Amber Archive Apr 2019: by subject

[AMBER] "Problem installing Miniconda"
- Seibold, Steve Allan (Thu Apr 18 2019 - 11:44:39 PDT)
- Hai Nguyen (Thu Apr 18 2019 - 11:00:05 PDT)
- David A Case (Thu Apr 18 2019 - 10:55:27 PDT)
- Hai Nguyen (Thu Apr 18 2019 - 08:57:55 PDT)
- Seibold, Steve Allan (Thu Apr 18 2019 - 08:43:30 PDT)
[AMBER] 2 job positions InterX Inc. Molecular Simulation and Molecular ForceField Scientists
- Ganesh Kamath (Sat Apr 06 2019 - 08:00:24 PDT)
- Ganesh Kamath (Fri Apr 05 2019 - 12:58:51 PDT)
[AMBER] [rok.ucsd.edu: AT19 cpptraj MPI build issue (Linux, x86_64, gnu)]
- David A Case (Tue Apr 30 2019 - 12:55:23 PDT)
[AMBER] A-DNA
- Charu Sharma (JRF) (Tue Apr 23 2019 - 11:51:09 PDT)
- David Case (Tue Apr 23 2019 - 05:13:52 PDT)
- Charu Sharma (JRF) (Mon Apr 22 2019 - 22:17:26 PDT)
[AMBER] AMBER - Heating MD Systems
- An Ta (Thu Apr 18 2019 - 10:58:58 PDT)
- Carlos Simmerling (Thu Apr 18 2019 - 08:43:54 PDT)
- Lin Song (Thu Apr 18 2019 - 08:38:30 PDT)
- An Ta (Thu Apr 18 2019 - 06:23:32 PDT)
- Carlos Simmerling (Thu Apr 18 2019 - 06:03:41 PDT)
- An Ta (Thu Apr 18 2019 - 05:48:37 PDT)
[AMBER] AmberTools19 - macOS 10.14.4 - Xcode 10.2.1 - clang
- Gustaf Olsson (Sun Apr 28 2019 - 14:12:38 PDT)
- David Case (Sun Apr 28 2019 - 09:49:13 PDT)
- Gustaf Olsson (Sat Apr 27 2019 - 11:25:03 PDT)
- Hai Nguyen (Sat Apr 27 2019 - 09:36:49 PDT)
- Gustaf Olsson (Sat Apr 27 2019 - 05:58:27 PDT)
[AMBER] AmberTools19 - macOS 10.14.4 - Xcode 10.2.1 - GCC8.3
- Gustaf Olsson (Sat Apr 27 2019 - 11:44:00 PDT)
[AMBER] Antechamber question
- David Poole (Thu Apr 25 2019 - 16:03:37 PDT)
[AMBER] Any help on how to implement it in cpptraj?
- Daniel Roe (Tue Apr 30 2019 - 06:43:21 PDT)
- Debarati DasGupta (Fri Apr 26 2019 - 09:25:11 PDT)
[AMBER] Atoms per processor
- David A Case (Mon Apr 15 2019 - 07:37:15 PDT)
- Charo del Genio (Mon Apr 15 2019 - 04:36:10 PDT)
[AMBER] Box with a “separator”
- Alessandro Mariani (Tue Apr 02 2019 - 02:59:01 PDT)
[AMBER] Calculate zero point energy for a protein (no ligand) system
- MOHD HOMAIDUR RAHMAN (Tue Apr 09 2019 - 11:49:17 PDT)
- Akshay Prabhakant (Tue Apr 09 2019 - 05:46:42 PDT)
- Carlos Simmerling (Tue Apr 09 2019 - 05:36:05 PDT)
- Akshay Prabhakant (Tue Apr 09 2019 - 05:32:19 PDT)
- Robert Molt (Tue Apr 09 2019 - 05:26:43 PDT)
- Carlos Simmerling (Tue Apr 09 2019 - 04:47:57 PDT)
- Akshay Prabhakant (Tue Apr 09 2019 - 04:42:58 PDT)
[AMBER] Can Amber constant pH run with CHARMM force field?
