Amber Archive Mar 2021: by author

A. Bakheit
- [AMBER] MMPBSA errors (Thu Mar 25 2021 - 03:15:11 PDT)
Aanshi Gandhi
- Re: [AMBER] CHARMM Output - Empty Restraint File (Mon Mar 29 2021 - 10:29:52 PDT)
- [AMBER] CHARMM Output - Empty Restraint File (Mon Mar 29 2021 - 08:46:46 PDT)
- [AMBER] Turning initial velocity off for continuous MD runs (Tue Mar 09 2021 - 09:35:24 PST)
Abhik Ghosh Moulick
- [AMBER] constant ph md (Thu Mar 11 2021 - 08:00:46 PST)
Abhilash J
- [AMBER] Clustering based on predefined centroids (Thu Mar 25 2021 - 13:17:27 PDT)
Adrian Roitberg
- Re: [AMBER] Using average frame for nmode entropy calculation? (Tue Mar 30 2021 - 09:20:37 PDT)
- Re: [AMBER] Addition of hydrogens - isoelectric point of protein (Thu Mar 25 2021 - 12:14:21 PDT)
- Re: [AMBER] CpHMD with structurally different protonation states? (Wed Mar 24 2021 - 10:22:59 PDT)
- Re: [AMBER] Why a target ion failed to move along the pathway in the simulated annealing version of Nudged Elastic Band (NEB) calculations? (Fri Mar 12 2021 - 12:20:54 PST)
- Re: [AMBER] constant ph md (Thu Mar 11 2021 - 08:16:40 PST)
- Re: [AMBER] Problem with CG minimization in implicit solvent (Thu Mar 11 2021 - 07:36:49 PST)
- Re: [AMBER] sander/orca/xtb ：Low parallel efficiency (Thu Mar 11 2021 - 06:11:30 PST)
- Re: [AMBER] Effect of different gamma_ln values (Mon Mar 01 2021 - 15:42:50 PST)
aishen.free.fr
- Re: [AMBER] Is it possible to create a deb for ubuntu or a pypi one ? (Mon Mar 29 2021 - 12:24:17 PDT)
- [AMBER] Is it possible to create a deb for ubuntu or a pypi one ? (Sun Mar 28 2021 - 08:22:59 PDT)
- Re: [AMBER] New In CPPTRAJ (Fri Mar 19 2021 - 00:29:02 PDT)
- Re: [AMBER] Visualizing NetCDF in VMD - ERROR (Wed Mar 17 2021 - 14:13:13 PDT)
- Re: [AMBER] Visualizing NetCDF in VMD - ERROR (Tue Mar 16 2021 - 01:49:59 PDT)
- Re: [AMBER] x=sequence (Mon Mar 15 2021 - 06:57:30 PDT)
- [AMBER] x=sequence (Mon Mar 15 2021 - 00:30:05 PDT)
- Re: [AMBER] AmberTools20 fails to compile with gcc10 (with workaround) (Sat Mar 13 2021 - 13:55:23 PST)
- Re: [AMBER] gcc9 (Thu Mar 04 2021 - 23:05:50 PST)
Alan
- [AMBER] Antechamber and mol2 file with .<TRIPOS>UNITY_ATOM_ATTR (Wed Mar 31 2021 - 00:18:12 PDT)
Alejandro Gil Ley
- Re: [AMBER] Problem with CG minimization in implicit solvent (Thu Mar 11 2021 - 13:56:26 PST)
- [AMBER] Problem with CG minimization in implicit solvent (Wed Mar 10 2021 - 11:17:05 PST)
Ali Saad Kusay
- [AMBER] Discrepancy in pb binding energy (MMPBSA.py tutorial) (Wed Mar 24 2021 - 06:33:10 PDT)
Aliakbartehrani Zahra
- [AMBER] Missing atom types for ligand with chlorine atoms (Tue Mar 16 2021 - 00:23:38 PDT)
Amit Sharma (Asstt. Prof., MCARS)
- Re: [AMBER] Seeking suggestions for breaking a covalent link between atoms (Wed Mar 24 2021 - 07:28:11 PDT)
- [AMBER] Seeking suggestions for breaking a covalent link between atoms (Tue Mar 23 2021 - 01:54:59 PDT)
An Ta
- Re: [AMBER] New In CPPTRAJ (Fri Mar 19 2021 - 03:41:58 PDT)
Anthony Cruz-Balberdy
- Re: [AMBER] LJ parameters (Wed Mar 10 2021 - 10:10:48 PST)
Ayesha Fatima
- Re: [AMBER] atom number difference in topology and simulated trajectory (Sun Mar 07 2021 - 08:50:12 PST)
- Re: [AMBER] atom number difference in topology and simulated trajectory (Sun Feb 28 2021 - 08:39:55 PST)
Bowleg, Jerrano
- Re: [AMBER] Single Point QM/MM energy using Amber-Q-Chem interface (Mon Mar 08 2021 - 09:56:48 PST)
- [AMBER] Single Point QM/MM energy using Amber-Q-Chem interface (Mon Mar 08 2021 - 07:55:54 PST)
Carlos Simmerling
- Re: [AMBER] Convert SIRAH coarse-grained model back to all-atomic pdb file format? (Wed Mar 31 2021 - 04:00:48 PDT)
- Re: [AMBER] CHARMM Output - Empty Restraint File (Mon Mar 29 2021 - 11:25:48 PDT)
- Re: [AMBER] CHARMM Output - Empty Restraint File (Mon Mar 29 2021 - 09:57:08 PDT)
