Amber Archive Apr 2018: by subject

[AMBER] "bad atom type: DU" error
- Elvis Martis (Fri Apr 13 2018 - 21:43:04 PDT)
- Sharon D. Morris (Fri Apr 13 2018 - 21:25:35 PDT)
[AMBER] (pmemd.cuda.MPI) Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
- David A Case (Sun Apr 15 2018 - 13:36:37 PDT)
- Amen Shamim (Sun Apr 15 2018 - 06:30:42 PDT)
[AMBER] A Problem about Alanine Scan of Proline
- 忠彦 (Wed Apr 04 2018 - 04:55:01 PDT)
[AMBER] accelerated MD cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered
- David A Case (Sat Apr 21 2018 - 06:02:10 PDT)
- David Cerutti (Fri Apr 20 2018 - 20:08:30 PDT)
- Ashutosh Shandilya (Fri Apr 20 2018 - 14:59:09 PDT)
[AMBER] Aligning frames and printing pdb files
- David A Case (Thu Apr 19 2018 - 10:58:43 PDT)
- Christopher Warren (Thu Apr 19 2018 - 10:04:05 PDT)
[AMBER] AMBER Digest, Vol 2256, Issue 1
- Sehrish Naz (Tue Apr 10 2018 - 07:01:01 PDT)
[AMBER] AMBER Digest, Vol 2271, Issue 1
- David A Case (Thu Apr 26 2018 - 10:12:21 PDT)
- Kadir Ozcan (Thu Apr 26 2018 - 09:07:59 PDT)
[AMBER] Amber Lipid Force Field Tutorial: update?
- Matthias.Nachtschatt.csiro.au (Thu Apr 26 2018 - 19:35:23 PDT)
[AMBER] Amber16+AT17: Several checks failing w/Intel Parallel Studio XE 2018.1
- David A Case (Mon Apr 09 2018 - 06:14:20 PDT)
[AMBER] Amber18 and Amber14
- David A Case (Fri Apr 20 2018 - 09:13:47 PDT)
- Günther H.J. Peters (Fri Apr 20 2018 - 08:48:56 PDT)
[AMBER] Amber18 and Titan V graphic cards
- Nikolay N. Kuzmich (Thu Apr 26 2018 - 06:19:50 PDT)
- David Cerutti (Mon Apr 23 2018 - 05:59:46 PDT)
- Nikolay N. Kuzmich (Mon Apr 23 2018 - 05:24:48 PDT)
[AMBER] Amber94 charges for neutral amino acids
- FyD (Fri Apr 13 2018 - 21:58:18 PDT)
- Rinsha Chk (Fri Apr 13 2018 - 21:33:23 PDT)
[AMBER] AmberError: FLAG ATOMIC_NUMBER
- Sharon D. Morris (Wed Apr 25 2018 - 23:14:24 PDT)
[AMBER] Ambertools17 error: 3D-RISM calculation
- David A Case (Thu Apr 12 2018 - 04:51:56 PDT)
- Leena Aggarwal (Thu Apr 12 2018 - 04:51:08 PDT)
- Fabian Herrera Olivares (Thu Apr 12 2018 - 00:49:40 PDT)
[AMBER] Amino acid GROMACS topology file
- roja rahmani (Mon Apr 23 2018 - 22:09:37 PDT)
- David A Case (Mon Apr 23 2018 - 14:41:48 PDT)
- roja rahmani (Mon Apr 23 2018 - 13:08:01 PDT)
- roja rahmani (Mon Apr 23 2018 - 06:50:41 PDT)
[AMBER] Analyzing Multidimensional REMD Simulations
- Christina Bergonzo (Wed Apr 25 2018 - 05:51:39 PDT)
- Jason Ku Wang (Wed Apr 25 2018 - 02:58:06 PDT)
[AMBER] Are the equations for FF14SB and FF15IPQ same or different
- David A Case (Wed Apr 04 2018 - 08:05:55 PDT)
- Dmitry Suplatov (Wed Apr 04 2018 - 06:32:52 PDT)
[AMBER] Atom position changes when setting up QM/MM calculation
- James Kress (Wed Apr 25 2018 - 11:19:03 PDT)
- Goetz, Andreas (Tue Apr 24 2018 - 22:26:38 PDT)
- David A Case (Tue Apr 24 2018 - 18:09:52 PDT)
- James Kress (Tue Apr 24 2018 - 11:37:54 PDT)
[AMBER] atomic radius data in amber library
- Rakesh Srivastava (Sat Apr 07 2018 - 21:49:10 PDT)
- David A Case (Sat Apr 07 2018 - 08:09:03 PDT)