- Jason Swails (Sun Apr 07 2019 - 17:19:37 PDT)
- Chen Yifan (Fri Apr 05 2019 - 19:12:56 PDT)
- Cruzeiro,Vinicius Wilian D (Fri Apr 05 2019 - 16:15:16 PDT)
- Feng, Zimin (Fri Apr 05 2019 - 13:56:57 PDT)
- Chen Yifan (Fri Apr 05 2019 - 11:51:35 PDT)
[AMBER] Capping RNA
- David A Case (Thu Apr 11 2019 - 07:03:46 PDT)
- Mihaljevic-Juric Paula (Mme) (Thu Apr 11 2019 - 02:56:08 PDT)
[AMBER] Change the trajectory format.
- Daniel Roe (Thu Apr 25 2019 - 04:54:18 PDT)
- Thomas Cheatham (Wed Apr 24 2019 - 23:15:14 PDT)
- Parviz Seifpanahi Shabane (Fri Apr 19 2019 - 12:12:39 PDT)
[AMBER] charge in constant redox cein file vs. prmtop file
- Feng, Zimin (Wed Apr 24 2019 - 11:10:41 PDT)
- Cruzeiro,Vinicius Wilian D (Wed Apr 24 2019 - 09:51:12 PDT)
- Feng, Zimin (Wed Apr 24 2019 - 09:14:30 PDT)
- Cruzeiro,Vinicius Wilian D (Tue Apr 23 2019 - 15:51:31 PDT)
- Feng, Zimin (Tue Apr 23 2019 - 15:03:24 PDT)
[AMBER] charged residue mutation free energy
- Hosein Geraili Daronkola (Fri Apr 12 2019 - 00:04:12 PDT)
[AMBER] COM Dihedral Restraint
- Kellon Belfon (Thu Apr 11 2019 - 09:34:45 PDT)
- Kung, Ryan (Thu Apr 11 2019 - 08:23:17 PDT)
[AMBER] Computing forces by trajectory post-processing with sander
- Casalini Tommaso (Wed Apr 24 2019 - 01:09:51 PDT)
- Daniel Roe (Tue Apr 23 2019 - 06:56:30 PDT)
- Yuliana Bosken (Mon Apr 22 2019 - 20:44:34 PDT)
- Alen Ahmetovic (Mon Apr 22 2019 - 16:50:40 PDT)
- Casalini Tommaso (Mon Apr 22 2019 - 12:54:10 PDT)
[AMBER] Confusion regarding ff14SB and ff99SBildn forcefields
- David Cerutti (Fri Apr 12 2019 - 00:36:01 PDT)
- RITUPARNA ROY (Fri Apr 12 2019 - 00:09:12 PDT)
[AMBER] constant-pressure equilibration with a water droplet
- David A Case (Mon Apr 29 2019 - 11:06:09 PDT)
- Carlos Simmerling (Mon Apr 29 2019 - 09:07:25 PDT)
- Anthony Bogetti (Mon Apr 29 2019 - 08:37:40 PDT)
[AMBER] CPPTRAJ gnu extension not working
- anu chandra (Tue Apr 30 2019 - 10:00:08 PDT)
[AMBER] Creating a water model from scratch
- David Cerutti (Mon Apr 08 2019 - 12:36:46 PDT)
- Gustavo Seabra (Mon Apr 08 2019 - 11:55:39 PDT)
[AMBER] cReAtInG PDB
- David A Case (Thu Apr 11 2019 - 07:06:11 PDT)
- Boutheïna KERKENI (Thu Apr 11 2019 - 03:13:20 PDT)
[AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed
- Ross Walker (Thu Apr 04 2019 - 07:36:32 PDT)
- bjyx20090941 (Wed Apr 03 2019 - 20:21:49 PDT)
[AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol ( GeForce RTX 2080)
- accuratefreeenergy.gmail.com (Wed Apr 03 2019 - 07:36:36 PDT)
- bjyx20090941 (Wed Apr 03 2019 - 07:24:23 PDT)
[AMBER] dihedral scanning with GAFF and GAFF2
- Qasim Pars (Fri Apr 26 2019 - 03:22:33 PDT)