- Re: [AMBER] Calculation halted on pmemd.cuda (Sun Mar 28 2021 - 04:25:19 PDT)
- Re: [AMBER] Calculation halted on pmemd.cuda (Fri Mar 26 2021 - 18:32:29 PDT)
- Re: [AMBER] Conversion of CHARMM optimized pdb to AMBER compatible pdb (Fri Mar 26 2021 - 09:36:44 PDT)
- Re: [AMBER] Selection of forcefield for protein-ligand simulations (Thu Mar 25 2021 - 12:49:54 PDT)
- Re: [AMBER] Apply Lennar-Jones potential between small molecules (Tue Mar 23 2021 - 03:35:23 PDT)
- Re: [AMBER] Pmemd to run TI on protein mutations (Mon Mar 22 2021 - 12:58:23 PDT)
- Re: [AMBER] SIRAH CG Protein with Implicit Solvent (Sun Mar 21 2021 - 07:00:45 PDT)
- Re: [AMBER] Apply Lennar-Jones potential between small molecules (Thu Mar 18 2021 - 08:05:49 PDT)
- Re: [AMBER] Apply Lennar-Jones potential between small molecules (Thu Mar 18 2021 - 03:35:40 PDT)
- Re: [AMBER] Apply Lennar-Jones potential between small molecules (Tue Mar 16 2021 - 06:41:38 PDT)
- Re: [AMBER] Apply Lennar-Jones potential between small molecules (Tue Mar 16 2021 - 05:32:12 PDT)
- Re: [AMBER] AmberTools20 fails to compile with gcc10 (with workaround) (Sun Mar 14 2021 - 14:18:33 PDT)
- Re: [AMBER] pmemd.cuda unstable with ff19SB+OPC and HMassRepartition (Wed Mar 10 2021 - 12:52:30 PST)
- Re: [AMBER] How to plot the Phi-Psi picture in Section 7 of “Tutorial 6.6 Nudged Elastic Band (NEB) simulations”? (Wed Mar 03 2021 - 06:19:36 PST)
Cato, Lee
- [AMBER] Conversion of CHARMM optimized pdb to AMBER compatible pdb (Fri Mar 26 2021 - 09:34:32 PDT)
Charo del Genio
- Re: [AMBER] Convert SIRAH coarse-grained model back to all-atomic pdb file format? (Wed Mar 31 2021 - 00:39:45 PDT)
- Re: [AMBER] AmberTools20 fails to compile with gcc10 (with workaround) (Mon Mar 15 2021 - 04:18:35 PDT)
- Re: [AMBER] AmberTools20 fails to compile with gcc10 (with workaround) (Sun Mar 14 2021 - 07:41:06 PDT)
- [AMBER] AmberTools20 fails to compile with gcc10 (with workaround) (Sat Mar 13 2021 - 12:06:20 PST)
Chris Neale
- Re: [AMBER] Problem with CG minimization in implicit solvent (Thu Mar 11 2021 - 20:33:37 PST)
Christina Bergonzo
- Re: [AMBER] Clustering based on predefined centroids (Fri Mar 26 2021 - 05:35:23 PDT)
- Re: [AMBER] x=sequence (Mon Mar 15 2021 - 04:07:31 PDT)
- Re: [AMBER] How to plot the Phi-Psi picture in Section 7 of “Tutorial 6.6 Nudged Elastic Band (NEB) simulations”? (Wed Mar 03 2021 - 06:17:30 PST)
Chuck is Busy
- Re: [AMBER] Running MMPBSA on protein membrane system built using CHARMMGUI (Sat Mar 13 2021 - 19:11:04 PST)
- Re: [AMBER] Running MMPBSA on protein membrane system built using CHARMMGUI (Sat Mar 13 2021 - 15:48:32 PST)
- Re: [AMBER] Running MMPBSA on protein membrane system built using CHARMMGUI (Sat Mar 13 2021 - 15:03:08 PST)
- [AMBER] Running MMPBSA on protein membrane system built using CHARMMGUI (Sat Mar 13 2021 - 09:51:09 PST)
Clorice Reinhardt
- Re: [AMBER] hbond cpptraj (Mon Mar 15 2021 - 15:27:27 PDT)
- Re: [AMBER] Single Point QM/MM energy using Amber-Q-Chem interface (Mon Mar 08 2021 - 13:53:08 PST)
- Re: [AMBER] Single Point QM/MM energy using Amber-Q-Chem interface (Mon Mar 08 2021 - 08:55:49 PST)
Cruzeiro, Vinicius
- Re: [AMBER] CpHMD with structurally different protonation states? (Wed Mar 24 2021 - 10:12:22 PDT)
Daniel Roe
- Re: [AMBER] Apply Lennar-Jones potential between small molecules (Wed Mar 24 2021 - 06:48:09 PDT)
- Re: [AMBER] Loading Topology & Trajectory Files (Wed Mar 24 2021 - 06:37:50 PDT)
- Re: [AMBER] saving pdb and rst at specific frames in trajectory (Mon Mar 22 2021 - 07:43:42 PDT)
- Re: [AMBER] Loading Topology & Trajectory Files (Mon Mar 22 2021 - 07:37:49 PDT)
- Re: [AMBER] cpptraj killed (Mon Mar 22 2021 - 07:25:50 PDT)