- Rakesh Srivastava (Sat Apr 07 2018 - 03:51:09 PDT)
[AMBER] ATP hydrolysis
- Abhilash J (Wed Apr 11 2018 - 00:42:36 PDT)
[AMBER] average between structures with different residue numbering
- Rosellen, Martin (Mon Apr 23 2018 - 08:30:37 PDT)
- Rosellen, Martin (Mon Apr 23 2018 - 08:03:35 PDT)
- Daniel Roe (Mon Apr 23 2018 - 07:58:19 PDT)
- Rosellen, Martin (Mon Apr 23 2018 - 07:43:54 PDT)
- Daniel Roe (Mon Apr 23 2018 - 07:30:48 PDT)
- Rosellen, Martin (Mon Apr 23 2018 - 07:22:22 PDT)
- Daniel Roe (Mon Apr 23 2018 - 06:43:24 PDT)
- Rosellen, Martin (Mon Apr 23 2018 - 04:31:52 PDT)
[AMBER] Boost not linking when compiling on Mac
- Scott Brozell (Fri Apr 27 2018 - 11:12:45 PDT)
- Gustaf Olsson (Fri Apr 27 2018 - 06:55:43 PDT)
- Stephan Schott (Fri Apr 27 2018 - 04:11:18 PDT)
- Gustaf Olsson (Thu Apr 26 2018 - 23:37:05 PDT)
- Hai Nguyen (Thu Apr 26 2018 - 12:18:14 PDT)
- David A Case (Thu Apr 26 2018 - 11:24:36 PDT)
- Stephan Schott (Thu Apr 26 2018 - 10:21:37 PDT)
- Gustaf Olsson (Thu Apr 26 2018 - 02:43:58 PDT)
- Gustaf Olsson (Thu Apr 26 2018 - 02:38:52 PDT)
- Stephan Schott (Thu Apr 26 2018 - 01:59:24 PDT)
- Gustaf Olsson (Thu Apr 26 2018 - 00:32:52 PDT)
- Hai Nguyen (Wed Apr 25 2018 - 16:26:55 PDT)
- Stephan Schott (Wed Apr 25 2018 - 07:53:54 PDT)
- Gustaf Olsson (Wed Apr 25 2018 - 06:25:42 PDT)
- David A Case (Wed Apr 25 2018 - 05:53:46 PDT)
- Gustaf Olsson (Wed Apr 25 2018 - 02:53:11 PDT)
[AMBER] Brand new GPU card testing
- Nikolay N. Kuzmich (Mon Apr 23 2018 - 03:09:21 PDT)
- Ross Walker (Fri Apr 20 2018 - 14:43:34 PDT)
- Nikolay N. Kuzmich (Fri Apr 20 2018 - 04:25:41 PDT)
- Ross Walker (Thu Apr 19 2018 - 05:11:50 PDT)
- Nikolay N. Kuzmich (Thu Apr 19 2018 - 00:28:06 PDT)
[AMBER] Building Amber16 CPU with Intel Compiler and GPU with GNU Compiler vs. MPI
- Scott Brozell (Sat Apr 14 2018 - 14:36:28 PDT)
- Daniel Roe (Fri Apr 13 2018 - 08:05:22 PDT)
- Ryan Novosielski (Thu Apr 12 2018 - 10:14:20 PDT)
[AMBER] Calculate minimum distance between two groups of atoms
- Daniel Roe (Tue Apr 10 2018 - 06:36:32 PDT)
- David Sáez (Sat Apr 07 2018 - 05:09:34 PDT)
- Daniel Roe (Thu Apr 05 2018 - 14:31:42 PDT)
- David Sáez (Thu Apr 05 2018 - 14:13:55 PDT)
[AMBER] Calculate water density in the protein water channel by Amber 16
- Daniel Roe (Tue Apr 10 2018 - 06:32:05 PDT)
[AMBER] Call for Papers, GCC 2018, 14th German Conference on Chemoinformatics
- Stefan.Guessregen.sanofi.com (Wed Apr 25 2018 - 05:35:41 PDT)
[AMBER] center of mass restraint in pmemd.cuda
- Rajarshi Roy (Tue Apr 03 2018 - 23:27:13 PDT)
[AMBER] Changing box size
- David A Case (Thu Apr 05 2018 - 07:53:23 PDT)
- M Conte (Wed Apr 04 2018 - 17:47:13 PDT)
[AMBER] Charmm36 modified forcefield in Amber
- David A Case (Tue Apr 24 2018 - 05:19:22 PDT)
- Midhun K Madhu (Tue Apr 24 2018 - 03:05:10 PDT)
[AMBER] Configure cuda
- David A Case (Fri Apr 27 2018 - 05:07:31 PDT)
- Kadir Ozcan (Thu Apr 26 2018 - 12:38:26 PDT)
- David A Case (Mon Apr 23 2018 - 17:51:51 PDT)
- Kadir Ozcan (Mon Apr 23 2018 - 11:41:27 PDT)