[AMBER] Electrostatic interactions in LIE method
- Debarati DasGupta (Thu Apr 11 2019 - 10:57:19 PDT)
[AMBER] Equilibration in multiple steps with decrement in force constants
- Carlos Simmerling (Mon Apr 01 2019 - 11:38:16 PDT)
- Priyabrata Das (Mon Apr 01 2019 - 10:04:08 PDT)
- Carlos Simmerling (Mon Apr 01 2019 - 06:29:41 PDT)
- Priyabrata Das (Mon Apr 01 2019 - 04:30:14 PDT)
- Carlos Simmerling (Mon Apr 01 2019 - 04:11:30 PDT)
- Priyabrata Das (Mon Apr 01 2019 - 03:19:34 PDT)
[AMBER] Error working with pytleap
- David A Case (Mon Apr 08 2019 - 04:44:42 PDT)
- ARITRA MITRA (Mon Apr 08 2019 - 03:58:33 PDT)
[AMBER] Fixing few box dimensions in semiisotropic/anisotropic pressure scaling
- David A Case (Tue Apr 16 2019 - 06:12:08 PDT)
- Kyeong-jun Jeong (Mon Apr 15 2019 - 13:56:54 PDT)
[AMBER] Force field for C-C Di-Tyrosine Linkage
- Bharat Manna (Thu Apr 18 2019 - 03:45:55 PDT)
[AMBER] Force field parameters for modified amino acid residues (carboxy glutamates)
- Tanusree S (Tue Apr 09 2019 - 21:42:30 PDT)
[AMBER] Fwd: AMBER Digest, Vol 2600, Issue 1
- SATYAJIT KHATUA (Mon Apr 01 2019 - 00:45:18 PDT)
[AMBER] Guidance on WHAM
- Zachary Fallon (Thu Apr 18 2019 - 12:35:43 PDT)
- Daniel Fernández Remacha (Thu Apr 18 2019 - 11:28:40 PDT)
- Zachary Fallon (Wed Apr 17 2019 - 10:21:56 PDT)
- Daniel Fernández Remacha (Wed Apr 17 2019 - 03:59:17 PDT)
- Carlos Simmerling (Tue Apr 16 2019 - 12:43:34 PDT)
- Zachary Fallon (Tue Apr 16 2019 - 12:23:01 PDT)
- Daniel Fernández Remacha (Sat Apr 13 2019 - 06:19:01 PDT)
[AMBER] How the instantaneous temperature is calculated in Amber ?
- Marek Maly (Mon Apr 01 2019 - 10:37:31 PDT)
- Carlos Simmerling (Mon Apr 01 2019 - 04:16:16 PDT)
- Marek Maly (Sun Mar 31 2019 - 20:20:18 PDT)
- Marek Maly (Sun Mar 31 2019 - 20:02:36 PDT)
- Marek Maly (Sun Mar 31 2019 - 17:35:05 PDT)
[AMBER] How to build the central fragment of a modified nucleotide in the AMBER force fields
- 21818674.zju.edu.cn (Sun Mar 31 2019 - 19:28:55 PDT)
[AMBER] How to select dihedral angles to reweight accelerated molecular dynamics simulation of protein
- Mayank Dixit (Thu Apr 18 2019 - 07:47:04 PDT)
- Chetna Tyagi (Wed Apr 17 2019 - 00:57:18 PDT)
- Mayank Dixit (Tue Apr 16 2019 - 17:48:47 PDT)
[AMBER] How to source oldff in tleap
- David A Case (Fri Apr 12 2019 - 05:47:29 PDT)
- Carlos Simmerling (Fri Apr 12 2019 - 05:00:25 PDT)
- Saikat Pal (Fri Apr 12 2019 - 04:43:24 PDT)
- Saikat Pal (Fri Apr 12 2019 - 04:32:54 PDT)
[AMBER] How to use GaMD in amber16
- ATUL KUMAR (Tue Apr 16 2019 - 01:35:25 PDT)
[AMBER] huge reference.frc in MMPBSA
- Antoine Marion (Sun Mar 31 2019 - 21:20:27 PDT)