- Re: [AMBER] Solvating my box with specified number of water molecules (Mon Mar 22 2021 - 07:22:32 PDT)
- [AMBER] New In CPPTRAJ (Thu Mar 18 2021 - 09:44:06 PDT)
- Re: [AMBER] Visualizing NetCDF in VMD - ERROR (Wed Mar 17 2021 - 11:22:54 PDT)
- Re: [AMBER] Secstruct error (Sat Mar 13 2021 - 05:52:32 PST)
- Re: [AMBER] makeDIST_RST (Tue Mar 09 2021 - 15:36:20 PST)
- Re: [AMBER] Superimpose (Thu Mar 04 2021 - 11:06:11 PST)
- Re: [AMBER] makeDIST_RST (Thu Mar 04 2021 - 08:17:50 PST)
David A Case
- Re: [AMBER] Antechamber and mol2 file with .<TRIPOS>UNITY_ATOM_ATTR (Wed Mar 31 2021 - 05:45:28 PDT)
- Re: [AMBER] MMPBSA per residue decomposition - Calculation speed (Wed Mar 31 2021 - 05:23:17 PDT)
- Re: [AMBER] erro: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered (Mon Mar 29 2021 - 09:36:08 PDT)
- Re: [AMBER] Is it possible to create a deb for ubuntu or a pypi one ? (Mon Mar 29 2021 - 05:28:53 PDT)
- Re: [AMBER] Is it possible to create a deb for ubuntu or a pypi one ? (Sun Mar 28 2021 - 14:06:07 PDT)
- Re: [AMBER] Using average frame for nmode entropy calculation? (Sun Mar 28 2021 - 13:43:20 PDT)
- Re: [AMBER] Using average frame for nmode entropy calculation? (Sun Mar 28 2021 - 05:37:30 PDT)
- Re: [AMBER] Calculation halted on pmemd.cuda (Sun Mar 28 2021 - 05:31:32 PDT)
- Re: [AMBER] Problem with packmol-memgen when I try to installing Amber20 in GPU (Fri Mar 26 2021 - 13:45:06 PDT)
- Re: [AMBER] Distance tolerance for identifying common atoms in thermodynamics integration (Fri Mar 26 2021 - 13:40:19 PDT)
- Re: [AMBER] Conversion of CHARMM optimized pdb to AMBER compatible pdb (Fri Mar 26 2021 - 13:34:39 PDT)
- Re: [AMBER] Problem with packmol-memgen when I try to installing Amber20 in GPU (Fri Mar 26 2021 - 04:58:58 PDT)
- Re: [AMBER] Electric Field Gradient (Thu Mar 25 2021 - 05:48:45 PDT)
- Re: [AMBER] MMPBSA errors (Thu Mar 25 2021 - 05:42:17 PDT)
- Re: [AMBER] Problem with AMBER20 compilation using Intel/20.4 compiler (Wed Mar 24 2021 - 13:50:45 PDT)
- Re: [AMBER] Seeking suggestions for breaking a covalent link between atoms (Wed Mar 24 2021 - 08:17:49 PDT)
- Re: [AMBER] erro: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered (Wed Mar 24 2021 - 08:07:13 PDT)
- Re: [AMBER] erro: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered (Wed Mar 24 2021 - 04:35:12 PDT)
- Re: [AMBER] Seeking suggestions for breaking a covalent link between atoms (Tue Mar 23 2021 - 06:40:29 PDT)
- Re: [AMBER] How to assess mutant-induced instability with MM-GBSA (Sat Mar 20 2021 - 06:08:07 PDT)
- Re: [AMBER] AMBER 18 Installation error (Fri Mar 19 2021 - 17:52:37 PDT)
- Re: [AMBER] MMPBSA per residue decomposition - Calculation speed (Fri Mar 19 2021 - 06:59:51 PDT)
- Re: [AMBER] AMBER 18 Installation error (Fri Mar 19 2021 - 06:56:18 PDT)
- Re: [AMBER] Apply Lennar-Jones potential between small molecules (Thu Mar 18 2021 - 07:51:06 PDT)
- Re: [AMBER] Visualizing NetCDF in VMD - ERROR (Wed Mar 17 2021 - 18:09:57 PDT)
- Re: [AMBER] segmentation fault error (Wed Mar 17 2021 - 06:58:54 PDT)
- Re: [AMBER] Missing atom types for ligand with chlorine atoms (Tue Mar 16 2021 - 06:03:08 PDT)
- Re: [AMBER] Apply Lennar-Jones potential between small molecules (Tue Mar 16 2021 - 05:55:43 PDT)
- Re: [AMBER] AmberTools20 fails to compile with gcc10 (with workaround) (Sun Mar 14 2021 - 13:25:33 PDT)
- Re: [AMBER] Energy minimization problem (Sun Mar 14 2021 - 05:56:48 PDT)
- Re: [AMBER] Running MMPBSA on protein membrane system built using CHARMMGUI (Sat Mar 13 2021 - 18:08:48 PST)
- Re: [AMBER] AmberTools20 fails to compile with gcc10 (with workaround) (Sat Mar 13 2021 - 18:02:18 PST)
- Re: [AMBER] Running MMPBSA on protein membrane system built using CHARMMGUI (Sat Mar 13 2021 - 14:08:06 PST)
