Amber Archive Apr 2019: by author

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

Amber Archive Apr 2019 by author