[AMBER] Issue with cpptraj.MPI
- Daniel Roe (Tue Apr 23 2019 - 06:34:31 PDT)
- Benard, Dany (Tue Apr 23 2019 - 06:01:36 PDT)
- Pratul Agarwal (Tue Apr 23 2019 - 05:58:41 PDT)
- Daniel Roe (Tue Apr 23 2019 - 05:52:46 PDT)
- Pratul Agarwal (Tue Apr 23 2019 - 05:52:05 PDT)
- Benard, Dany (Tue Apr 23 2019 - 05:44:23 PDT)
[AMBER] issues with pmemd.cuda
- Veenis, Andrew Jay (Fri Apr 26 2019 - 07:08:02 PDT)
- David A Case (Thu Apr 25 2019 - 10:43:32 PDT)
- Veenis, Andrew Jay (Thu Apr 25 2019 - 08:11:46 PDT)
[AMBER] KeyError: 4018 for iron containing enzyme (prolyl hydroxylase)
- Mahesh kumar Teli (Wed Apr 03 2019 - 19:14:48 PDT)
- Aashish Bhatt (Wed Apr 03 2019 - 05:48:11 PDT)
- Mahesh kumar Teli (Tue Apr 02 2019 - 22:06:32 PDT)
[AMBER] leap duplicates bond ('triangular' bond) warning
- Pietro Aronica (Tue Apr 02 2019 - 05:45:04 PDT)
- Fabian Glaser (Tue Apr 02 2019 - 05:16:39 PDT)
[AMBER] Ligand Splitting Issue
- David Case (Sun Apr 07 2019 - 18:22:03 PDT)
- Tamsila Parveen (Sun Apr 07 2019 - 04:21:59 PDT)
[AMBER] location related redox-potential?
- Feng, Zimin (Sun Apr 07 2019 - 14:34:05 PDT)
- Cruzeiro,Vinicius Wilian D (Fri Apr 05 2019 - 16:31:36 PDT)
- Feng, Zimin (Fri Apr 05 2019 - 09:15:00 PDT)
[AMBER] mdgx CreateBellyMask error
- David Cerutti (Mon Apr 15 2019 - 08:02:08 PDT)
- Anthony Bogetti (Mon Apr 15 2019 - 07:50:02 PDT)
[AMBER] metal parameters
- Pengfei Li (Sat Apr 06 2019 - 14:39:29 PDT)
- Fabian Glaser (Fri Apr 05 2019 - 21:56:51 PDT)
[AMBER] metal-oxide-metal interactions
- Pengfei Li (Thu Apr 04 2019 - 17:44:44 PDT)
[AMBER] Mg2+_preparation_general_rule
- Antonio Amber Carlesso (Wed Apr 17 2019 - 09:53:47 PDT)
- Antonio Amber Carlesso (Wed Apr 17 2019 - 08:27:11 PDT)
[AMBER] MM PBSA - clarification
- Thomas Evangelidis (Mon Apr 22 2019 - 06:31:00 PDT)
- Prasanth G, Research Scholar (Sun Apr 21 2019 - 23:17:41 PDT)
- Ray Luo (Fri Apr 19 2019 - 06:35:12 PDT)
- Prasanth G, Research Scholar (Fri Apr 19 2019 - 06:14:33 PDT)
[AMBER] mmpbsa
- Chris Moth (Tue Apr 09 2019 - 19:30:18 PDT)
- MYRIAN TORRES RICO (Tue Apr 09 2019 - 01:22:16 PDT)
[AMBER] mmpbsa error
- MYRIAN TORRES RICO (Tue Apr 30 2019 - 09:28:57 PDT)
- David A Case (Tue Apr 30 2019 - 04:28:17 PDT)
- MYRIAN TORRES RICO (Tue Apr 30 2019 - 02:01:54 PDT)
- Daniel Roe (Fri Apr 05 2019 - 08:06:08 PDT)
- MYRIAN TORRES RICO (Thu Apr 04 2019 - 02:07:07 PDT)
- MYRIAN TORRES RICO (Thu Apr 04 2019 - 01:08:44 PDT)
[AMBER] mol2 files for FEW
- Zhonghua Xia (Tue Apr 30 2019 - 07:48:28 PDT)
- David A Case (Wed Apr 17 2019 - 05:06:50 PDT)
- Zhonghua Xia (Wed Apr 17 2019 - 01:33:24 PDT)
[AMBER] More macOS compilation issues....