- Re: [AMBER] AmberTools20 fails to compile with gcc10 (with workaround) (Sat Mar 13 2021 - 14:03:57 PST)
- Re: [AMBER] Tleap Fatal error (Fri Mar 12 2021 - 04:54:30 PST)
- Re: [AMBER] Problem with CG minimization in implicit solvent (Thu Mar 11 2021 - 13:18:35 PST)
- Re: [AMBER] GPU installation error amber18 (Thu Mar 11 2021 - 05:54:22 PST)
- Re: [AMBER] pmemd.cuda unstable with ff19SB+OPC and HMassRepartition (Thu Mar 11 2021 - 05:48:30 PST)
- Re: [AMBER] makeDIST_RST (Tue Mar 09 2021 - 17:58:43 PST)
- Re: [AMBER] Turning initial velocity off for continuous MD runs (Tue Mar 09 2021 - 13:12:03 PST)
- Re: [AMBER] Problem with AMBER20 compilation using Intel/20.4 compiler (Tue Mar 09 2021 - 09:15:56 PST)
- Re: [AMBER] Generating library from cif file. (Mon Mar 08 2021 - 08:31:40 PST)
- Re: [AMBER] Error when compiling AMBER20 (Mon Mar 08 2021 - 05:13:29 PST)
- Re: [AMBER] makeDIST_RST (Sun Mar 07 2021 - 05:06:17 PST)
- Re: [AMBER] MMPBSA/ Parmed error (Sat Mar 06 2021 - 05:48:55 PST)
- Re: [AMBER] Ambertools20 with amber18 (Fri Mar 05 2021 - 11:44:27 PST)
- Re: [AMBER] Practical questions on NMR-refinment (Thu Mar 04 2021 - 13:20:27 PST)
- Re: [AMBER] makeDIST_RST (Thu Mar 04 2021 - 05:41:04 PST)
- Re: [AMBER] Practical questions on NMR-refinment (Wed Mar 03 2021 - 18:31:08 PST)
- Re: [AMBER] Simulation of optimized ligand without docking (Wed Mar 03 2021 - 05:37:09 PST)
- Re: [AMBER] MMPBSA/ Parmed error (Wed Mar 03 2021 - 05:30:52 PST)
- Re: [AMBER] positional and NMR distance restraints together (Tue Mar 02 2021 - 06:13:25 PST)
David Cerutti
- [AMBER] Pending deprecation of paramfit: Amber21 or Amber22? (Fri Mar 05 2021 - 08:01:22 PST)
- Re: [AMBER] Parametrization of Virtual sites in Halogens (Fri Mar 05 2021 - 07:28:51 PST)
Dr. Anselm Horn
- Re: [AMBER] Convert SIRAH coarse-grained model back to all-atomic pdb file format? (Wed Mar 31 2021 - 01:08:58 PDT)
- [AMBER] Force field parameters for TYS ? (Fri Mar 26 2021 - 11:44:11 PDT)
- Re: [AMBER] CpHMD with structurally different protonation states? (Thu Mar 25 2021 - 01:18:32 PDT)
- [AMBER] CpHMD with structurally different protonation states? (Wed Mar 24 2021 - 04:58:04 PDT)
- Re: [AMBER] Pair interaction energy (Wed Mar 10 2021 - 00:15:22 PST)
- Re: [AMBER] Pair interaction energy (Tue Mar 09 2021 - 11:50:42 PST)
Dr. Gerardo Pérez Hernández
- Re: [AMBER] Problem with packmol-memgen when I try to installing Amber20 in GPU (Fri Mar 26 2021 - 13:10:09 PDT)
- [AMBER] Problem with packmol-memgen when I try to installing Amber20 in GPU (Fri Mar 26 2021 - 04:00:07 PDT)
Eduardo R. Almeida
- Re: [AMBER] Pair interaction energy (Wed Mar 10 2021 - 05:23:41 PST)
- Re: [AMBER] Pair interaction energy (Tue Mar 09 2021 - 14:33:43 PST)
- Re: [AMBER] Pair interaction energy (Tue Mar 09 2021 - 12:04:46 PST)
- [AMBER] Pair interaction energy (Tue Mar 09 2021 - 06:53:50 PST)
Elvis A F Martis
- Re: [AMBER] atom number difference in topology and simulated trajectory (Sun Mar 07 2021 - 21:24:11 PST)
- Re: [AMBER] atom number difference in topology and simulated trajectory (Sun Feb 28 2021 - 22:10:24 PST)
fmying.xmu.edu.cn
- [AMBER] Error when compiling AMBER20 (Sun Mar 07 2021 - 22:38:32 PST)
George M. Giambasu
- Re: [AMBER] 3D-RISM solvent placement with MoFT (Tue Mar 23 2021 - 18:31:53 PDT)
George Madalin Giambasu
- Re: [AMBER] 3D-RISM solvent placement with MoFT (Sun Mar 28 2021 - 18:42:25 PDT)
Gerald Monard
- Re: [AMBER] pmemd.cuda unstable with ff19SB+OPC and HMassRepartition (Thu Mar 11 2021 - 03:47:07 PST)
Goetz, Andreas
- Re: [AMBER] Using DFT-D3(BJ) during QM/MM calculations (Tue Mar 02 2021 - 12:05:27 PST)
Gould, Ian R
- Re: [AMBER] Installation Ambertools20 Mac M1 (arm64) (Mon Mar 15 2021 - 01:12:52 PDT)
Gustaf Olsson