- David A Case (Fri Apr 20 2018 - 05:22:20 PDT)
- Kadir Ozcan (Thu Apr 19 2018 - 07:26:50 PDT)
- David A Case (Mon Apr 16 2018 - 17:58:16 PDT)
- Kadir Ozcan (Mon Apr 16 2018 - 16:53:15 PDT)
[AMBER] Configure cuda (David A Case)
- David A Case (Tue Apr 17 2018 - 13:45:33 PDT)
- Kadir Ozcan (Tue Apr 17 2018 - 12:27:37 PDT)
[AMBER] Constant Redox potential MD simulations
- Cruzeiro,Vinicius Wilian D (Sun Apr 22 2018 - 12:15:23 PDT)
- Fernando Ogata (Sat Apr 21 2018 - 14:20:51 PDT)
[AMBER] Continuous hydrogen bond time correlation function S(t)
- Tousif Hossen (Sat Apr 28 2018 - 04:07:06 PDT)
[AMBER] convert psf to prmtop
- Jason Swails (Tue Apr 17 2018 - 05:52:35 PDT)
- David A Case (Mon Apr 16 2018 - 18:06:55 PDT)
- Ashutosh Shandilya (Mon Apr 16 2018 - 17:00:04 PDT)
[AMBER] Converting gromacs TRX file to mdcrd.nc and mdvel.nc
- Daniel Roe (Tue Apr 10 2018 - 06:34:05 PDT)
- Mohd Farid Ismail (Wed Apr 04 2018 - 03:20:15 PDT)
[AMBER] Count water in active site
- Daniel Roe (Tue Apr 10 2018 - 06:17:39 PDT)
[AMBER] Cpptraj and Sander Question
- Portillo, Jennifer (Mon Apr 16 2018 - 14:10:42 PDT)
- David A Case (Wed Apr 11 2018 - 05:15:53 PDT)
- Portillo, Jennifer (Tue Apr 10 2018 - 17:24:58 PDT)
[AMBER] Cremer Pucker values using Pytraj
- Hai Nguyen (Mon Apr 30 2018 - 14:26:32 PDT)
- Vivek Bharadwaj (Mon Apr 30 2018 - 11:13:38 PDT)
[AMBER] eCheminfo Milano July 16-29, Training and Innovation Course in Drug Design 2018, bursary and early-bird deadline ending soon
- Thomas Exner (Thu Apr 19 2018 - 03:40:13 PDT)
[AMBER] Error compiling AmberTools18 cpptraj with Intel 16
- Niel Henriksen (Fri Apr 20 2018 - 10:10:39 PDT)
- Daniel Roe (Fri Apr 20 2018 - 05:37:09 PDT)
- David A Case (Fri Apr 20 2018 - 04:58:36 PDT)
- Niel Henriksen (Thu Apr 19 2018 - 07:34:38 PDT)
[AMBER] Error generating gau_job.inp
- Giovanni Grazioso (Thu Apr 19 2018 - 03:16:47 PDT)
[AMBER] ERROR TUTORIAL AMBER --- Step 3.3.3) "Visualizing the trajectories with VMD"
- Edjan Silva (Thu Apr 12 2018 - 08:05:41 PDT)
- David A Case (Sat Apr 07 2018 - 08:02:11 PDT)
- Diego Gomes (Fri Apr 06 2018 - 05:20:12 PDT)
- Edjan Silva (Fri Apr 06 2018 - 05:07:09 PDT)
[AMBER] Extracting forces from the mdcrd file
- Nikolay N. Kuzmich (Fri Apr 13 2018 - 15:08:14 PDT)
- Daniel Roe (Thu Apr 12 2018 - 08:28:02 PDT)
- Nikolay N. Kuzmich (Wed Apr 11 2018 - 06:09:49 PDT)
- Daniel Roe (Tue Apr 10 2018 - 06:14:12 PDT)
- Nikolay N. Kuzmich (Tue Apr 10 2018 - 03:41:16 PDT)
- Daniel Roe (Mon Apr 09 2018 - 11:53:54 PDT)
- Nikolay N. Kuzmich (Mon Apr 09 2018 - 10:09:01 PDT)
- Daniel Roe (Mon Apr 09 2018 - 05:13:08 PDT)
- Nikolay N. Kuzmich (Mon Apr 09 2018 - 04:28:06 PDT)
[AMBER] Fix for fixed sized cmd in nab
- David A Case (Mon Apr 09 2018 - 06:01:43 PDT)
- Åke Sandgren (Thu Apr 05 2018 - 09:56:23 PDT)
- Åke Sandgren (Thu Apr 05 2018 - 03:35:29 PDT)
[AMBER] Forces on atoms
- David A Case (Sat Apr 28 2018 - 04:12:17 PDT)
- Yuliana Bosken (Sat Apr 28 2018 - 01:29:54 PDT)
[AMBER] Fwd: Paramfit issues - Improvement of R^2 value.
