Amber Archive Feb 2022: by date

Tuesday, 1 February 2022
- [AMBER] boron nitride Victor Nazarychev
- Re: [AMBER] boron nitride David A Case
- [AMBER] Amber20 Installation run_cmake problem Manuel Fernandez Merino
- Re: [AMBER] Modifying prmtop/inpcrd files Kenneth Huang
- Re: [AMBER] Amber20 Installation run_cmake problem David A Case
- Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) Michael Coleman
Wednesday, 2 February 2022
- Re: [AMBER] Amber20 Installation run_cmake problem Manuel Fernandez Merino
- Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) David A Case
- Re: [AMBER] Amber20 Installation run_cmake problem David A Case
- [AMBER] Mass-weighted covariance matrix gmx
- [AMBER] problem finding packmol.f90 David A Case
- Re: [AMBER] Mass-weighted covariance matrix Daniel Roe
- [AMBER] Void bubbles forming in minimization with single nucleoside/solvent? Kenneth Huang
- Re: [AMBER] Mass-weighted covariance matrix gmx
- Re: [AMBER] Void bubbles forming in minimization with single nucleoside/solvent? Carlos Simmerling
- Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) Michael Coleman
- Re: [AMBER] Modifying prmtop/inpcrd files Sam Walsworth (Researcher)
Thursday, 3 February 2022
- [AMBER] MMPBSA.py.MPI error Fabian Glaser
- Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) David A Case
- Re: [AMBER] Modifying prmtop/inpcrd files David A Case
- [AMBER] iron-sulphur clusters Ayesha Fatima
- Re: [AMBER] Amber20 Installation run_cmake problem Manuel Fernandez Merino
- [AMBER] MCPB error for organometallic complex Alexej Jerschow
- [AMBER] Query regarding 3DRISM calculation Rakesh Srivastava
- Re: [AMBER] Modifying prmtop/inpcrd files Sam Walsworth (Researcher)
- Re: [AMBER] Modifying prmtop/inpcrd files David A Case
- Re: [AMBER] Query regarding 3DRISM calculation David A Case
- Re: [AMBER] Modifying prmtop/inpcrd files Sam Walsworth (Researcher)
- Re: [AMBER] Modifying prmtop/inpcrd files Kenneth Huang
- Re: [AMBER] Modifying prmtop/inpcrd files Sam Walsworth (Researcher)
- Re: [AMBER] Modifying prmtop/inpcrd files Sam Walsworth (Researcher)
- [AMBER] Could not import Amber Python modules! Centos 7 Suguna Sakkiah
- Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) Michael Coleman
Friday, 4 February 2022
- Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) David A Case
- Re: [AMBER] Modifying prmtop/inpcrd files David A Case
- Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) Ross Walker
- Re: [AMBER] Could not import Amber Python modules! Centos 7 David A Case
- [AMBER] Same initial velocities with ig=NNN and NTT=1 (on GPU)? Dr. Anselm Horn
- [AMBER] MCPB error for organometallic complex Alexej Jerschow
- Re: [AMBER] Same initial velocities with ig=NNN and NTT=1 (on GPU)? Carlos Simmerling
- Re: [AMBER] Could not import Amber Python modules! Centos 7 Suguna Sakkiah
- [AMBER] amber gaff parameters resource?? Debarati DasGupta
- Re: [AMBER] Same initial velocities with ig=NNN and NTT=1 (on GPU)? Dr. Anselm Horn
- Re: [AMBER] Same initial velocities with ig=NNN and NTT=1 (on GPU)? Adrian Roitberg
- Re: [AMBER] Same initial velocities with ig=NNN and NTT=1 (on GPU)? Carlos Simmerling
- Re: [AMBER] Same initial velocities with ig=NNN and NTT=1 (on GPU)? Dr. Anselm Horn
- Re: [AMBER] Same initial velocities with ig=NNN and NTT=1 (on GPU)? Carlos Simmerling
- Re: [AMBER] Same initial velocities with ig=NNN and NTT=1 (on GPU)? Dr. Anselm Horn
- Re: [AMBER] Same initial velocities with ig=NNN and NTT=1 (on GPU)? Carlos Simmerling
- Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) Michael Coleman
- Re: [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI) Michael Coleman
Saturday, 5 February 2022
- Re: [AMBER] Could not import Amber Python modules! Centos 7 David A Case
