST)
- Nicolas Feldman (Tue Jan 28 2020 - 07:13:37 PST)
- Gustaf Olsson (Tue Jan 28 2020 - 07:08:14 PST)
- Gustaf Olsson (Tue Jan 28 2020 - 05:21:47 PST)
- Nicolas Feldman (Tue Jan 28 2020 - 04:33:33 PST)
- Nicolas Feldman (Tue Jan 28 2020 - 04:27:06 PST)
- Gustaf Olsson (Tue Jan 28 2020 - 04:22:32 PST)
- Elvis Martis (Tue Jan 28 2020 - 04:19:42 PST)
- Nicolas Feldman (Tue Jan 28 2020 - 04:14:39 PST)
[AMBER] Any help on the error
- David Case (Tue Jan 07 2020 - 05:59:45 PST)
- Debarati DasGupta (Mon Jan 06 2020 - 12:22:52 PST)
[AMBER] Autoimage problem
- Agata Sowińska I34 (Fri Jan 24 2020 - 08:41:14 PST)
[AMBER] Calculation of mask for TI input
- Carlos Simmerling (Tue Jan 28 2020 - 02:40:09 PST)
- Airy Sanjeev (Mon Jan 27 2020 - 20:22:34 PST)
[AMBER] charting Ligand's movement in the binding pocket
- Markowska (Thu Jan 09 2020 - 12:02:08 PST)
- Prasanth G, Research Scholar (Thu Jan 09 2020 - 02:58:01 PST)
[AMBER] compatible graphics card
- Antonio Bauzá (Sun Jan 12 2020 - 09:01:29 PST)
[AMBER] convergence of Ref energies in cpHMD
- Cruzeiro,Vinicius Wilian D (Thu Jan 23 2020 - 14:38:23 PST)
- Kolattukudy P. Santo (Wed Jan 22 2020 - 06:37:44 PST)
- Cruzeiro,Vinicius Wilian D (Tue Jan 21 2020 - 23:43:35 PST)
- Kolattukudy P. Santo (Tue Jan 21 2020 - 06:13:47 PST)
- Cruzeiro,Vinicius Wilian D (Mon Jan 20 2020 - 14:27:11 PST)
- Kolattukudy P. Santo (Mon Jan 20 2020 - 12:41:18 PST)
- Cruzeiro,Vinicius Wilian D (Mon Jan 20 2020 - 12:15:54 PST)
- Kolattukudy P. Santo (Mon Jan 20 2020 - 10:43:20 PST)
[AMBER] Cpptraj - Density Action Command Units
- An Ta (Thu Jan 09 2020 - 13:11:53 PST)
[AMBER] CPPTRAJ-Hbonds
- Daniel Roe (Mon Jan 13 2020 - 09:08:01 PST)
- Rui Chen (Mon Jan 13 2020 - 07:49:11 PST)
[AMBER] cpptraj_clucster
- Thayer, Kelly (Wed Jan 29 2020 - 07:13:49 PST)
- Lod King (Tue Jan 21 2020 - 19:16:44 PST)
[AMBER] Custom language module(s) for AMBER file types for common text editors?
- Matias Machado (Wed Jan 15 2020 - 12:23:52 PST)
- Makay Murray (Sat Jan 11 2020 - 18:17:06 PST)
[AMBER] defining a progress variable to be the z-component of some atom or group of atoms?
- Stephan Schott (Mon Jan 20 2020 - 07:12:55 PST)
- Feng Pan (Sun Jan 19 2020 - 08:31:08 PST)
- Gerardo Zerbetto De Palma (Sat Jan 18 2020 - 18:26:19 PST)
- Goetz, Andreas (Sat Jan 18 2020 - 18:01:59 PST)
- David Case (Sat Jan 18 2020 - 05:14:29 PST)
[AMBER] Does anyone here use a99SB-disp force field and how did you obtain it?