- David Cerutti (Mon Apr 30 2018 - 20:05:25 PDT)
- David Cerutti (Fri Apr 27 2018 - 07:43:58 PDT)
- Alechania Misturini (Fri Apr 27 2018 - 07:29:19 PDT)
[AMBER] Fwd: Postdoctoral Positions in Computational Biophysics at Westlake University
- Pengfei Li (Tue Apr 03 2018 - 09:00:38 PDT)
[AMBER] GPU
- Scott Brozell (Mon Apr 16 2018 - 11:56:25 PDT)
- David Cerutti (Mon Apr 16 2018 - 11:55:36 PDT)
- Atila Petrosian (Mon Apr 16 2018 - 11:13:23 PDT)
- Setyanto Md (Sun Apr 15 2018 - 15:22:42 PDT)
- Atila Petrosian (Sat Apr 14 2018 - 22:57:53 PDT)
- Scott Brozell (Sat Apr 14 2018 - 14:06:49 PDT)
- Atila Petrosian (Sat Apr 14 2018 - 08:59:32 PDT)
[AMBER] GTX 1080Ti Problem.
- David Cerutti (Sun Apr 29 2018 - 05:42:51 PDT)
- 汪盛 (Sun Apr 29 2018 - 03:16:54 PDT)
[AMBER] Help with building a non-standard RNA structure
- Debostuti Ghoshdastidar (Wed Apr 11 2018 - 23:52:47 PDT)
[AMBER] Help with mdcrd in VMD
- Abdul-Rashid III Sampaco (Sat Mar 31 2018 - 10:35:54 PDT)
[AMBER] How can I run PMEMD with multiple distance restraints?
- David A Case (Thu Apr 12 2018 - 09:55:20 PDT)
- Markowska (Thu Apr 12 2018 - 06:32:17 PDT)
[AMBER] How fast is Amber's new GPU code? Are CPUs ever coming back?
- Ross Walker (Wed Apr 18 2018 - 06:34:19 PDT)
- David A Case (Tue Apr 17 2018 - 13:40:18 PDT)
- David Cerutti (Tue Apr 17 2018 - 08:40:14 PDT)
[AMBER] How to solve the problem of molecule box jumping?
- Daniel Roe (Sat Apr 21 2018 - 09:52:27 PDT)
- g.bakrani.sci.ui.ac.ir (Fri Apr 20 2018 - 23:39:54 PDT)
- golshan bakrani (Wed Apr 18 2018 - 21:42:54 PDT)
[AMBER] installation problem
- David A Case (Fri Apr 20 2018 - 04:50:56 PDT)
- wuxc (Fri Apr 20 2018 - 01:53:06 PDT)
[AMBER] Issue running alanine scanning
- pancham lal Gupta (Thu Apr 26 2018 - 08:35:36 PDT)
- Núbia Prates (Wed Apr 25 2018 - 12:00:00 PDT)
- David A Case (Tue Apr 24 2018 - 18:15:57 PDT)
- Núbia Prates (Tue Apr 24 2018 - 14:49:23 PDT)
[AMBER] Jumping from simulation box
- Daniel Roe (Mon Apr 23 2018 - 06:50:01 PDT)
- g.bakrani.sci.ui.ac.ir (Sun Apr 22 2018 - 12:49:33 PDT)
[AMBER] mac installation problem
- Jiyong Su (Sun Apr 22 2018 - 18:41:28 PDT)
- Hai Nguyen (Sun Apr 22 2018 - 14:07:22 PDT)
- Jiyong Su (Sun Apr 22 2018 - 00:22:20 PDT)
- Jiyong Su (Sun Apr 22 2018 - 00:21:32 PDT)
- David A Case (Fri Apr 20 2018 - 04:44:28 PDT)
- Jiyong Su (Thu Apr 19 2018 - 21:54:22 PDT)
[AMBER] md simulation of modified nucleotides in RNA
- FyD (Mon Apr 16 2018 - 21:30:41 PDT)
- David A Case (Sat Apr 14 2018 - 18:18:36 PDT)
- leila karami (Sat Apr 14 2018 - 08:47:19 PDT)
[AMBER] MM-GBSA on pH constant MD simulations
- Giovanni Grazioso (Thu Apr 12 2018 - 07:27:43 PDT)
[AMBER] MMGBSA calculation for complex with two ligangs using three trajectoris