- Gustaf Olsson (Fri Apr 26 2019 - 22:48:25 PDT)
- David A Case (Fri Apr 26 2019 - 06:48:32 PDT)
- Gustaf Olsson (Thu Apr 25 2019 - 23:49:37 PDT)
- Gustaf Olsson (Thu Apr 25 2019 - 13:08:51 PDT)
- Gustaf Olsson (Mon Apr 22 2019 - 22:20:11 PDT)
- David A Case (Mon Apr 22 2019 - 13:07:11 PDT)
- Gustaf Olsson (Sun Apr 21 2019 - 13:37:05 PDT)
- Gustaf Olsson (Sun Apr 21 2019 - 03:31:39 PDT)
- David A Case (Thu Apr 18 2019 - 10:33:25 PDT)
- Hai Nguyen (Thu Apr 18 2019 - 06:47:08 PDT)
- Gustaf Olsson (Thu Apr 18 2019 - 01:20:39 PDT)
[AMBER] namd and amber md energies do not match
- Akshay Prabhakant (Mon Apr 15 2019 - 23:00:28 PDT)
- David A Case (Fri Apr 12 2019 - 05:37:56 PDT)
- Akshay Prabhakant (Thu Apr 11 2019 - 11:33:01 PDT)
[AMBER] Negative dihedral angle n glycan simulation
- Rajarshi Roy (Fri Apr 26 2019 - 19:20:08 PDT)
- Lachele Foley (Fri Apr 26 2019 - 18:10:18 PDT)
- Rajarshi Roy (Thu Apr 11 2019 - 10:01:20 PDT)
- Rajarshi Roy (Thu Apr 11 2019 - 09:45:11 PDT)
- Irfan Alibay (Thu Apr 11 2019 - 04:43:51 PDT)
- Lachele Foley (Wed Apr 10 2019 - 12:13:57 PDT)
- Lachele Foley (Tue Apr 09 2019 - 10:32:58 PDT)
- Rajarshi Roy (Tue Apr 09 2019 - 00:55:44 PDT)
- Lachele Foley (Mon Apr 08 2019 - 08:49:58 PDT)
- Lachele Foley (Mon Apr 08 2019 - 08:24:16 PDT)
- Rajarshi Roy (Tue Apr 02 2019 - 04:04:58 PDT)
[AMBER] New compile-issue macOS, CPPTRAJ
- Gustaf Olsson (Mon Apr 08 2019 - 06:48:20 PDT)
- David A Case (Mon Apr 08 2019 - 04:57:11 PDT)
- David A Case (Fri Apr 05 2019 - 06:01:56 PDT)
- Gustaf Olsson (Thu Apr 04 2019 - 06:54:53 PDT)
- Daniel Roe (Thu Apr 04 2019 - 06:30:51 PDT)
- Gustaf Olsson (Thu Apr 04 2019 - 06:16:01 PDT)
- David A Case (Wed Apr 03 2019 - 07:36:59 PDT)
- Hai Nguyen (Wed Apr 03 2019 - 05:59:45 PDT)
- Hai Nguyen (Wed Apr 03 2019 - 05:54:30 PDT)
- David A Case (Wed Apr 03 2019 - 05:24:27 PDT)
- Gustaf Olsson (Tue Apr 02 2019 - 23:36:19 PDT)
- Hai Nguyen (Tue Apr 02 2019 - 07:20:23 PDT)
- Gustaf Olsson (Tue Apr 02 2019 - 06:40:03 PDT)
- Hai Nguyen (Tue Apr 02 2019 - 06:26:56 PDT)
- Gustaf Olsson (Tue Apr 02 2019 - 06:23:48 PDT)
- Gustaf Olsson (Tue Apr 02 2019 - 00:27:58 PDT)
- Daniel Roe (Mon Apr 01 2019 - 08:18:46 PDT)
- David A Case (Mon Apr 01 2019 - 07:45:28 PDT)
- Gustaf Olsson (Mon Apr 01 2019 - 05:04:14 PDT)
[AMBER] NFE error: Cannot read &abmd namelist
- Feng Pan (Tue Apr 02 2019 - 16:56:47 PDT)
- Jason Imamoto (Mon Apr 01 2019 - 00:54:59 PDT)
