Amber Archive Dec 2016: by date

Wednesday, 30 November 2016
- [AMBER] Collective Variable not "Strictly" Enforced: Adaptively Biased MD Simulations of type "COM_ANGLE" using "FLOODING" Emmanuel
- [AMBER] clustering doubt Mary Varughese
Thursday, 1 December 2016
- [AMBER] Atom type for middle nitrogen in dycyanamide? Mohd Farid Ismail
- Re: [AMBER] clustering doubt Achim Sandmann
- [AMBER] question about pol_h in ambertool15 Thibaud von Erlach
- Re: [AMBER] clustering doubt Mary Varughese
- Re: [AMBER] clustering doubt Achim Sandmann
- Re: [AMBER] Fw: Problems with imaging Mark Waterhouse [RPG]
- Re: [AMBER] Atom type for middle nitrogen in dycyanamide? David A Case
- Re: [AMBER] question about pol_h in ambertool15 David A Case
- Re: [AMBER] question about pol_h in ambertool15 Anon
- [AMBER] trajectory analysis Carlos Romero
- Re: [AMBER] trajectory analysis Elvis Martis
Friday, 2 December 2016
- Re: [AMBER] question about pol_h in ambertool15 Thibaud von Erlach
- [AMBER] multiple residues and solvatebox command Azade Yazdan Yar
- Re: [AMBER] multiple residues and solvatebox command David A Case
- [AMBER] Slowly reducing restraints Dd H
- Re: [AMBER] Slowly reducing restraints Elvis Martis
- Re: [AMBER] Collective Variable not "Strictly" Enforced: Adaptively Biased MD Simulations of type "COM_ANGLE" using "FLOODING" Feng Pan
- Re: [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD Brian Radak
Monday, 5 December 2016
- [AMBER] ReCpHMD Optimal values of ntcnstph, ntrelax, nstlim and numexchg Fabrício Bracht
- Re: [AMBER] ReCpHMD Optimal values of ntcnstph, ntrelax, nstlim and numexchg Jason Swails
- Re: [AMBER] ReCpHMD Optimal values of ntcnstph, ntrelax, nstlim and numexchg Adrian Roitberg
- Re: [AMBER] ReCpHMD Optimal values of ntcnstph, ntrelax, nstlim and numexchg Jason Swails
- [AMBER] CpHMD tutorial: how to generate the titration_curves.dat file in an automated way Eric Lang
- Re: [AMBER] CpHMD tutorial: how to generate the titration_curves.dat file in an automated way Fabrício Bracht
- Re: [AMBER] CpHMD tutorial: how to generate the titration_curves.dat file in an automated way Jason Swails
- Re: [AMBER] CpHMD tutorial: how to generate the titration_curves.dat file in an automated way Eric Lang
- Re: [AMBER] Paramfit for multiple molecules Robin Betz
- [AMBER] MMGBSA vs MMPBSA Aronica, Pietro
- Re: [AMBER] MMGBSA vs MMPBSA Hai Nguyen
Tuesday, 6 December 2016
- [AMBER] Parmchk2 and dihedral parameters Andreas Gavrielides
- [AMBER] How to turn off non-bonded interactions A kS
- Re: [AMBER] Parmchk2 and dihedral parameters David A Case
- Re: [AMBER] How to turn off non-bonded interactions David A Case
- Re: [AMBER] Parmchk2 and dihedral parameters Andreas Gavrielides
- [AMBER] GIST: nan (not a number) in unreferenced water-water energy of the grid Bruno Falcone
- Re: [AMBER] Parmchk2 and dihedral parameters David A Case
- Re: [AMBER] GIST: nan (not a number) in unreferenced water-water energy of the grid Steven Ramsey
- Re: [AMBER] MMGBSA vs MMPBSA Ray Luo
- Re: [AMBER] GIST: nan (not a number) in unreferenced water-water energy of the grid Bruno Falcone
- Re: [AMBER] GIST: nan (not a number) in unreferenced water-water energy of the grid Steven Ramsey
- Re: [AMBER] GIST: nan (not a number) in unreferenced water-water energy of the grid Daniel Roe