- Re: [AMBER] Loading Topology & Trajectory Files (Wed Mar 24 2021 - 07:00:36 PDT)
- Re: [AMBER] Loading Topology & Trajectory Files (Tue Mar 23 2021 - 02:51:24 PDT)
- Re: [AMBER] cpptraj killed (Tue Mar 23 2021 - 00:45:34 PDT)
- Re: [AMBER] Visualizing NetCDF in VMD - ERROR (Thu Mar 18 2021 - 02:02:29 PDT)
- Re: [AMBER] saving pdb and rst at specific frames in trajectory (Thu Mar 18 2021 - 02:01:06 PDT)
- Re: [AMBER] saving pdb and rst at specific frames in trajectory (Thu Mar 18 2021 - 01:39:51 PDT)
- Re: [AMBER] saving pdb and rst at specific frames in trajectory (Wed Mar 17 2021 - 06:48:58 PDT)
- Re: [AMBER] Visualizing NetCDF in VMD - ERROR (Wed Mar 17 2021 - 00:51:29 PDT)
- Re: [AMBER] Visualizing NetCDF in VMD - ERROR (Tue Mar 16 2021 - 04:59:09 PDT)
- Re: [AMBER] Visualizing NetCDF in VMD - ERROR (Tue Mar 16 2021 - 02:50:11 PDT)
- Re: [AMBER] Visualizing NetCDF in VMD - ERROR (Tue Mar 16 2021 - 01:00:38 PDT)
- Re: [AMBER] gcc9 (Thu Mar 04 2021 - 23:44:45 PST)
Gustavo Seabra
- Re: [AMBER] New In CPPTRAJ (Thu Mar 18 2021 - 16:52:51 PDT)
- Re: [AMBER] Practical questions on NMR-refinment (Thu Mar 04 2021 - 08:56:18 PST)
- [AMBER] Practical questions on NMR-refinment (Wed Mar 03 2021 - 12:33:51 PST)
Hai Nguyen
- Re: [AMBER] Visualizing NetCDF in VMD - ERROR (Wed Mar 17 2021 - 20:47:15 PDT)
- Re: [AMBER] Visualizing NetCDF in VMD - ERROR (Wed Mar 17 2021 - 09:47:40 PDT)
- Re: [AMBER] MMPBSA/ Parmed error (Wed Mar 03 2021 - 18:18:53 PST)
He, Amy
- Re: [AMBER] 3D-RISM solvent placement with MoFT (Mon Mar 29 2021 - 22:16:06 PDT)
- Re: [AMBER] 3D-RISM solvent placement with MoFT (Wed Mar 24 2021 - 21:59:06 PDT)
- Re: [AMBER] 3D-RISM solvent placement with MoFT (Mon Mar 22 2021 - 10:32:12 PDT)
- [AMBER] 3D-RISM solvent placement with MoFT (Sun Mar 21 2021 - 19:10:45 PDT)
Hector Martinez-Seara
- [AMBER] Request for the sha256sum od amber20 (Sat Mar 13 2021 - 02:43:07 PST)
Helena Damtoft Tjørnelund
- [AMBER] Free Energy Calculations using LIE and FEW (Tue Mar 02 2021 - 02:21:27 PST)
Hrishikesh Dhondge
- Re: [AMBER] Is it possible to create a deb for ubuntu or a pypi one ? (Mon Mar 29 2021 - 00:13:29 PDT)
Jaime Rubio Martinez
- Re: [AMBER] Selection of forcefield for protein-ligand simulations (Sun Mar 28 2021 - 02:46:33 PDT)
James Kress
- Re: [AMBER] Electric Field Gradient (Thu Mar 25 2021 - 09:23:29 PDT)
- Re: [AMBER] use orca in amber (Tue Mar 02 2021 - 14:41:20 PST)
Jatin Kashyap
- Re: [AMBER] MMPBSA per residue decomposition - Calculation speed (Tue Mar 30 2021 - 21:51:53 PDT)
- [AMBER] Loading Topology & Trajectory Files (Fri Mar 19 2021 - 14:24:41 PDT)
- Re: [AMBER] New In CPPTRAJ (Fri Mar 19 2021 - 03:46:35 PDT)
- [AMBER] MMPBSA per residue decomposition - Calculation speed (Fri Mar 19 2021 - 03:11:52 PDT)
- Re: [AMBER] Visualizing NetCDF in VMD - ERROR (Wed Mar 17 2021 - 15:50:53 PDT)
- Re: [AMBER] Visualizing NetCDF in VMD - ERROR (Wed Mar 17 2021 - 13:54:09 PDT)
- Re: [AMBER] Visualizing NetCDF in VMD - ERROR (Tue Mar 16 2021 - 18:20:46 PDT)
- [AMBER] Visualizing NetCDF in VMD - ERROR (Mon Mar 15 2021 - 21:23:07 PDT)
Jenny 148
- Re: [AMBER] MMPBSA/ Parmed error (Mon Mar 08 2021 - 07:16:02 PST)
- Re: [AMBER] MMPBSA/ Parmed error (Fri Mar 05 2021 - 23:02:56 PST)
- Re: [AMBER] MMPBSA/ Parmed error (Wed Mar 03 2021 - 06:18:46 PST)
- [AMBER] MMPBSA/ Parmed error (Tue Mar 02 2021 - 22:39:15 PST)
Jon Uranga
- [AMBER] hbond cpptraj (Mon Mar 15 2021 - 06:47:17 PDT)
Juraj Dobias
- Re: [AMBER] Missing atom types for ligand with chlorine atoms (Tue Mar 16 2021 - 01:27:05 PDT)
Kellon Belfon
- Re: [AMBER] How to define COM for groups in ASMD (Tue Mar 09 2021 - 18:37:38 PST)
Kenneth Huang
- Re: [AMBER] Ligand moving out of active site after 250ns (Sat Mar 13 2021 - 08:43:09 PST)