[AMBER] Novel Force Field Parameters for Aromatic Dihedrals
- Erdem Yeler (Sun Apr 28 2019 - 13:09:41 PDT)
[AMBER] NpT simulations in interfacial system
- David Case (Sun Apr 28 2019 - 09:56:50 PDT)
- Lucas Bandeira (Sat Apr 27 2019 - 07:38:33 PDT)
[AMBER] outtraj question
- Daniel Roe (Tue Apr 30 2019 - 07:23:30 PDT)
- Xiaoyu Wang (Fri Apr 05 2019 - 15:35:10 PDT)
[AMBER] parameters for isolated zwitter ion tyrosine
- Elvis Martis (Wed Apr 10 2019 - 23:50:29 PDT)
- angad sharma (Wed Apr 10 2019 - 23:15:25 PDT)
[AMBER] Patches for AmberTools18
- Hai Nguyen (Wed Apr 10 2019 - 13:19:11 PDT)
- Stephan Schott (Wed Apr 10 2019 - 05:38:58 PDT)
- viktor drobot (Wed Apr 10 2019 - 04:26:12 PDT)
[AMBER] pdb4amber install w/ conda
- Hai Nguyen (Fri Apr 12 2019 - 23:14:10 PDT)
- Hai Nguyen (Fri Apr 12 2019 - 09:49:23 PDT)
- Paul, Austin (Fri Apr 12 2019 - 09:16:21 PDT)
[AMBER] pKa calculation
- Tanmoy Paul (Tue Apr 16 2019 - 23:18:58 PDT)
[AMBER] pmemd.CUDA vs pmemd.MPI for equilibration of protein-ligand and trajectory identification for mmpbsa
- Prasanth G, Research Scholar (Fri Apr 05 2019 - 23:47:01 PDT)
[AMBER] possible bug in charmmlipid2amber.py
- liu junjun (Mon Apr 22 2019 - 00:14:17 PDT)
[AMBER] preparing a new pdb
- Boutheïna KERKENI (Sun Apr 07 2019 - 03:56:11 PDT)
[AMBER] Problem calculating water density over distance
- Lucas Bandeira (Thu Apr 04 2019 - 13:35:38 PDT)
[AMBER] Problem calculating water mass density over distance
- Gerardo Zerbetto De Palma (Thu Apr 11 2019 - 07:54:08 PDT)
- Lucas Bandeira (Thu Apr 11 2019 - 09:48:23 PDT)
- Gerardo Zerbetto De Palma (Thu Apr 11 2019 - 09:37:30 PDT)
- Lucas Bandeira (Thu Apr 11 2019 - 09:08:47 PDT)
- Gerardo Zerbetto De Palma (Thu Apr 11 2019 - 09:05:18 PDT)
- Lucas Bandeira (Thu Apr 11 2019 - 09:00:23 PDT)
[AMBER] problem in locating Aqvist Mg2+ parameter in amber
- David Case (Tue Apr 23 2019 - 05:23:49 PDT)
- ATUL KUMAR (Mon Apr 22 2019 - 21:52:18 PDT)
[AMBER] Problem in setting parameters for non standard DG residue:O6-Methylguanine
- Xiaoting Mao (Sat Apr 13 2019 - 02:48:14 PDT)
[AMBER] Problem in setting parameters for the modified nucleotide
- Xiaoting Mao (Mon Apr 08 2019 - 06:10:58 PDT)
[AMBER] Problem with heating the system
- Pratul Agarwal (Wed Apr 24 2019 - 05:14:12 PDT)
- ATUL KUMAR (Wed Apr 24 2019 - 04:53:58 PDT)
- David A Case (Wed Apr 24 2019 - 04:47:18 PDT)