- Re: [AMBER] amber gaff parameters resource?? David A Case
- Re: [AMBER] Could not import Amber Python modules! Centos 7 Suguna Sakkiah
- Re: [AMBER] Query regarding 3DRISM calculation Rakesh Srivastava
- Re: [AMBER] Could not import Amber Python modules! Centos 7 David A Case
- Re: [AMBER] Could not import Amber Python modules! Centos 7 Suguna Sakkiah
Sunday, 6 February 2022
- Re: [AMBER] Could not import Amber Python modules! Centos 7 David A Case
- [AMBER] when amber22 is going to be released? Albert
- [AMBER] mpi4py Problem Ilyas Yildirim
Monday, 7 February 2022
- Re: [AMBER] when amber22 is going to be released? David A Case
- Re: [AMBER] Could not import Amber Python modules! Centos 7 Daniel Roe
- Re: [AMBER] Could not import Amber Python modules! Centos 7 Suguna Sakkiah
- [AMBER] trouble finding vdW parameters for methanol Debarati DasGupta
- Re: [AMBER] mpi4py Problem David A Case
- [AMBER] In development of dihedral angle parameters; negative PK and negative PHASE values Cenk Andac
- Re: [AMBER] In development of dihedral angle parameters; negative PK and negative PHASE values Carlos Simmerling
- [AMBER] test cuda parallel error message Suguna Sakkiah
- Re: [AMBER] Could not import Amber Python modules! Centos 7 Suguna Sakkiah
- [AMBER] Simulation of proteins with D-amino acids nguerin
- Re: [AMBER] Simulation of proteins with D-amino acids Carlos Simmerling
- Re: [AMBER] trouble finding vdW parameters for methanol David A Case
- Re: [AMBER] test cuda parallel error message David A Case
- Re: [AMBER] mpi4py Problem Ilyas Yildirim
Tuesday, 8 February 2022
- Re: [AMBER] mpi4py Problem David A Case
- Re: [AMBER] trouble finding vdW parameters for methanol Debarati DasGupta
- Re: [AMBER] trouble finding vdW parameters for methanol Carlos Simmerling
- Re: [AMBER] mpi4py Problem Ilyas Yildirim
- Re: [AMBER] trouble finding vdW parameters for methanol Debarati DasGupta
- Re: [AMBER] trouble finding vdW parameters for methanol Carlos Simmerling
- [AMBER] Symmetric or mirrored boundary condition? Tucker Burgin
- Re: [AMBER] Simulation of proteins with D-amino acids Nathan Guerin
- [AMBER] Reg: Modified LYS residues - Can I use Gaff if so how to link with hybrid AMBERff14SB and GAFF Lara rajam
- Re: [AMBER] mpi4py Problem Jason Swails
- Re: [AMBER] mpi4py Problem Jason Swails
- Re: [AMBER] mpi4py Problem Ilyas Yildirim
Wednesday, 9 February 2022
- Re: [AMBER] Symmetric or mirrored boundary condition? David A Case
- Re: [AMBER] mpi4py Problem David A Case
- Re: [AMBER] Same initial velocities with ig=NNN and NTT=1 (on GPU)? Dr. Anselm Horn
- [AMBER] xleap problem Ibrahim Said
- Re: [AMBER] xleap problem Clorice Reinhardt
- Re: [AMBER] Reg: Modified LYS residues - Can I use Gaff if so how to link with hybrid AMBERff14SB and GAFF Dr. Anselm Horn
- Re: [AMBER] xleap problem David A Case
- [AMBER] Issues with make test.parallel during installation of parallel version of Amber IPSITA Banerjee
- [AMBER] solvation failed with Amber 20 Qinghua Liao
- Re: [AMBER] Creating .lib files from prmtop/inpcrd files David A Case
- [AMBER] Problem with make test.parallel during installation of parallel version of Amber Charlotta Lebedenko
- Re: [AMBER] Issues with make test.parallel during installation of parallel version of Amber David A Case
- Re: [AMBER] Creating .lib files from prmtop/inpcrd files Sam Walsworth (Researcher)
- Re: [AMBER] Query regarding 3DRISM calculation ABDUL BASIT
Thursday, 10 February 2022
- Re: [AMBER] solvation failed with Amber 20 Dr. Anselm Horn
- Re: [AMBER] xleap problem Ibrahim Said
- [AMBER] MMPBSA internal energy when using idecomp 4 Tue
- Re: [AMBER] solvation failed with Amber 20 Qinghua Liao
- Re: [AMBER] xleap problem Dr. Anselm Horn