- Re: [AMBER] Tleap Fatal error (Fri Mar 12 2021 - 22:16:12 PST)
Kodituwakku,Dimuthu Nirmani
- [AMBER] Secstruct error (Wed Mar 10 2021 - 19:48:34 PST)
Lennart Gundelach
- [AMBER] Unknown PB option use_sav=0 (Sat Mar 20 2021 - 01:07:50 PDT)
Leung, Jeremy
- Re: [AMBER] SIRAH CG Protein with Implicit Solvent (Mon Mar 22 2021 - 08:59:09 PDT)
- [AMBER] SIRAH CG Protein with Implicit Solvent (Sat Mar 20 2021 - 10:09:31 PDT)
Li Dailin
- [AMBER] 答复: Why a target ion failed to move along the pathway in the simulated annealing version of Nudged Elastic Band (NEB) calculations? (Fri Mar 12 2021 - 16:26:57 PST)
- [AMBER] Why a target ion failed to move along the pathway in the simulated annealing version of Nudged Elastic Band (NEB) calculations? (Thu Mar 11 2021 - 17:55:57 PST)
- [AMBER] 答复: How to plot the Phi-Psi picture in Section 7 of “Tutorial 6.6 Nudged Elastic Band (NEB) simulations”? (Fri Mar 05 2021 - 18:38:33 PST)
- [AMBER] 答复: How to plot the Phi-Psi picture in Section 7 of “Tutorial 6.6 Nudged Elastic Band (NEB) simulations”? (Fri Mar 05 2021 - 18:37:16 PST)
- [AMBER] How to plot the Phi-Psi picture in Section 7 of “Tutorial 6.6 Nudged Elastic Band (NEB) simulations”? (Tue Mar 02 2021 - 20:10:01 PST)
Liao
- Re: [AMBER] Using average frame for nmode entropy calculation? (Wed Mar 31 2021 - 20:07:49 PDT)
- Re: [AMBER] Using average frame for nmode entropy calculation? (Mon Mar 29 2021 - 11:05:42 PDT)
- Re: [AMBER] Using average frame for nmode entropy calculation? (Sun Mar 28 2021 - 07:48:03 PDT)
- [AMBER] Using average frame for nmode entropy calculation? (Sat Mar 27 2021 - 12:10:42 PDT)
- [AMBER] Effect of different gamma_ln values (Mon Mar 01 2021 - 12:29:29 PST)
Loo Kang
- [AMBER] Calculating SASA using Surf and Molsurf (Mon Mar 29 2021 - 19:10:28 PDT)
LOZANO ORDOÑEZ, HECTOR
- Re: [AMBER] LJ parameters (Wed Mar 10 2021 - 09:48:51 PST)
- [AMBER] LJ parameters (Wed Mar 10 2021 - 08:59:33 PST)
Luis Simon
- Re: [AMBER] LJ parameters (Wed Mar 10 2021 - 09:14:57 PST)
- [AMBER] Is it possible to obtain vacuum charges (and only vacuum charges) with mdgx? (Mon Mar 08 2021 - 01:48:10 PST)
Mailing list
- Re: [AMBER] Installation Ambertools20 Mac M1 (arm64) (Mon Mar 15 2021 - 01:38:43 PDT)
- [AMBER] Installation Ambertools20 Mac M1 (arm64) (Sun Mar 14 2021 - 05:59:40 PDT)
Mani Radh
- [AMBER] Electric Field Gradient (Thu Mar 25 2021 - 04:24:42 PDT)
Mariano Curti
- Re: [AMBER] cpptraj killed (Tue Mar 23 2021 - 01:28:07 PDT)
- Re: [AMBER] The issue regarding to list index out of range (Mon Mar 08 2021 - 04:21:37 PST)
Matias Machado
- Re: [AMBER] Convert SIRAH coarse-grained model back to all-atomic pdb file format? (Wed Mar 31 2021 - 08:26:05 PDT)
- Re: [AMBER] Solvating my box with specified number of water molecules (Sun Mar 21 2021 - 08:08:00 PDT)
- Re: [AMBER] SIRAH CG Protein with Implicit Solvent (Sun Mar 21 2021 - 07:55:38 PDT)
Matthew Guberman-Pfeffer
- [AMBER] How to assess mutant-induced instability with MM-GBSA (Fri Mar 19 2021 - 13:49:37 PDT)
- [AMBER] How to define COM for groups in ASMD (Sat Mar 06 2021 - 00:12:38 PST)
- [AMBER] Problem Running E-REMD on GPUs (Thu Mar 04 2021 - 19:13:20 PST)
Michael Shokhen
- [AMBER] Convert SIRAH coarse-grained model back to all-atomic pdb file format? (Tue Mar 30 2021 - 23:39:57 PDT)
Ming Tang
- Re: [AMBER] Apply Lennar-Jones potential between small molecules (Wed Mar 24 2021 - 15:55:41 PDT)
- Re: [AMBER] Apply Lennar-Jones potential between small molecules (Tue Mar 23 2021 - 16:20:59 PDT)
- Re: [AMBER] Apply Lennar-Jones potential between small molecules (Mon Mar 22 2021 - 21:31:19 PDT)
- Re: [AMBER] Apply Lennar-Jones potential between small molecules (Thu Mar 18 2021 - 07:53:33 PDT)
- Re: [AMBER] Apply Lennar-Jones potential between small molecules (Wed Mar 17 2021 - 21:15:18 PDT)