- cuiyinglukitty (Sun Apr 08 2018 - 01:36:55 PDT)
[AMBER] MMPBSA runs GB but fails in PB for RNA-ligand complex
- Ray Luo (Wed Apr 11 2018 - 18:54:47 PDT)
- Kasprzak, Wojciech (NIH/NCI) [C] (Wed Apr 11 2018 - 12:47:02 PDT)
- Ray Luo (Wed Apr 11 2018 - 09:46:32 PDT)
- Kasprzak, Wojciech (NIH/NCI) [C] (Wed Apr 11 2018 - 07:47:44 PDT)
[AMBER] MMPBSA.py.MPI TypeError when using &pb
- Eiros Zamora, Juan (Mon Apr 30 2018 - 10:49:48 PDT)
[AMBER] Multi-Dimensional REMD: rem.log shows exchanges along Hamiltonian dimension, but .mdout files do not
- Jason Ku Wang (Fri Apr 27 2018 - 13:20:20 PDT)
- Cruzeiro,Vinicius Wilian D (Fri Apr 27 2018 - 11:43:20 PDT)
- Jason Ku Wang (Fri Apr 27 2018 - 10:54:23 PDT)
- Cruzeiro,Vinicius Wilian D (Wed Apr 25 2018 - 18:29:08 PDT)
- Jason Ku Wang (Wed Apr 25 2018 - 17:44:45 PDT)
[AMBER] Multisander: No scale up
- David A Case (Wed Apr 18 2018 - 06:09:21 PDT)
- Aravind Ravichandran (Tue Apr 17 2018 - 23:31:57 PDT)
[AMBER] native contacts
- Sowmya Indrakumar (Thu Apr 19 2018 - 09:26:27 PDT)
[AMBER] NEB simulations: Inputs from TMD ?
- Aravind Ravichandran (Sat Apr 21 2018 - 02:10:43 PDT)
- Carlos Simmerling (Fri Apr 20 2018 - 04:50:26 PDT)
- Aravind Ravichandran (Fri Apr 20 2018 - 02:36:24 PDT)
- Aravind Ravichandran (Fri Apr 20 2018 - 02:33:41 PDT)
[AMBER] no output results for heating process
- David A Case (Tue Apr 03 2018 - 08:23:58 PDT)
- Carlos Simmerling (Mon Apr 02 2018 - 06:13:08 PDT)
- wangjy.dicp.ac.cn (Mon Apr 02 2018 - 01:47:11 PDT)
[AMBER] packmol-memgen and parmed packages import error
- Chetna Tyagi (Thu Apr 26 2018 - 04:16:58 PDT)
- Stephan Schott (Thu Apr 26 2018 - 03:25:44 PDT)
- Chetna Tyagi (Thu Apr 26 2018 - 03:04:09 PDT)
[AMBER] Paramfit issues - Improvement of R^2 value
- Alechania Misturini (Wed Apr 25 2018 - 07:51:54 PDT)
[AMBER] Parmchk
- Premila Samuel Mohan Dass (Tue Apr 24 2018 - 21:55:06 PDT)
- roja rahmani (Tue Apr 24 2018 - 21:11:57 PDT)
- David A Case (Tue Apr 24 2018 - 18:13:02 PDT)
- roja rahmani (Tue Apr 24 2018 - 11:52:40 PDT)
[AMBER] parmed CharmmError: Could not convert dihedral phase to <type 'float'>
- Sadegh Faramarzi Ganjabad (Tue Apr 10 2018 - 09:42:45 PDT)
- David A Case (Mon Apr 09 2018 - 06:04:19 PDT)
- Sadegh Faramarzi Ganjabad (Wed Apr 04 2018 - 11:05:50 PDT)
[AMBER] PB calculation is failing
- varun dewaker (Tue Apr 10 2018 - 07:54:38 PDT)
[AMBER] pH as a Dimension in Multidimensional (2D) Replica Exchange
- Cruzeiro,Vinicius Wilian D (Fri Apr 20 2018 - 11:59:24 PDT)
- Jason Ku Wang (Fri Apr 20 2018 - 11:08:57 PDT)
[AMBER] pmemd.cuda error; Exiting due to the presence of inconsistent SHAKEH hydrogen clusters
- Sadegh Faramarzi Ganjabad (Mon Apr 23 2018 - 09:17:29 PDT)