- Re: [AMBER] GIST: nan (not a number) in unreferenced water-water energy of the grid Bruno Falcone
- Re: [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD Daniel Roe
- Re: [AMBER] clustering doubt Daniel Roe
- Re: [AMBER] Paramfit for multiple molecules (Robin Betz) Sven Hackbusch
- Re: [AMBER] MMGBSA vs MMPBSA Aronica, Pietro
- Re: [AMBER] clustering doubt Mary Varughese
Wednesday, 7 December 2016
- [AMBER] Amber 16: ** NFE-Error ** : Cannot read &colvar namelist! Ruth Helena Tichauer
- [AMBER] Explicit solvent CpHMD calculation with Amber14 Tsibela German Tebello Mofokeng
- Re: [AMBER] Explicit solvent CpHMD calculation with Amber14 Jason Swails
- Re: [AMBER] Explicit solvent CpHMD calculation with Amber14 Carlos Simmerling
- Re: [AMBER] Explicit solvent CpHMD calculation with Amber14 Tsibela German Tebello Mofokeng
- Re: [AMBER] Amber 16: ** NFE-Error ** : Cannot read &colvar namelist! Daniel Roe
- Re: [AMBER] MMGBSA vs MMPBSA Ray Luo
- Re: [AMBER] Amber 16: ** NFE-Error ** : Cannot read &colvar namelist! Ruth Helena Tichauer
- Re: [AMBER] Amber 16: ** NFE-Error ** : Cannot read &colvar namelist! Feng Pan
- Re: [AMBER] GIST: nan (not a number) in unreferenced water-water energy of the grid Bruno Falcone
- Re: [AMBER] GIST: nan (not a number) in unreferenced water-water energy of the grid Daniel Roe
- [AMBER] The AmberTools 16 build errors Juwen
- Re: [AMBER] The AmberTools 16 build errors Nhai
- Re: [AMBER] The AmberTools 16 build errors Nhai
- Re: [AMBER] The AmberTools 16 build errors Juwen
- Re: [AMBER] The AmberTools 16 build errors Nhai
- [AMBER] Query regarding Ligand Binding Metalloprotein with MCPB.py Abhilash J
Thursday, 8 December 2016
- [AMBER] Parallel installation of MMPBSA.py.MPI failed MOHD HOMAIDUR RAHMAN
- [AMBER] NADH antechamber Andreas Tosstorff
- [AMBER] QM/MM/MD g09 interface issues, David Poole
- Re: [AMBER] NADH antechamber FyD
- Re: [AMBER] Parallel installation of MMPBSA.py.MPI failed Jason Swails
- Re: [AMBER] QM/MM/MD g09 interface issues, Fabrício Bracht
- Re: [AMBER] Amber 16: ** NFE-Error ** : Cannot read &colvar namelist! Ruth Helena Tichauer
- Re: [AMBER] NADH antechamber David A Case
- [AMBER] Installation of AMBER on Centos Rocks 6.2 Yasir Israr
- Re: [AMBER] Installation of AMBER on Centos Rocks 6.2 Elvis Martis
- Re: [AMBER] Installation of AMBER on Centos Rocks 6.2 Yasir Israr
- Re: [AMBER] Installation of AMBER on Centos Rocks 6.2 Elvis Martis
Friday, 9 December 2016
- Re: [AMBER] NADH antechamber Andreas Tosstorff
- [AMBER] Fitting of rms2d Mike Nemec
- Re: [AMBER] Fitting of rms2d Carlos Simmerling
- [AMBER] Eigenvector visualization in Nmode JPB
- [AMBER] HMR with ParmEd for PSF/PDB inputs? Brian Radak
- Re: [AMBER] HMR with ParmEd for PSF/PDB inputs? Hai Nguyen
- Re: [AMBER] HMR with ParmEd for PSF/PDB inputs? Brian Radak
- Re: [AMBER] HMR with ParmEd for PSF/PDB inputs? Hai Nguyen
- Re: [AMBER] HMR with ParmEd for PSF/PDB inputs? Brian Radak
- Re: [AMBER] HMR with ParmEd for PSF/PDB inputs? Hai Nguyen
- [AMBER] Freeze Atoms in Nab The Cromicus Productions
- Re: [AMBER] Eigenvector visualization in Nmode The Cromicus Productions
- Re: [AMBER] Eigenvector visualization in Nmode The Cromicus Productions
- [AMBER] error 睿 ?