- ATUL KUMAR (Wed Apr 24 2019 - 02:06:52 PDT)
- Bill Ross (Wed Apr 24 2019 - 01:49:56 PDT)
- ATUL KUMAR (Wed Apr 24 2019 - 01:57:34 PDT)
[AMBER] Problems calculating density over distance
- Lucas Bandeira (Mon Apr 01 2019 - 09:13:25 PDT)
[AMBER] Problems in forcefield parameterization of Mercury
- Pengfei Li (Fri Apr 19 2019 - 08:42:20 PDT)
- Muthukumaran Rajagopalan (Tue Apr 16 2019 - 22:36:14 PDT)
- Pengfei Li (Tue Apr 16 2019 - 18:31:35 PDT)
- Muthukumaran Rajagopalan (Tue Apr 16 2019 - 10:24:35 PDT)
[AMBER] Problems in setting parameters for the modified nucleotide
- Xiaoting Mao (Fri Apr 12 2019 - 06:08:43 PDT)
[AMBER] processing trajectories subjected to GIST analysis
- Daniel Roe (Tue Apr 30 2019 - 06:58:42 PDT)
- Alfredo Quevedo (Tue Apr 23 2019 - 23:19:47 PDT)
[AMBER] Question about chemical reaction in vacuum with adding an extra reaction field (Specify dielectric constant in vacuum)
- 王婷婷 (Thu Apr 11 2019 - 18:40:46 PDT)
- David A Case (Thu Apr 11 2019 - 06:57:52 PDT)
- 王婷婷 (Wed Apr 10 2019 - 18:03:59 PDT)
[AMBER] Question about NEB
- Lillian Chong (Fri Apr 12 2019 - 06:02:57 PDT)
[AMBER] Question about QM/MM simulation in vacuum connecting Amber and Gaussian 09 package
- Roitberg,Adrian E (Mon Apr 08 2019 - 17:41:56 PDT)
- 王婷婷 (Mon Apr 08 2019 - 17:36:31 PDT)
[AMBER] Regarding cosine content calculation in AMBER
- Rajarshi Roy (Tue Apr 30 2019 - 10:39:37 PDT)
- Pratul Agarwal (Tue Apr 30 2019 - 09:46:56 PDT)
- Rajarshi Roy (Tue Apr 30 2019 - 09:14:09 PDT)
- Pratul Agarwal (Tue Apr 30 2019 - 08:53:56 PDT)
- Rajarshi Roy (Tue Apr 30 2019 - 08:47:39 PDT)
- Daniel Roe (Tue Apr 30 2019 - 06:16:45 PDT)
- Rajarshi Roy (Mon Apr 29 2019 - 22:22:40 PDT)
[AMBER] REGARDING MPI
- Charu Sharma (JRF) (Wed Apr 10 2019 - 11:06:10 PDT)
[AMBER] regarding radius of gyration
- Carlos Simmerling (Mon Apr 22 2019 - 07:02:36 PDT)
- angad sharma (Mon Apr 22 2019 - 06:03:04 PDT)
[AMBER] regarding simulation
- David A Case (Tue Apr 02 2019 - 05:20:38 PDT)
- Charu Sharma (JRF) (Tue Apr 02 2019 - 00:55:53 PDT)
[AMBER] Release of AmberTools19
- David Case (Fri Apr 26 2019 - 17:59:43 PDT)
[AMBER] rms2d analysis
- Debarati DasGupta (Wed Apr 03 2019 - 06:20:20 PDT)
- Daniel Roe (Tue Apr 02 2019 - 12:43:54 PDT)
- Debarati DasGupta (Tue Apr 02 2019 - 11:38:26 PDT)
[AMBER] RTX 2070 GPU Card
- Ajeet Kumar Yadav (Mon Apr 15 2019 - 03:02:01 PDT)
[AMBER] RTX-2070 supported(untested)?