- David A Case (Sat Apr 21 2018 - 06:07:37 PDT)
- Sadegh Faramarzi Ganjabad (Fri Apr 20 2018 - 10:49:31 PDT)
[AMBER] PMF analysis
- Tousif Hossen (Wed Apr 25 2018 - 07:13:38 PDT)
- David A Case (Tue Apr 24 2018 - 05:25:51 PDT)
- Tousif Hossen (Tue Apr 24 2018 - 04:06:16 PDT)
[AMBER] Problem building Amber16 with -cuda
- Ryan Novosielski (Wed Apr 11 2018 - 07:57:57 PDT)
- Ryan Novosielski (Wed Apr 11 2018 - 07:53:42 PDT)
- David A Case (Wed Apr 11 2018 - 05:19:39 PDT)
- Ryan Novosielski (Wed Apr 11 2018 - 00:28:19 PDT)
[AMBER] Problem in disance restraints for atom groups
- Huan He (Wed Apr 11 2018 - 06:37:02 PDT)
- David A Case (Wed Apr 11 2018 - 05:28:37 PDT)
- Huan He (Wed Apr 11 2018 - 04:20:42 PDT)
- Huan He (Wed Apr 11 2018 - 04:00:36 PDT)
[AMBER] Problem with g++ compiler with boost (AmberTools18)
- Abdul-Rashid III Sampaco (Thu Apr 26 2018 - 02:30:06 PDT)
- Stephan Schott (Wed Apr 25 2018 - 16:23:53 PDT)
- Abdul-Rashid III Sampaco (Wed Apr 25 2018 - 14:49:09 PDT)
- Stephan Schott (Wed Apr 25 2018 - 09:08:48 PDT)
- David A Case (Tue Apr 24 2018 - 05:11:13 PDT)
- Abdul-Rashid III Sampaco (Mon Apr 23 2018 - 22:48:11 PDT)
[AMBER] problem with membrane embedding
- Gould, Ian R (Sun Apr 29 2018 - 02:00:47 PDT)
- Stephan Schott (Sat Apr 28 2018 - 17:17:26 PDT)
- Mohammad Salem (Sat Apr 28 2018 - 15:29:12 PDT)
[AMBER] Problem with parallel install
- Maria Clelia Milletti (Mon Apr 02 2018 - 12:59:52 PDT)
[AMBER] protons
- Carlos Romero (Mon Apr 09 2018 - 21:45:54 PDT)
- David A Case (Mon Apr 09 2018 - 18:42:38 PDT)
- Carlos Romero (Mon Apr 09 2018 - 16:36:13 PDT)
[AMBER] Python installation while installing AmberTools18
- David A Case (Thu Apr 19 2018 - 05:46:48 PDT)
- Debostuti Ghoshdastidar (Thu Apr 19 2018 - 02:04:22 PDT)
[AMBER] QM/MM minimization issue using sander (AMBER 18)
- Abhilash J (Mon Apr 30 2018 - 01:16:17 PDT)
[AMBER] QM/MM-MD charges
- Goetz, Andreas (Wed Apr 25 2018 - 12:34:34 PDT)
- Thakur, Abhishek (Wed Apr 25 2018 - 08:38:17 PDT)
[AMBER] QM/MM-MD Mulliken Charge calculation output atom name changed
- Thakur, Abhishek (Thu Apr 26 2018 - 13:41:48 PDT)
- Goetz, Andreas (Thu Apr 26 2018 - 13:20:23 PDT)
- Thakur, Abhishek (Thu Apr 26 2018 - 11:50:54 PDT)
[AMBER] QMMM Replica exchange with TeraChem
- Goetz, Andreas (Wed Apr 18 2018 - 13:30:19 PDT)
- Raimon Fabregat (Tue Apr 17 2018 - 08:12:58 PDT)
[AMBER] Query about Constant pH cpout file
- Cruzeiro,Vinicius Wilian D (Thu Apr 05 2018 - 10:04:20 PDT)
- Saikat Dutta chowdhury (Thu Apr 05 2018 - 05:33:07 PDT)
[AMBER] Query for force field parameters of 'R' and 'S' enantiomers
- Carlos Simmerling (Wed Apr 04 2018 - 05:27:14 PDT)
- FyD (Wed Apr 04 2018 - 02:01:07 PDT)