- [AMBER] problem in the protein-ligand system Renato Araujo
- Re: [AMBER] MMPBSA internal energy when using idecomp 4 Tue
- Re: [AMBER] Problem with make test.parallel during installation of parallel version of Amber David A Case
- Re: [AMBER] Query regarding 3DRISM calculation David A Case
- Re: [AMBER] Query regarding 3DRISM calculation ABDUL BASIT
- Re: [AMBER] problem in the protein-ligand system Alan
- Re: [AMBER] problem in the protein-ligand system Renato Araujo
- Re: [AMBER] problem in the protein-ligand system Alan
- [AMBER] Unexpected TER chars with pdb4amber and phosphorylated amino acids Brian Radak
- Re: [AMBER] Query regarding 3DRISM calculation tluchko
- Re: [AMBER] Simulation of proteins with D-amino acids Piotr Cieplak
Friday, 11 February 2022
- Re: [AMBER] MMPBSA.py.MPI error Jason Swails
Saturday, 12 February 2022
- [AMBER] Ambrtool16 make install error spss4.iacs.res.in
- Re: [AMBER] Ambrtool16 make install error Daniel Roe
- Re: [AMBER] Ambrtool16 make install error spss4.iacs.res.in
Sunday, 13 February 2022
- Re: [AMBER] Ambrtool16 make install error David A Case
- [AMBER] Bug in mmpbsa.py internal energy when idecomp is 3 or 4 Tue Boesen
Monday, 14 February 2022
- [AMBER] Cannot heat the lipid system Vic De Roo
- Re: [AMBER] In development of dihedral angle parameters; negative PK and negative PHASE values Cenk Andac
- Re: [AMBER] In development of dihedral angle parameters; negative PK and negative PHASE values Barış KURT
- Re: [AMBER] In development of dihedral angle parameters; negative PK and negative PHASE values Cenk Andac
- Re: [AMBER] In development of dihedral angle parameters; negative PK and negative PHASE values Carlos Simmerling
- [AMBER] MD simulations for POPC membrane King Wu
- Re: [AMBER] In development of dihedral angle parameters; negative PK and negative PHASE values Cenk Andac
- Re: [AMBER] In development of dihedral angle parameters; negative PK and negative PHASE values Carlos Simmerling
- Re: [AMBER] Potential PDB and .lib file atom order mismatch Carlos Simmerling
- Re: [AMBER] In development of dihedral angle parameters; negative PK and negative PHASE values Cenk Andac
- Re: [AMBER] In development of dihedral angle parameters; negative PK and negative PHASE values Cenk Andac
- [AMBER] Cpptrj : How to give two hbond calculation at the same time. Lara rajam
- Re: [AMBER] In development of dihedral angle parameters; negative PK and negative PHASE values Barış KURT
- Re: [AMBER] Cpptrj : How to give two hbond calculation at the same time. Daniel Roe
- Re: [AMBER] CPPTRAJ, Comparing H-bonding in two trajectories Kenneth Huang
- Re: [AMBER] Cpptrj : How to give two hbond calculation at the same time. Lara rajam
- Re: [AMBER] Cpptrj : How to give two hbond calculation at the same time. Rodrigo Galindo-Murillo
- Re: [AMBER] CPPTRAJ, Comparing H-bonding in two trajectories Daniel Roe
- Re: [AMBER] CPPTRAJ, Comparing H-bonding in two trajectories Matthew Guberman-Pfeffer
Tuesday, 15 February 2022
- [AMBER] How to run 3drism.snglpnt calculations in amber20 without rst or traj files Daniel Fowles
- [AMBER] Running amber executable on multiple GPUs Prithviraj Nandigrami
- Re: [AMBER] Running amber executable on multiple GPUs Adrian Roitberg
- [AMBER] MD simulations for POPC membrane King Wu
- Re: [AMBER] MD simulations for POPC membrane Carlos Simmerling
- Re: [AMBER] MD simulations for POPC membrane King Wu
- Re: [AMBER] MD simulations for POPC membrane Carlos Simmerling
- Re: [AMBER] MD simulations for POPC membrane Elvis Martis
- Re: [AMBER] MD simulations for POPC membrane King Wu
- Re: [AMBER] How to run 3drism.snglpnt calculations in amber20 without rst or traj files tluchko
- Re: [AMBER] MD simulations for POPC membrane King Wu