- Casalini Tommaso (Thu Jan 23 2020 - 07:05:43 PST)
- Anthony Cruz-Balberdy (Thu Jan 23 2020 - 04:56:36 PST)
- Homeo Morphism (Thu Jan 23 2020 - 02:44:52 PST)
[AMBER] DOPC lipid bilayer deformation in Implicit MD simulation using Lipid14 force field in Amber18
- Gould, Ian R (Tue Jan 07 2020 - 00:37:25 PST)
- Bhat Zahoor (Mon Jan 06 2020 - 23:16:55 PST)
[AMBER] Doubt regarding Collision frequency during NEB simulations
- SHAUNAK BADANI (Fri Jan 31 2020 - 11:37:03 PST)
[AMBER] Drug parameter generation
- Carlos Simmerling (Fri Jan 03 2020 - 10:22:19 PST)
- Madhur Aggarwal (Fri Jan 03 2020 - 10:09:16 PST)
[AMBER] DUMPAVE digits
- Santiago Movilla (Mon Jan 20 2020 - 14:29:33 PST)
[AMBER] empty cein file redox potential calculations
- Cruzeiro,Vinicius Wilian D (Thu Jan 09 2020 - 07:01:11 PST)
- Vaibhav Dixit (Mon Jan 06 2020 - 00:59:37 PST)
[AMBER] error
- Gustaf Olsson (Wed Jan 08 2020 - 22:54:22 PST)
- MYRIAN TORRES RICO (Wed Jan 08 2020 - 07:07:38 PST)
[AMBER] Error in installing parallel version of AMBER18
- Scott Brozell (Thu Jan 30 2020 - 11:55:53 PST)
- dilrajl.bii.a-star.edu.sg (Thu Jan 30 2020 - 06:51:57 PST)
[AMBER] Error with using dpeaks clustering in CPPTRAJ
- Yinglong Miao (Fri Jan 17 2020 - 07:45:10 PST)
- Daniel Roe (Fri Jan 17 2020 - 07:35:57 PST)
- Yinglong Miao (Fri Jan 17 2020 - 07:09:34 PST)
- Daniel Roe (Fri Jan 17 2020 - 06:41:09 PST)
- Daniel Roe (Fri Jan 17 2020 - 06:37:12 PST)
- Daniel Roe (Fri Jan 17 2020 - 06:34:12 PST)
- yinglong.miao.gmail.com (Tue Jan 14 2020 - 09:34:22 PST)
- Yinglong Miao (Tue Jan 14 2020 - 08:05:11 PST)
- Daniel Roe (Tue Jan 14 2020 - 07:46:30 PST)
- Yinglong Miao (Mon Jan 13 2020 - 17:10:04 PST)
- Daniel Roe (Mon Jan 13 2020 - 16:20:42 PST)
- yinglong.miao.gmail.com (Mon Jan 13 2020 - 15:50:49 PST)
[AMBER] esp charge
- Rui Chen (Fri Jan 03 2020 - 16:49:52 PST)
[AMBER] ff99SBnmr2 Force field implemented in AMBER18
- Carlos Simmerling (Fri Jan 10 2020 - 17:58:30 PST)
- Lod King (Fri Jan 10 2020 - 17:41:14 PST)
[AMBER] Fwd: CalcError: /truba/sw/centos6.4/app/amber/amber14/bin/sander failed with prmtop gas.complex.prmtop!