- FyD (Wed Apr 04 2018 - 01:47:39 PDT)
- David A Case (Sun Apr 01 2018 - 08:17:12 PDT)
- Chetna Tyagi (Sun Apr 01 2018 - 03:32:55 PDT)
[AMBER] query regarding nonlinear pbsa
- Rakesh Srivastava (Mon Apr 16 2018 - 01:02:15 PDT)
[AMBER] Questions about SEBOMD with Divide and Conqure method
- Gerald Monard (Fri Apr 06 2018 - 08:18:17 PDT)
- Mingyuan (Fri Apr 06 2018 - 04:47:10 PDT)
- Mingyuan_xu (Fri Apr 06 2018 - 04:35:07 PDT)
[AMBER] RED Server deriving charges for hybrid molecule using GLYCAM ff
- FyD (Tue Apr 10 2018 - 05:36:17 PDT)
- Neha Gandhi (Sun Apr 08 2018 - 23:26:32 PDT)
[AMBER] Regarding AuCl force field
- Pengfei Li (Wed Apr 18 2018 - 14:27:17 PDT)
- David A Case (Mon Apr 16 2018 - 18:15:47 PDT)
- Aashish Bhatt (Mon Apr 16 2018 - 06:58:08 PDT)
[AMBER] Regarding input files
- Daniel Roe (Tue Apr 10 2018 - 06:40:09 PDT)
- David A Case (Tue Apr 10 2018 - 04:28:12 PDT)
- Midhun K Madhu (Mon Apr 09 2018 - 23:45:01 PDT)
[AMBER] Release of Amber18 and AmberTools18
- David A Case (Tue Apr 17 2018 - 14:28:42 PDT)
[AMBER] Replica exchange in explicit solvent
- Maya Hauss (Wed Apr 18 2018 - 08:15:04 PDT)
- Cruzeiro,Vinicius Wilian D (Tue Apr 17 2018 - 07:49:47 PDT)
- Maya Hauss (Tue Apr 17 2018 - 05:59:02 PDT)
- Cruzeiro,Vinicius Wilian D (Fri Apr 13 2018 - 12:36:20 PDT)
- Maya Hauss (Fri Apr 13 2018 - 12:23:12 PDT)
[AMBER] Replica Exchange: an illegal memory access was encountered launching kernel kClearForces
- Jason Ku Wang (Thu Apr 05 2018 - 14:37:46 PDT)
- Jason Ku Wang (Thu Apr 05 2018 - 13:58:35 PDT)
[AMBER] residue looks like it is not a part of protein
- Carlos Simmerling (Thu Apr 12 2018 - 08:56:27 PDT)
- Thakur, Abhishek (Thu Apr 12 2018 - 08:41:55 PDT)
- Rajarshi Roy (Mon Apr 09 2018 - 20:21:11 PDT)
- David A Case (Mon Apr 09 2018 - 18:34:09 PDT)
- Thakur, Abhishek (Mon Apr 09 2018 - 14:54:27 PDT)
[AMBER] Resume AMD simulation
- Daniel Roe (Tue Apr 10 2018 - 06:25:58 PDT)
[AMBER] RNA with Amber16
- Christina Bergonzo (Wed Apr 04 2018 - 05:58:36 PDT)
- Elisa FREZZA (Wed Apr 04 2018 - 04:05:57 PDT)
[AMBER] Segmentation fault - invalid memory reference, during the minimization
- David A Case (Fri Apr 27 2018 - 09:02:11 PDT)
- Nikolay N. Kuzmich (Fri Apr 27 2018 - 08:20:27 PDT)
[AMBER] Simple normal mode analysis in amber
- David A Case (Mon Apr 23 2018 - 18:11:11 PDT)
- Lorena.Rosaleny.uv.es (Mon Apr 23 2018 - 12:42:43 PDT)
- Lorena.Rosaleny.uv.es (Thu Apr 19 2018 - 00:49:05 PDT)
- David A Case (Tue Apr 17 2018 - 07:50:15 PDT)
- Lorena.Rosaleny.uv.es (Tue Apr 17 2018 - 07:20:02 PDT)
- David A Case (Mon Apr 16 2018 - 05:59:11 PDT)
- Lorena.Rosaleny.uv.es (Sun Apr 15 2018 - 23:08:57 PDT)
[AMBER] Simulation between DNA and small molecules.