- Re: [AMBER] MD simulations for POPC membrane Carlos Simmerling
- [AMBER] DNA breaking down during the simulation b.ercig.nki.nl
- Re: [AMBER] MD simulations for POPC membrane Vic De Roo
- Re: [AMBER] DNA breaking down during the simulation Carlos Simmerling
- Re: [AMBER] DNA breaking down during the simulation Thomas Cheatham
- Re: [AMBER] MD simulations for POPC membrane King Wu
- Re: [AMBER] Ambrtool16 make install error spss4.iacs.res.in
Wednesday, 16 February 2022
- Re: [AMBER] Ambrtool16 make install error 王世玉
- Re: [AMBER] DNA breaking down during the simulation Jiri Sponer
- [AMBER] Move a specific residue parallel using cpptraj Eugene huh
- Re: [AMBER] DNA breaking down during the simulation Vlad Cojocaru
- Re: [AMBER] DNA breaking down during the simulation Jiri Sponer
- Re: [AMBER] Ambrtool16 make install error David A Case
- Re: [AMBER] Ambrtool16 make install error spss4.iacs.res.in
- [AMBER] Unused parameters in tip4pew? Rosemary Millmore
- Re: [AMBER] Unused parameters in tip4pew? Jason Swails
- Re: [AMBER] Move a specific residue parallel using cpptraj Daniel Roe
- [AMBER] Fast 3-point water residue error Artur Hermano
- Re: [AMBER] CPPTRAJ, Comparing H-bonding in two trajectories Daniel Roe
- Re: [AMBER] Ambrtool16 make install error David A Case
Thursday, 17 February 2022
- [AMBER] Restart using Nosé-Hoover GIULIA BIFFI
- Re: [AMBER] Amber simulation of cyclic peptide saranya.cbmm.lodz.pl
- Re: [AMBER] Amber simulation of cyclic peptide Carlos Simmerling
- Re: [AMBER] Amber simulation of cyclic peptide Dr. Anselm Horn
- Re: [AMBER] Amber simulation of cyclic peptide saranya.cbmm.lodz.pl
- Re: [AMBER] Bug in mmpbsa.py internal energy when idecomp is 3 or 4 Jason Swails
- Re: [AMBER] Bug in mmpbsa.py internal energy when idecomp is 3 or 4 Tue Boesen
- [AMBER] Protocol to optimize bonded parameters for GAFF2 ABEL Stephane
- Re: [AMBER] Cannot heat the lipid system David A Case
Friday, 18 February 2022
- Re: [AMBER] Bug in mmpbsa.py internal energy when idecomp is 3 or 4 Jason Swails
- Re: [AMBER] Fast 3-point water residue error Jason Swails
- Re: [AMBER] Query regarding 3DRISM calculation tluchko
- [AMBER] Running Umbrella Sampling simulations Osman, Roman
- Re: [AMBER] Bug in mmpbsa.py internal energy when idecomp is 3 or 4 Tue Boesen
- [AMBER] MMPBSA.py for membrane proteins with per-residue decomposition Ravi Abrol
- Re: [AMBER] Bug in mmpbsa.py internal energy when idecomp is 3 or 4 Thomas Cheatham
Saturday, 19 February 2022
- Re: [AMBER] Bug in mmpbsa.py internal energy when idecomp is 3 or 4 Tue Boesen
- [AMBER] Single-Molecule Mixing of Force Fields Nathan Black
- Re: [AMBER] boron nitride Erdem Yeler
Sunday, 20 February 2022
- Re: [AMBER] MMPBSA.py for membrane proteins with per-residue decomposition Ray Luo
- Re: [AMBER] MMPBSA.py for membrane proteins with per-residue decomposition Ravi Abrol
- [AMBER] Problems of sander.quick.cuda xmgign.126.com
- Re: [AMBER] Problems of sander.quick.cuda Vinicius Wilian Cruzeiro
Monday, 21 February 2022
- Re: [AMBER] Workstation Recommendations Sushil Mishra
- Re: [AMBER] Single-Molecule Mixing of Force Fields Dr. Anselm Horn
- Re: [AMBER] Single-Molecule Mixing of Force Fields Nathan Black
- Re: [AMBER] Single-Molecule Mixing of Force Fields Carlos Simmerling
- Re: [AMBER] Meaning of "Multiple 'e' in NUMBER-like thing" Scott Brozell
- [AMBER] bulk properties for SPAM in mixed solvents David Poole
Tuesday, 22 February 2022
- Re: [AMBER] Single-Molecule Mixing of Force Fields Dr. Anselm Horn
- [AMBER] Removing AmberTools binary files installed on .pyenv/shims Tony Myung Keun Cho
- Re: [AMBER] Single-Molecule Mixing of Force Fields Nathan Black
- Re: [AMBER] Bug in mmpbsa.py internal energy when idecomp is 3 or 4 Jason Swails