- Rana Rehan Khalid (Mon Jan 27 2020 - 08:51:02 PST)
[AMBER] Fwd: Periodic box problem when simulating Membrane system
- Tiejun Wei (Mon Jan 13 2020 - 06:26:41 PST)
[AMBER] Fwd: Problems using groups to provide centre for solvent caps in tLeap
- David Wright (Tue Jan 07 2020 - 03:41:40 PST)
- David Case (Mon Jan 06 2020 - 06:34:20 PST)
- David Wright (Mon Jan 06 2020 - 03:37:59 PST)
[AMBER] gaff with and without gaff atom types
- Erdem Yeler (Tue Jan 07 2020 - 00:27:24 PST)
- David Case (Sun Jan 05 2020 - 10:42:28 PST)
- Erdem Yeler (Sun Jan 05 2020 - 08:32:08 PST)
[AMBER] Generalized Born and entropy
- Carlos Simmerling (Mon Jan 13 2020 - 05:04:43 PST)
- Rosellen, Martin (Mon Jan 13 2020 - 04:48:19 PST)
- David Case (Wed Jan 08 2020 - 07:30:25 PST)
- Martin Rosellen (Wed Jan 08 2020 - 06:03:51 PST)
[AMBER] generating g-quadruplex DNA structures from a sequence
- Satyaseelan C (Thu Jan 23 2020 - 00:53:24 PST)
- Vaibhav Dixit (Wed Jan 22 2020 - 21:09:14 PST)
- David Case (Wed Jan 22 2020 - 05:05:18 PST)
- Vaibhav Dixit (Tue Jan 21 2020 - 22:51:39 PST)
[AMBER] Generating parameters for iron-sulfur protein
- Pengfei Li (Sat Jan 18 2020 - 16:39:57 PST)
- Baker, Joseph (Tue Jan 14 2020 - 20:51:28 PST)
[AMBER] Glycoprotein MD error in Amber18: an illegal memory access was encountered launching kernel kNLSkinTest
- zizhang sheng (Tue Jan 07 2020 - 07:47:45 PST)
[AMBER] Glycosylation issue: Atom xx was assigned a lower molecule # than previous atom.
- Lachele Foley (Fri Jan 03 2020 - 15:49:35 PST)
- zz sheng (Fri Jan 03 2020 - 15:43:14 PST)
- Lachele Foley (Fri Jan 03 2020 - 14:44:14 PST)
- zizhang sheng (Fri Jan 03 2020 - 13:44:04 PST)
[AMBER] gnuplot
- MYRIAN TORRES RICO (Wed Jan 29 2020 - 02:18:56 PST)
- MYRIAN TORRES RICO (Wed Jan 29 2020 - 02:17:48 PST)
[AMBER] GPU-AMBER18 installation on RTX2080Ti
- ke.gohda.camm-kansai.org (Mon Jan 20 2020 - 03:30:38 PST)
- Ross Walker (Sat Jan 18 2020 - 11:32:13 PST)
- ke.gohda.camm-kansai.org (Sat Jan 18 2020 - 02:29:48 PST)
[AMBER] Harmless bug in Lipid11-17 residue libraries causing tleap to split fragments in saved PDB
- Matias Machado (Wed Jan 15 2020 - 08:32:38 PST)
[AMBER] Help building a model of a 2F-2S protein with MDPB.py
- MENDOZA Cesar (Wed Jan 29 2020 - 12:27:36 PST)
- MENDOZA Cesar (Wed Jan 29 2020 - 12:25:47 PST)
- Gustavo Seabra (Wed Jan 29 2020 - 10:57:18 PST)
[AMBER] hiii
- David Case (Sat Jan 04 2020 - 14:18:12 PST)
- ankita mehta (Sat Jan 04 2020 - 05:54:40 PST)
[AMBER] hiiiii
- ankita mehta (Sun Jan 05 2020 - 23:43:51 PST)
- Cory Ayres (Mon Jan 06 2020 - 03:19:12 PST)
- ankita mehta (Sun Jan 05 2020 - 20:02:52 PST)
- David Case (Sun Jan 05 2020 - 10:32:44 PST)
- ankita mehta (Sun Jan 05 2020 - 07:37:54 PST)
- Carlos Simmerling (Sun Jan 05 2020 - 07:28:38 PST)
- ankita mehta (Sun Jan 05 2020 - 07:20:44 PST)
- Carlos Simmerling (Sun Jan 05 2020 - 06:32:56 PST)
- ankita mehta (Sun Jan 05 2020 - 06:18:43 PST)
- David Case (Sun Jan 05 2020 - 05:47:26 PST)
- ankita mehta (Sat Jan 04 2020 - 23:01:39 PST)
[AMBER] hiiiiii
- ankita mehta (Sat Jan 04 2020 - 07:17:42 PST)
[AMBER] how does one reply to a thread in a mailing list
- David Case (Wed Jan 29 2020 - 11:08:18 PST)
- Homeo Morphism (Wed Jan 29 2020 - 07:26:57 PST)
[AMBER] How to use polarizable water model in Amber 18?