- Edjan Silva (Mon Apr 16 2018 - 11:49:13 PDT)
- Edjan Silva (Mon Apr 16 2018 - 05:44:46 PDT)
- David A Case (Thu Apr 12 2018 - 09:58:48 PDT)
- Edjan Silva (Thu Apr 12 2018 - 08:35:37 PDT)
[AMBER] Simulation of bilayer with negative pressure
- Debostuti Ghoshdastidar (Thu Apr 26 2018 - 02:13:10 PDT)
[AMBER] simulation with duration of 5000 Ps
- Edjan Silva (Wed Apr 25 2018 - 08:21:36 PDT)
- Gustaf Olsson (Wed Apr 25 2018 - 07:20:29 PDT)
- Edjan Silva (Wed Apr 25 2018 - 06:52:29 PDT)
[AMBER] Solvateoct Distance Parameter
- Kung, Ryan (Wed Apr 25 2018 - 15:42:09 PDT)
[AMBER] Suggestions to pick up right methodology
- anu chandra (Fri Apr 27 2018 - 02:52:00 PDT)
[AMBER] superimpose two atoms in cpptraj
- David A Case (Sun Apr 01 2018 - 08:29:21 PDT)
- Mark Rance (Sun Apr 01 2018 - 05:55:34 PDT)
[AMBER] Temperatured-Based Replica Exchange: an illegal memory access was encountered launching kernel kClearForces
- Jason Ku Wang (Thu Apr 05 2018 - 14:45:06 PDT)
[AMBER] Thermodynamic integration with sander + using nosoftcore
- David A Case (Mon Apr 30 2018 - 17:11:43 PDT)
- Khabiri, Morteza (Mon Apr 30 2018 - 10:58:32 PDT)
[AMBER] Thioester Bond:leap
- David A Case (Wed Apr 11 2018 - 05:23:04 PDT)
- Aravind Ravichandran (Wed Apr 11 2018 - 02:54:12 PDT)
[AMBER] topology file
- roja rahmani (Mon Apr 30 2018 - 03:41:46 PDT)
- David A Case (Thu Apr 26 2018 - 04:20:39 PDT)
- roja rahmani (Wed Apr 25 2018 - 05:51:18 PDT)
[AMBER] Trouble Running/Understanding Wavelet Analysis
- Daniel Roe (Thu Apr 26 2018 - 10:40:36 PDT)
- Moataz Noureddine (Tue Apr 24 2018 - 10:42:01 PDT)
[AMBER] Two-Dimensional Replica Exchange in AMBER
- Daniel Roe (Fri Apr 13 2018 - 07:55:13 PDT)
- Cruzeiro,Vinicius Wilian D (Fri Apr 13 2018 - 04:15:53 PDT)
- Jason Ku Wang (Fri Apr 13 2018 - 00:56:17 PDT)
[AMBER] Unable to perform MD because of Fortran runtime error: End of file
- David A Case (Mon Apr 09 2018 - 05:50:08 PDT)
- Sehrish Naz (Mon Apr 09 2018 - 03:28:18 PDT)
[AMBER] variety of errors in membrane/umbrella sampling simulations
- Stephan Schott (Mon Apr 30 2018 - 00:49:08 PDT)
- Baker, Joseph (Sun Apr 29 2018 - 19:09:10 PDT)
- David Cerutti (Sun Apr 29 2018 - 18:15:26 PDT)
- Baker, Joseph (Sun Apr 29 2018 - 17:39:55 PDT)
- David A Case (Sun Apr 29 2018 - 14:00:42 PDT)
- Baker, Joseph (Sun Apr 29 2018 - 11:47:40 PDT)
- Gould, Ian R (Sun Apr 29 2018 - 02:28:43 PDT)
- Baker, Joseph (Sat Apr 28 2018 - 19:08:31 PDT)
- Stephan Schott (Sat Apr 28 2018 - 17:13:42 PDT)
- Baker, Joseph (Sat Apr 28 2018 - 11:51:13 PDT)
[AMBER] Volume occupied during MD
- Daniel Roe (Tue Apr 10 2018 - 06:24:00 PDT)
[AMBER] Weight the xyz components of restraints
- Huan He (Tue Apr 17 2018 - 06:24:03 PDT)
[AMBER] When did SCEE and SCNB make it into the force-field files
- Karl Kirschner (Thu Apr 05 2018 - 23:49:26 PDT)
- Ross Walker (Thu Apr 05 2018 - 13:18:42 PDT)
- David Cerutti (Wed Apr 04 2018 - 16:37:09 PDT)
- Karl Kirschner (Wed Apr 04 2018 - 06:28:08 PDT)
[AMBER] ZnS force field parameters
- David A Case (Mon Apr 02 2018 - 07:57:47 PDT)
- roja rahmani (Sun Apr 01 2018 - 11:17:43 PDT)

Amber Archive Apr 2018 by subject