- Re: [AMBER] Apply Lennar-Jones potential between small molecules (Mon Mar 15 2021 - 16:28:21 PDT)
- Re: [AMBER] makeDIST_RST (Sun Mar 14 2021 - 01:01:37 PST)
- Re: [AMBER] makeDIST_RST (Wed Mar 10 2021 - 17:39:08 PST)
- Re: [AMBER] makeDIST_RST (Tue Mar 09 2021 - 14:51:09 PST)
- Re: [AMBER] makeDIST_RST (Sat Mar 06 2021 - 18:20:58 PST)
- [AMBER] makeDIST_RST (Wed Mar 03 2021 - 21:04:27 PST)
mohamed marzouk
- Re: [AMBER] Superimpose (Sat Mar 27 2021 - 03:57:47 PDT)
- [AMBER] Superimpose (Mon Mar 01 2021 - 10:07:43 PST)
MYRIAN TORRES RICO
- Re: [AMBER] cpptraj killed (Mon Mar 22 2021 - 10:18:51 PDT)
- [AMBER] cpptraj killed (Mon Mar 22 2021 - 02:37:51 PDT)
Nikolay N. Kuzmich
- Re: [AMBER] New in CPPTRAJ (Fri Mar 19 2021 - 12:35:57 PDT)
Pinky Mazumder
- [AMBER] Calculating displacement from PMF (Wed Mar 31 2021 - 06:58:49 PDT)
- [AMBER] Calculating displacement from PMF (Tue Mar 30 2021 - 10:10:08 PDT)
- [AMBER] Ambertools20 with amber18 (Fri Mar 05 2021 - 10:32:17 PST)
Prasanth G, Research Scholar
- Re: [AMBER] Addition of hydrogens - isoelectric point of protein (Fri Mar 26 2021 - 18:25:39 PDT)
- [AMBER] Selection of forcefield for protein-ligand simulations (Fri Mar 26 2021 - 17:24:26 PDT)
- [AMBER] Selection of forcefield for protein-ligand simulations (Thu Mar 25 2021 - 12:22:18 PDT)
- [AMBER] Addition of hydrogens - isoelectric point of protein (Thu Mar 25 2021 - 12:11:49 PDT)
Qinghua Liao
- [AMBER] positional and NMR distance restraints together (Mon Mar 01 2021 - 17:15:31 PST)
Ramanathan Rajesh
- [AMBER] Simulation of optimized ligand without docking (Wed Mar 03 2021 - 04:19:38 PST)
Rana Rehan Khalid
- [AMBER] MCPB.py ZINC Mediated interactions parameterization (Mon Mar 15 2021 - 14:56:17 PDT)
Ray Luo
- Re: [AMBER] Unknown PB option use_sav=0 (Sun Mar 21 2021 - 17:04:37 PDT)
- Re: [AMBER] Running MMPBSA on protein membrane system built using CHARMMGUI (Sat Mar 13 2021 - 18:33:34 PST)
- Re: [AMBER] Running MMPBSA on protein membrane system built using CHARMMGUI (Sat Mar 13 2021 - 15:31:44 PST)
Renato Araujo
- Re: [AMBER] erro: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered (Mon Mar 29 2021 - 10:42:07 PDT)
- Re: [AMBER] erro: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered (Mon Mar 29 2021 - 10:16:47 PDT)
- Re: [AMBER] erro: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered (Mon Mar 29 2021 - 05:47:19 PDT)
- Re: [AMBER] erro: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered (Wed Mar 24 2021 - 06:30:11 PDT)
- Re: [AMBER] erro: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered (Wed Mar 24 2021 - 05:06:27 PDT)
- [AMBER] erro: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered (Wed Mar 24 2021 - 04:19:17 PDT)
- [AMBER] GPU installation error amber18 (Thu Mar 11 2021 - 04:53:14 PST)
richa anand
- [AMBER] segmentation fault error (Tue Mar 16 2021 - 23:29:45 PDT)
- [AMBER] Energy minimization problem (Sun Mar 14 2021 - 00:15:39 PST)
- Re: [AMBER] AMBER Digest, Vol 3300, Issue 1 (Sat Mar 13 2021 - 00:29:36 PST)
- [AMBER] Tleap Fatal error (Fri Mar 12 2021 - 03:09:37 PST)
- [AMBER] Error in tleap (Fri Mar 12 2021 - 02:04:28 PST)
Richard Kullmann
- [AMBER] GB-HCP Example File and Setup (Wed Mar 24 2021 - 08:07:46 PDT)
Rinsha Chk
- [AMBER] Amber-forcefield for QM/MM calculation (Mon Mar 01 2021 - 05:05:28 PST)
Rituparna Roy
- Re: [AMBER] AMBER 18 Installation error (Fri Mar 19 2021 - 07:29:44 PDT)
- [AMBER] AMBER 18 Installation error (Fri Mar 19 2021 - 01:35:13 PDT)
Sadaf Rani
- Re: [AMBER] saving pdb and rst at specific frames in trajectory (Thu Mar 18 2021 - 00:40:22 PDT)
- Re: [AMBER] saving pdb and rst at specific frames in trajectory (Wed Mar 17 2021 - 07:09:53 PDT)