- David Case (Sun Jan 19 2020 - 17:46:57 PST)
- Markowska (Sat Jan 18 2020 - 10:01:14 PST)
- Markowska (Fri Jan 17 2020 - 00:22:11 PST)
- Carlos Simmerling (Wed Jan 15 2020 - 10:23:48 PST)
- Matias Machado (Wed Jan 15 2020 - 08:46:11 PST)
- Markowska (Wed Jan 15 2020 - 05:39:39 PST)
[AMBER] installing amber on wsl
- Ayesha Fatima (Mon Jan 13 2020 - 06:59:49 PST)
- Ayesha Fatima (Sun Jan 12 2020 - 22:54:28 PST)
- ALAMGIR KHAN (Sun Jan 12 2020 - 20:04:17 PST)
- David Case (Sun Jan 12 2020 - 11:56:35 PST)
- Ayesha Fatima (Sun Jan 12 2020 - 05:29:26 PST)
[AMBER] Is error bar necessary for umbrella sampling?
- Carlos Simmerling (Tue Jan 14 2020 - 03:30:35 PST)
- Qing Lv (Mon Jan 13 2020 - 18:48:06 PST)
- Carlos Simmerling (Mon Jan 13 2020 - 06:42:49 PST)
- Qing Lv (Mon Jan 13 2020 - 06:36:15 PST)
[AMBER] Is minimization and equilibration needed in umbrella sampling?
- Qing Lv (Fri Jan 10 2020 - 07:46:29 PST)
[AMBER] Is NPT ensemble necessary for the protein-water system?
- Qing Lv (Fri Jan 10 2020 - 07:55:57 PST)
[AMBER] Is there any sense in even trying to model large conformational dynamics with molecular dynamics?
- Carlos Simmerling (Mon Jan 20 2020 - 11:59:07 PST)
- Gerardo Zerbetto De Palma (Mon Jan 20 2020 - 11:24:30 PST)
- Homeo Morphism (Mon Jan 20 2020 - 11:15:52 PST)
[AMBER] Issues with Umbrella Sampling Simulations involving lipid bilayer
- Charles Lin (Tue Jan 21 2020 - 06:30:36 PST)
- Stephan Schott (Mon Jan 20 2020 - 07:01:36 PST)
- Casalini Tommaso (Fri Jan 17 2020 - 01:24:23 PST)
- Stephan Schott (Thu Jan 16 2020 - 14:37:43 PST)
- Casalini Tommaso (Thu Jan 16 2020 - 04:37:26 PST)
- Stephan Schott (Thu Jan 16 2020 - 04:13:59 PST)
- Casalini Tommaso (Thu Jan 16 2020 - 01:30:58 PST)
[AMBER] kindly guide me
- ALAMGIR KHAN (Wed Jan 29 2020 - 01:43:08 PST)
- Gustaf Olsson (Tue Jan 28 2020 - 22:42:49 PST)
- ALAMGIR KHAN (Tue Jan 28 2020 - 21:00:54 PST)
[AMBER] ligand clustering
- Neha Gandhi (Wed Jan 01 2020 - 21:47:51 PST)
[AMBER] ligand split
- MYRIAN TORRES RICO (Fri Jan 17 2020 - 07:32:27 PST)
