Amber Archive Apr 2018: by author

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

Amber Archive Apr 2018 by author