- [AMBER] saving pdb and rst at specific frames in trajectory (Wed Mar 17 2021 - 06:23:17 PDT)
Samuel Mohan Dass, Premila
- Re: [AMBER] Problem with AMBER20 compilation using Intel/20.4 compiler (Wed Mar 24 2021 - 14:10:22 PDT)
- Re: [AMBER] Problem with AMBER20 compilation using Intel/20.4 compiler (Tue Mar 09 2021 - 09:23:34 PST)
- Re: [AMBER] Problem with AMBER20 compilation using Intel/20.4 compiler (Mon Mar 08 2021 - 11:25:09 PST)
- [AMBER] Problem with AMBER20 compilation using Intel/20.4 compiler (Mon Mar 08 2021 - 11:20:52 PST)
SATYAJIT KHATUA
- Re: [AMBER] Interaction energy by MM-PBSA for a superantigen with important Zn(II) center (Fri Mar 05 2021 - 02:53:07 PST)
Shakir Ali Siddiqui
- [AMBER] Unit of Electric field frequency (Sun Mar 28 2021 - 12:03:21 PDT)
- [AMBER] Unit of Electric Field Frequency (Thu Mar 18 2021 - 04:05:13 PDT)
Shawn Brown
- Re: [AMBER] Problem with AMBER20 compilation using Intel/20.4 compiler (Thu Mar 25 2021 - 05:20:16 PDT)
- Re: [AMBER] Problem with AMBER20 compilation using Intel/20.4 compiler (Wed Mar 24 2021 - 06:43:36 PDT)
Song, Lin
- Re: [AMBER] erro: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered (Mon Mar 29 2021 - 10:37:33 PDT)
sriram raghavan
- [AMBER] Generating library from cif file. (Mon Mar 08 2021 - 07:24:10 PST)
Sruthi Sudhakar
- [AMBER] Ligand moving out of active site after 250ns (Fri Mar 12 2021 - 22:08:23 PST)
- Re: [AMBER] MMPBSA/ Parmed error (Wed Mar 03 2021 - 06:32:24 PST)
Stephan Schott
- Re: [AMBER] Problem with packmol-memgen when I try to installing Amber20 in GPU (Fri Mar 26 2021 - 05:21:12 PDT)
Thomas Cheatham
- Re: [AMBER] Selection of forcefield for protein-ligand simulations (Fri Mar 26 2021 - 17:52:47 PDT)
Tucker Burgin
- Re: [AMBER] pmemd.cuda unstable with ff19SB+OPC and HMassRepartition (Mon Mar 22 2021 - 08:10:42 PDT)
- [AMBER] pmemd.cuda unstable with ff19SB+OPC and HMassRepartition (Wed Mar 10 2021 - 11:25:22 PST)
wangjianing_mail
- [AMBER] sander/orca/xtb ：Low parallel efficiency (Wed Mar 10 2021 - 20:12:58 PST)
- Re: [AMBER] use orca in amber (Tue Mar 02 2021 - 02:31:31 PST)
- [AMBER] use orca in amber (Tue Mar 02 2021 - 01:37:05 PST)
Zhiyi Wu
- Re: [AMBER] Using DFT-D3(BJ) during QM/MM calculations (Tue Mar 02 2021 - 12:12:32 PST)
- [AMBER] Using DFT-D3(BJ) during QM/MM calculations (Tue Mar 02 2021 - 02:22:02 PST)
zz sheng
- Re: [AMBER] Distance tolerance for identifying common atoms in thermodynamics integration (Fri Mar 26 2021 - 13:56:59 PDT)
- [AMBER] Distance tolerance for identifying common atoms in thermodynamics integration (Fri Mar 26 2021 - 11:19:11 PDT)
- Re: [AMBER] Pmemd to run TI on protein mutations (Thu Mar 25 2021 - 07:09:38 PDT)
- [AMBER] Pmemd to run TI on protein mutations (Mon Mar 22 2021 - 11:00:27 PDT)
ışılay öztürk
- Re: [AMBER] Visualizing NetCDF in VMD - ERROR (Tue Mar 16 2021 - 05:35:12 PDT)
- Re: [AMBER] Visualizing NetCDF in VMD - ERROR (Tue Mar 16 2021 - 03:00:09 PDT)
- Re: [AMBER] Visualizing NetCDF in VMD - ERROR (Tue Mar 16 2021 - 02:39:28 PDT)
Игорь Злотников
- Re: [AMBER] Benchmarks for new RTX3060 (Tue Mar 23 2021 - 10:52:15 PDT)
- [AMBER] Benchmarks for new RTX3060 (Tue Mar 23 2021 - 10:43:23 PDT)
库米尔
- Re: [AMBER] Calculation halted on pmemd.cuda (Sun Mar 28 2021 - 00:22:04 PDT)
- [AMBER] Calculation halted on pmemd.cuda (Fri Mar 26 2021 - 17:10:06 PDT)
- [AMBER] Solvating my box with specified number of water molecules (Sat Mar 20 2021 - 09:20:21 PDT)
辛志宏
- [AMBER] About the extract snapshop as input files from a trajectory files (Sun Mar 14 2021 - 03:09:37 PDT)
- Re: [AMBER] The issue regarding to list index out of range (???) (Mon Mar 08 2021 - 16:07:57 PST)
- [AMBER] The issue regarding to list index out of range (Mon Mar 08 2021 - 04:12:03 PST)

Amber Archive Mar 2021 by author