- Carlos Simmerling (Fri Jan 17 2020 - 07:24:07 PST)
- MYRIAN TORRES RICO (Fri Jan 17 2020 - 07:15:52 PST)
- Carlos Simmerling (Wed Jan 15 2020 - 10:22:33 PST)
- MYRIAN TORRES RICO (Wed Jan 15 2020 - 04:52:20 PST)
- Carlos Simmerling (Wed Jan 15 2020 - 03:07:00 PST)
- MYRIAN TORRES RICO (Wed Jan 15 2020 - 02:44:40 PST)
- Carlos Simmerling (Wed Jan 15 2020 - 02:31:48 PST)
- MYRIAN TORRES RICO (Wed Jan 15 2020 - 02:26:22 PST)
- David Case (Tue Jan 14 2020 - 11:25:48 PST)
- MYRIAN TORRES RICO (Tue Jan 14 2020 - 09:07:35 PST)
[AMBER] Lipid bilayer imaging problem
- Bhat Zahoor (Thu Jan 09 2020 - 04:59:41 PST)
- Chetna Tyagi (Thu Jan 09 2020 - 03:48:47 PST)
- Bhat Zahoor (Thu Jan 09 2020 - 03:58:07 PST)
[AMBER] Long syntax error on complex molecule
- Thomas Cheatham (Fri Jan 17 2020 - 20:11:19 PST)
- Manisha Yadav (Fri Jan 17 2020 - 20:00:20 PST)
[AMBER] MD error in Amber18: an illegal memory access was encountered launching kernel kNLSkinTest
- zizhang sheng (Fri Jan 10 2020 - 13:43:01 PST)
- David Case (Fri Jan 10 2020 - 12:54:26 PST)
- zizhang sheng (Fri Jan 10 2020 - 09:29:32 PST)
- David Case (Thu Jan 09 2020 - 10:01:48 PST)
- zizhang sheng (Thu Jan 09 2020 - 06:18:32 PST)
[AMBER] Membrane simulation with PSM
- cpimenta (Wed Jan 15 2020 - 11:09:24 PST)
[AMBER] MMPBSA error
- Ray Luo (Sat Jan 04 2020 - 17:41:50 PST)
- Rui Chen (Fri Jan 03 2020 - 12:59:10 PST)
- Ray Luo (Fri Jan 03 2020 - 12:05:06 PST)
- Rui Chen (Fri Jan 03 2020 - 08:58:42 PST)
- Ray Luo (Thu Jan 02 2020 - 22:15:58 PST)
- Rui Chen (Thu Jan 02 2020 - 21:37:14 PST)
- Ray Luo (Thu Jan 02 2020 - 16:37:15 PST)
- Rui Chen (Thu Jan 02 2020 - 16:27:54 PST)
[AMBER] MMPBSA run failure
- Billiot, Eugene (Sat Jan 18 2020 - 04:45:31 PST)
[AMBER] MMPBSA standard deviation (Geng Dong)
- Ray Luo (Sun Jan 05 2020 - 07:46:29 PST)
- 东庚 (Sun Jan 05 2020 - 03:30:01 PST)
[AMBER] modeling a Schiff base with GAFF atom types
- David Case (Wed Jan 15 2020 - 05:54:42 PST)
- Sally Pias (Tue Jan 14 2020 - 15:16:57 PST)
[AMBER] Molecule is wrapped out of the cell.