Wednesday, 23 February 2022
- Re: [AMBER] Ambrtool16 make install error spss4.iacs.res.in
Thursday, 24 February 2022
- [AMBER] To know about the Forcefield of Pyrrolysine amino acid. PRIYANKA PUROHIT
- [AMBER] pH replica exchange MD (pH-REMD) in explicit solvent, using CUDA MPI in AMBER 18 Laura Milena Pedraza-González
- [AMBER] LEaP Not Reading a Parameter in .frcmod File Nathan Black
- Re: [AMBER] LEaP Not Reading a Parameter in .frcmod File Carlos Simmerling
- Re: [AMBER] LEaP Not Reading a Parameter in .frcmod File Nathan Black
- [AMBER] Segmentation Fault (Core Dumped) in xLEaP Nathan Black
- Re: [AMBER] LEaP Not Reading a Parameter in .frcmod File Carlos Simmerling
- Re: [AMBER] Segmentation Fault (Core Dumped) in xLEaP Carlos Simmerling
- Re: [AMBER] Segmentation Fault (Core Dumped) in xLEaP Nathan Black
- Re: [AMBER] Segmentation Fault (Core Dumped) in xLEaP Carlos Simmerling
- Re: [AMBER] Segmentation Fault (Core Dumped) in xLEaP Nathan Black
- Re: [AMBER] LEaP Not Reading a Parameter in .frcmod File Nathan Black
- Re: [AMBER] pH replica exchange MD (pH-REMD) in explicit solvent, using CUDA MPI in AMBER 18 Vinicius Wilian Cruzeiro
- Re: [AMBER] Segmentation Fault (Core Dumped) in xLEaP Nathan Black
- Re: [AMBER] Problems of sander.quick.cuda aa
Friday, 25 February 2022
- [AMBER] Fwd: Ambrtool16 make install error spss4.iacs.res.in
- Re: [AMBER] pH replica exchange MD (pH-REMD) in explicit solvent, using CUDA MPI in AMBER 18 Laura Milena Pedraza-González
- Re: [AMBER] pH replica exchange MD (pH-REMD) in explicit solvent, using CUDA MPI in AMBER 18 Laura Milena Pedraza-González
- Re: [AMBER] Fwd: Ambrtool16 make install error David A Case
- Re: [AMBER] Problems of sander.quick.cuda Jason Swails
- Re: [AMBER] Segmentation Fault (Core Dumped) in xLEaP Carlos Simmerling
- Re: [AMBER] Segmentation Fault (Core Dumped) in xLEaP Nathan Black
- Re: [AMBER] Segmentation Fault (Core Dumped) in xLEaP Carlos Simmerling
- Re: [AMBER] pH replica exchange MD (pH-REMD) in explicit solvent, using CUDA MPI in AMBER 18 Vinicius Wilian Cruzeiro
- Re: [AMBER] Problems of sander.quick.cuda Vinicius Wilian Cruzeiro
- Re: [AMBER] pH replica exchange MD (pH-REMD) in explicit solvent, using CUDA MPI in AMBER 18 Laura Milena Pedraza-González
- Re: [AMBER] Segmentation Fault (Core Dumped) in xLEaP Nathan Black
- Re: [AMBER] pH replica exchange MD (pH-REMD) in explicit solvent, using CUDA MPI in AMBER 18 Vinicius Wilian Cruzeiro
- [AMBER] coordinate and topology not generated Sadaf Rani
Saturday, 26 February 2022
- Re: [AMBER] coordinate and topology not generated Maria Nagan
- Re: [AMBER] Fortran runtime error: End of file Stephan Schott
- Re: [AMBER] Fwd: Ambrtool16 make install error spss4.iacs.res.in
- [AMBER] Clarification in 3DRISM Alexis Azucena
Sunday, 27 February 2022
- Re: [AMBER] Segmentation Fault (Core Dumped) in xLEaP Dr. Anselm Horn
- [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces Állan Ferrari
Monday, 28 February 2022
- Re: [AMBER] pH replica exchange MD (pH-REMD) in explicit solvent, using CUDA MPI in AMBER 18 Laura Milena Pedraza-González
- [AMBER] Finding percentage occupancy of pi-pi interactions Sruthi Sudhakar
- Re: [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces Carlos Simmerling
- Re: [AMBER] Segmentation Fault (Core Dumped) in xLEaP Nathan Black
- Re: [AMBER] Segmentation Fault (Core Dumped) in xLEaP Nathan Black
- Re: [AMBER] pH replica exchange MD (pH-REMD) in explicit solvent, using CUDA MPI in AMBER 18 Vinicius Wilian Cruzeiro
- [AMBER] CUDART lib not found during install Charlotta Lebedenko

Last message date: Mon Feb 28 2022 - 10:30:03 PST
Archived on: Wed Apr 24 2024 - 05:56:08 PDT

Amber Archive Feb 2022 by date