- Bill Ross (Fri Apr 19 2019 - 05:11:25 PDT)
- Carlos Simmerling (Fri Apr 19 2019 - 05:05:48 PDT)
- David Cerutti (Thu Apr 18 2019 - 14:28:33 PDT)
- Yeyue Xiong (Thu Apr 18 2019 - 13:29:28 PDT)
[AMBER] Save RST from mdcrd containing velocities
- Daniel Roe (Thu Apr 18 2019 - 10:59:21 PDT)
- Yuliana Bosken (Sat Apr 13 2019 - 02:40:05 PDT)
[AMBER] saving output of Gaussian accelerated MD
- Qinghua Liao (Tue Apr 23 2019 - 07:41:28 PDT)
[AMBER] secondary structure
- Carlos Simmerling (Wed Apr 24 2019 - 04:59:50 PDT)
- angad sharma (Wed Apr 24 2019 - 04:32:53 PDT)
[AMBER] secstruct issue in CPPTRAJ
- Daniel Roe (Tue Apr 16 2019 - 05:26:58 PDT)
- Daniel Roe (Wed Apr 10 2019 - 12:16:06 PDT)
- Daniel Roe (Wed Apr 10 2019 - 11:28:42 PDT)
- SARAH JEANNE LEFAVE (Mon Apr 08 2019 - 13:22:18 PDT)
[AMBER] setting up triplicate runs
- David Cerutti (Thu Apr 25 2019 - 19:02:45 PDT)
- Yin, Guowei (Thu Apr 25 2019 - 18:08:00 PDT)
[AMBER] silver parameters
- Christina Bergonzo (Fri Apr 12 2019 - 06:48:50 PDT)
- Uroš Javornik (Fri Apr 12 2019 - 06:29:12 PDT)
[AMBER] Simulation with Protein, cofactor and Ligand
- Prasanth G, Research Scholar (Thu Apr 25 2019 - 11:41:05 PDT)
[AMBER] smflags in configure script
- David A Case (Mon Apr 22 2019 - 13:03:56 PDT)
- Charles Lin (Mon Apr 22 2019 - 12:52:10 PDT)
- viktor drobot (Fri Apr 19 2019 - 07:19:24 PDT)
[AMBER] styrene sulfonate molecule building using xleap
- David A Case (Wed Apr 24 2019 - 04:45:08 PDT)
- Shilpa Gupta (Tue Apr 23 2019 - 23:32:36 PDT)
[AMBER] Suggestions on running a qm-mm simulation for studying a group transfer reaction
- Prayagraj Fandilolu (Mon Apr 22 2019 - 05:43:24 PDT)
[AMBER] T4 vs RTX2080Ti
- David Cerutti (Fri Apr 12 2019 - 08:21:38 PDT)
- Shenglong Wang (Thu Apr 11 2019 - 08:03:00 PDT)
- Giovanni Grazioso (Thu Apr 11 2019 - 08:00:42 PDT)
[AMBER] Targeted MD
- Carlos Simmerling (Thu Apr 25 2019 - 05:01:37 PDT)
- Elena Gomez (Thu Apr 25 2019 - 01:08:18 PDT)
[AMBER] tests with different # of threads
- Vaibhav Dixit (Thu Apr 04 2019 - 08:11:38 PDT)
- David A Case (Wed Apr 03 2019 - 05:30:44 PDT)
- Vaibhav Dixit (Wed Apr 03 2019 - 03:26:04 PDT)
[AMBER] trouble in amberFATA: Atom doesn't have a type
- Sally Pias (Fri Apr 19 2019 - 12:09:19 PDT)
- Maximilien BERNE (Fri Apr 19 2019 - 09:19:14 PDT)
[AMBER] varying pressure conditions?
- Carlos Simmerling (Mon Apr 01 2019 - 08:23:06 PDT)
- Shayna Hilburg (Mon Apr 01 2019 - 08:21:07 PDT)
[AMBER] WHAM umbrella PMF of ligand Z diffusion on lipid molecule
- zmatovic.kg.ac.rs (Mon Apr 29 2019 - 04:05:27 PDT)
[AMBER] Why is SPAM throwing errors when I see none in my input files or trajectories.
- Daniel Roe (Tue Apr 30 2019 - 06:12:07 PDT)
- Debarati DasGupta (Mon Apr 29 2019 - 13:25:58 PDT)
[AMBER] xleap display
- Gustaf Olsson (Sun Apr 28 2019 - 05:58:47 PDT)
- Bill Ross (Sat Apr 27 2019 - 21:28:56 PDT)
- Yin, Guowei (Sat Apr 27 2019 - 19:54:15 PDT)
- Bill Ross (Sat Apr 27 2019 - 16:31:50 PDT)
- Pratul Agarwal (Sat Apr 27 2019 - 16:02:31 PDT)
- Bill Ross (Sat Apr 27 2019 - 15:57:41 PDT)
- Bill Ross (Sat Apr 27 2019 - 15:49:56 PDT)
- Yin, Guowei (Sat Apr 27 2019 - 14:49:20 PDT)
secstruct issue in CPPTRAJ
- SARAH JEANNE LEFAVE (Tue Apr 16 2019 - 05:44:35 PDT)

Amber Archive Apr 2019 by subject