- Petro (Tue Jan 07 2020 - 09:32:41 PST)
- David Case (Mon Jan 06 2020 - 07:07:43 PST)
- Petro (Mon Jan 06 2020 - 02:44:51 PST)
[AMBER] Multiple GPU imstallation of AMBER 18 error
- Elvis Martis (Sat Jan 25 2020 - 18:45:45 PST)
- Sruthi Sudhakar (Fri Jan 24 2020 - 22:25:09 PST)
- Sruthi Sudhakar (Fri Jan 24 2020 - 20:48:14 PST)
- Elvis Martis (Fri Jan 24 2020 - 03:51:15 PST)
- Sruthi Sudhakar (Fri Jan 24 2020 - 02:13:20 PST)
- Sruthi Sudhakar (Thu Jan 23 2020 - 07:53:41 PST)
- Elvis Martis (Thu Jan 23 2020 - 07:38:03 PST)
- Sruthi Sudhakar (Thu Jan 23 2020 - 07:24:01 PST)
- David Case (Thu Jan 23 2020 - 06:39:31 PST)
- Elvis Martis (Thu Jan 23 2020 - 05:15:11 PST)
- Sruthi Sudhakar (Thu Jan 23 2020 - 03:39:54 PST)
- Sruthi Sudhakar (Thu Jan 23 2020 - 02:10:05 PST)
- Sruthi Sudhakar (Thu Jan 23 2020 - 02:08:46 PST)
- Elvis Martis (Thu Jan 23 2020 - 01:33:20 PST)
- Sruthi Sudhakar (Thu Jan 23 2020 - 00:17:11 PST)
- Elvis Martis (Thu Jan 23 2020 - 00:06:36 PST)
- Sruthi Sudhakar (Wed Jan 22 2020 - 22:54:08 PST)
[AMBER] NEB Simulations in Amber
- Carlos Simmerling (Mon Jan 20 2020 - 13:55:31 PST)
- SHAUNAK BADANI (Mon Jan 20 2020 - 12:25:26 PST)
[AMBER] NMR distance restrained MD
- maya nair (Tue Jan 28 2020 - 23:44:59 PST)
- maya nair (Mon Jan 06 2020 - 04:21:57 PST)
- maya nair (Mon Jan 06 2020 - 04:17:14 PST)
- Christina Bergonzo (Thu Jan 02 2020 - 05:45:30 PST)
- David Case (Thu Jan 02 2020 - 05:41:00 PST)
- maya nair (Wed Jan 01 2020 - 23:56:32 PST)
[AMBER] Normal mode analysis using trajectory files
- Elvis Martis (Thu Jan 23 2020 - 00:08:52 PST)
- Divya Rai (Wed Jan 22 2020 - 22:26:31 PST)
[AMBER] NPT density equilibration
- Debarati DasGupta (Wed Jan 08 2020 - 12:43:00 PST)
[AMBER] P2 correlation functions questions
- David Case (Tue Jan 07 2020 - 18:29:27 PST)
- erik zuiderweg (Tue Jan 07 2020 - 09:08:28 PST)
[AMBER] Parameter Files for Nanopore made of Si3N4(Silicon Nitride)
- Vishal Reddy (Thu Jan 23 2020 - 02:05:25 PST)
[AMBER] parameters for Si3N4
- Akshay Prabhakant (Mon Jan 13 2020 - 08:38:24 PST)
[AMBER] parmed issue
- David Case (Sat Jan 04 2020 - 14:16:27 PST)
- Ayesha Fatima (Sat Jan 04 2020 - 05:50:11 PST)
[AMBER] pdb to mol2 conversion via antechamber
- Liao (Fri Jan 17 2020 - 00:20:02 PST)
- Sruthi Sudhakar (Thu Jan 16 2020 - 22:54:51 PST)
[AMBER] Periodic box problem when simulating Membrane system
- Bhat Zahoor (Mon Jan 13 2020 - 07:09:40 PST)
- Gustaf Olsson (Mon Jan 13 2020 - 06:44:36 PST)
[AMBER] pmemd.cuda.MPI run error
- Sruthi Sudhakar (Mon Jan 27 2020 - 05:11:08 PST)
- Gerardo Zerbetto De Palma (Mon Jan 27 2020 - 04:31:08 PST)
- Sruthi Sudhakar (Mon Jan 27 2020 - 04:55:00 PST)
- Sruthi Sudhakar (Mon Jan 27 2020 - 04:49:12 PST)
- Elvis Martis (Mon Jan 27 2020 - 03:58:28 PST)
- Gerardo Zerbetto De Palma (Mon Jan 27 2020 - 03:52:05 PST)
- Sruthi Sudhakar (Mon Jan 27 2020 - 04:21:04 PST)
[AMBER] pmemd.cuda:command not found
- Liao (Sat Jan 04 2020 - 23:56:35 PST)
- Sruthi Sudhakar (Sat Jan 04 2020 - 23:28:32 PST)
[AMBER] postdoc DNA/RNA simulations
- Nicolas Feldman (Thu Jan 30 2020 - 10:14:06 PST)
- Jiri Sponer (Thu Jan 30 2020 - 09:36:31 PST)
[AMBER] printing charges in pdb
- Vaibhav Dixit (Mon Jan 06 2020 - 09:04:05 PST)
- David Case (Mon Jan 06 2020 - 07:04:07 PST)
- Vaibhav Dixit (Mon Jan 06 2020 - 01:44:53 PST)
[AMBER] Problem in Amber update
- Kshatresh Dutta Dubey (Sun Jan 19 2020 - 05:14:27 PST)
- David Case (Sat Jan 18 2020 - 05:27:10 PST)
- Kshatresh Dutta Dubey (Sat Jan 18 2020 - 00:07:50 PST)
[AMBER] Problem regarding umbrella sampling
- David Case (Mon Jan 20 2020 - 05:44:45 PST)
- Rituparna Roy (Sun Jan 19 2020 - 20:31:13 PST)
- roomno sixtysix (Sun Jan 19 2020 - 06:45:41 PST)
[AMBER] Problems using groups to provide centre for solvent caps in tLeap
- David Wright (Sat Jan 04 2020 - 05:10:03 PST)
[AMBER] query
- ankita mehta (Fri Jan 03 2020 - 02:50:20 PST)
- ankita mehta (Fri Jan 03 2020 - 02:42:39 PST)
- David Case (Thu Jan 02 2020 - 12:13:55 PST)
- ankita mehta (Thu Jan 02 2020 - 08:45:08 PST)
[AMBER] Question about addtobox
- David Case (Thu Jan 09 2020 - 10:03:14 PST)
- David Cerutti (Thu Jan 09 2020 - 06:52:13 PST)
- Petro (Wed Jan 08 2020 - 15:19:41 PST)
- David Case (Wed Jan 08 2020 - 07:22:21 PST)
- Petro (Tue Jan 07 2020 - 22:28:09 PST)
[AMBER] RDF: corrupted trajectory
- emanuele falbo (Wed Jan 22 2020 - 01:40:51 PST)
- Daniel Roe (Tue Jan 21 2020 - 11:00:46 PST)
- emanuele falbo (Mon Jan 20 2020 - 02:24:06 PST)
- Daniel Roe (Fri Jan 17 2020 - 10:47:57 PST)
- emanuele falbo (Fri Jan 17 2020 - 08:02:09 PST)
[AMBER] Reg. Centering of Molecule and Periodic Boundary Conditions
- Daniel Roe (Thu Jan 16 2020 - 12:26:02 PST)
- DHEERAJ CHITARA (Thu Jan 16 2020 - 00:46:32 PST)
[AMBER] Reg. working of Periodic Boundary Conditions
- David Case (Tue Jan 21 2020 - 09:38:10 PST)
- DHEERAJ CHITARA (Tue Jan 21 2020 - 06:25:23 PST)
[AMBER] Regarding clustering using mmtsb toolkit
- David Case (Thu Jan 02 2020 - 05:35:57 PST)
- Carlos Simmerling (Thu Jan 02 2020 - 04:58:17 PST)
- Sruthi Sudhakar (Wed Jan 01 2020 - 22:37:22 PST)
[AMBER] Resolving overlapping atoms.
- Petro (Thu Jan 09 2020 - 10:19:36 PST)
- David Case (Thu Jan 09 2020 - 06:23:04 PST)
- Petro (Thu Jan 09 2020 - 01:54:12 PST)
[AMBER] RESP fitting
- Elvis Martis (Wed Jan 15 2020 - 04:53:12 PST)
- Sruthi Sudhakar (Wed Jan 15 2020 - 04:58:56 PST)
[AMBER] rror: an illegal memory access was encountered launching kernel kNLSkinTest
- David Case (Sat Jan 18 2020 - 05:31:36 PST)
- Sruthi Sudhakar (Sat Jan 18 2020 - 04:30:58 PST)
[AMBER] saxs
- Adrian Roitberg (Tue Jan 07 2020 - 12:41:25 PST)
[AMBER] saxs_md
- Christina Bergonzo (Wed Jan 08 2020 - 09:25:11 PST)
- Buteler,Maria del Pilar (Wed Jan 08 2020 - 08:49:02 PST)
[AMBER] Semi-empirical QMMD on all molecules
- Goetz, Andreas (Fri Jan 03 2020 - 03:36:43 PST)
- Abdullah Faheem (Thu Jan 02 2020 - 23:43:39 PST)
[AMBER] Several alpha-helices stitched together - how would you stress-test it with MD?
- Carlos Simmerling (Tue Jan 28 2020 - 02:52:49 PST)
- Homeo Morphism (Tue Jan 28 2020 - 02:48:35 PST)
[AMBER] Shaw DE RNA ff in Amber format
- amirhossein taghavi (Thu Jan 23 2020 - 13:59:17 PST)
[AMBER] sqm calculation with external charges not working
- Goetz, Andreas (Tue Jan 21 2020 - 21:58:43 PST)
- Anthony Bogetti (Mon Jan 20 2020 - 07:53:08 PST)
[AMBER] steered MD question
- Baker, Joseph (Thu Jan 23 2020 - 12:10:50 PST)
[AMBER] sulfonamide parameters for correct geometry
- Annachiara TINIVELLA (Wed Jan 29 2020 - 04:31:25 PST)
[AMBER] TI data collection of DU/Dlambda at constant volume
- Debarati DasGupta (Tue Jan 07 2020 - 09:00:20 PST)
[AMBER] Tleap naming problem
- David Case (Thu Jan 02 2020 - 05:30:41 PST)
- Rui Chen (Wed Jan 01 2020 - 13:19:00 PST)
[AMBER] Tracking ligand position throughout equilibration stages
- Carlos Simmerling (Mon Jan 13 2020 - 02:29:32 PST)
- Dr. Anselm Horn (Mon Jan 13 2020 - 01:34:40 PST)
- Debarati DasGupta (Sat Jan 11 2020 - 07:21:37 PST)
[AMBER] Umbrella sampling sufficient overlap test
- Martin Rosellen (Mon Jan 06 2020 - 04:20:06 PST)
[AMBER] usefrcascoords calculations
- Lambach, Lauren (Thu Jan 30 2020 - 14:25:28 PST)
[AMBER] ValueError: could not convert string to float: ********* Error occured on rank 0. Exiting. All files have been retained.
- David Case (Thu Jan 16 2020 - 05:36:00 PST)
- Neha Gandhi (Wed Jan 15 2020 - 20:35:09 PST)
[AMBER] vanilla Nose-Hoover thermostat availability
- Sally Pias (Wed Jan 22 2020 - 17:41:00 PST)
- David Case (Fri Jan 17 2020 - 06:43:07 PST)
- Sally Pias (Thu Jan 16 2020 - 14:19:39 PST)
[AMBER] Wanting to get synchronized trajectory files
- Abdullah Bin Faheem (Wed Jan 22 2020 - 10:58:14 PST)
- Carlos Simmerling (Wed Jan 22 2020 - 09:10:16 PST)
- Abdullah Bin Faheem (Wed Jan 22 2020 - 08:06:01 PST)
- Carlos Simmerling (Wed Jan 22 2020 - 07:43:43 PST)
- Abdullah Bin Faheem (Wed Jan 22 2020 - 07:05:28 PST)
- Gustaf Olsson (Wed Jan 22 2020 - 05:47:36 PST)
- David Case (Wed Jan 22 2020 - 05:09:18 PST)
- Abdullah Bin Faheem (Wed Jan 22 2020 - 02:53:50 PST)
[AMBER] weights for the lambda values
- Carlos Simmerling (Fri Jan 10 2020 - 03:30:35 PST)
- Debarati DasGupta (Thu Jan 09 2020 - 11:30:49 PST)
[AMBER] Workshop on Free Energy calculations in Muenster March 11-13 2020
- Vlad Cojocaru (Fri Jan 17 2020 - 01:32:27 PST)
NPT density equilibration
- Debarati DasGupta (Wed Jan 08 2020 - 12:44:41 PST)

Amber Archive Jan 2020 by subject