- Re: [AMBER] Freeze Atoms in Nab David A Case
- Re: [AMBER] Eigenvector visualization in Nmode David A Case
- Re: [AMBER] error Hai Nguyen
- Re: [AMBER] error 睿翟
Saturday, 10 December 2016
- Re: [AMBER] Installation of AMBER on Centos Rocks 6.2 yasir.orionsolutions.co.in
- Re: [AMBER] Installation of AMBER on Centos Rocks 6.2 Hai Nguyen
- Re: [AMBER] Installation of AMBER on Centos Rocks 6.2 yasir.orionsolutions.co.in
- Re: [AMBER] Installation of AMBER on Centos Rocks 6.2 Hai Nguyen
- Re: [AMBER] Installation of AMBER on Centos Rocks 6.2 yasir.orionsolutions.co.in
- Re: [AMBER] Installation of AMBER on Centos Rocks 6.2 yasir.orionsolutions.co.in
- Re: [AMBER] Installation of AMBER on Centos Rocks 6.2 yasir.orionsolutions.co.in
- Re: [AMBER] error David A Case
- Re: [AMBER] Installation of AMBER on Centos Rocks 6.2 David A Case
- Re: [AMBER] HMR with ParmEd for PSF/PDB inputs? Jason Swails
Sunday, 11 December 2016
- Re: [AMBER] HMR with ParmEd for PSF/PDB inputs? Brian Radak
- [AMBER] 10. QM/MM/MD g09 interface issues, now tleap David Poole
- [AMBER] Questions regarding Installation of AMBER 16 James Kress
- Re: [AMBER] Questions regarding Installation of AMBER 16 Hai Nguyen
- [AMBER] [Amber] Calculation of Velocity Autocorrelation Function The Cromicus Productions
- Re: [AMBER] HMR with ParmEd for PSF/PDB inputs? Jason Swails
- [AMBER] Untwisting a molecule The Cromicus Productions
- [AMBER] different frequencies for mdout/mdinfo writes? Bill Ross
- Re: [AMBER] Untwisting a molecule David A Case
- Re: [AMBER] Untwisting a molecule Bill Ross
- Re: [AMBER] Untwisting a molecule The Cromicus Productions
- Re: [AMBER] Untwisting a molecule Bill Ross
- [AMBER] Magnesium ion and MMPBSA/GBSA Francesco Gentile
- Re: [AMBER] Magnesium ion and MMPBSA/GBSA Elvis Martis
Monday, 12 December 2016
- Re: [AMBER] Untwisting a molecule Josh Berryman
- [AMBER] AmberTools16 installation problem a.jarmula.nencki.gov.pl
- Re: [AMBER] Untwisting a molecule Christina Bergonzo
- Re: [AMBER] AmberTools16 installation problem David A Case
- Re: [AMBER] AmberTools16 installation problem David A Case
- Re: [AMBER] Untwisting a molecule Daniel Roe
- [AMBER] acdoctor: Warning: There are no hydrogen and halogens in this molecule, it is highly possible that this molecule has open valence Andreas Tosstorff
- Re: [AMBER] [Amber] Calculation of Velocity Autocorrelation Function Daniel Roe
- [AMBER] Editing residue in PDB file Nikolay N. Kuzmich
- Re: [AMBER] HMR with ParmEd for PSF/PDB inputs? Brian Radak
- Re: [AMBER] HMR with ParmEd for PSF/PDB inputs? Nhai
- Re: [AMBER] HMR with ParmEd for PSF/PDB inputs? Nhai
- Re: [AMBER] Editing residue in PDB file David A Case
- Re: [AMBER] acdoctor: Warning: There are no hydrogen and halogens in this molecule, it is highly possible that this molecule has open valence David A Case
- Re: [AMBER] Magnesium ion and MMPBSA/GBSA David A Case
- Re: [AMBER] Magnesium ion and MMPBSA/GBSA Ray Luo
- Re: [AMBER] Magnesium ion and MMPBSA/GBSA Brian Radak
- Re: [AMBER] different frequencies for mdout/mdinfo writes? Daniel Roe
- Re: [AMBER] Questions regarding Installation of AMBER 16 Daniel Roe
- Re: [AMBER] different frequencies for mdout/mdinfo writes? Lorenzo Gontrani
- [AMBER] pka of CYS Sowmya Indrakumar
- [AMBER] REMD with pressure coupling Neale, Christopher Andrew
- Re: [AMBER] REMD with pressure coupling Daniel Roe
- [AMBER] Problems during solvation of molecule from Protein Data Bank The Cromicus Productions
- Re: [AMBER] Problems during solvation of molecule from Protein Data Bank The Cromicus Productions
- Re: [AMBER] Problems during solvation of molecule from Protein Data Bank Carlos Simmerling
- Re: [AMBER] Problems during solvation of molecule from Protein Data Bank David A Case
- [AMBER] MMPBSA Quasi-Harmonic Entropy Sachin Natesh
- Re: [AMBER] pka of CYS Eric Lang
Tuesday, 13 December 2016
- Re: [AMBER] acdoctor: Warning: There are no hydrogen and halogens in this molecule, it is highly possible that this molecule has open valence Andreas Tosstorff
- Re: [AMBER] acdoctor: Warning: There are no hydrogen and halogens in this molecule, it is highly possible that this molecule has open valence Andreas Tosstorff
- [AMBER] Zinc Oxide and protein simulation with AMBER vivek m
- Re: [AMBER] Problems during solvation of molecule from Protein Data Bank Sowmya Indrakumar
- Re: [AMBER] pka of CYS Carlos Simmerling
- [AMBER] Minimum distance between imgaes A kS
- Re: [AMBER] pka of CYS Eric Lang
- Re: [AMBER] Minimum distance between imgaes Daniel Roe
- Re: [AMBER] Minimum distance between imgaes A kS
- Re: [AMBER] Minimum distance between imgaes Daniel Roe
- Re: [AMBER] Minimum distance between imgaes A kS
- Re: [AMBER] acdoctor: Warning: There are no hydrogen and halogens in this molecule, it is highly possible that this molecule has open valence David A Case
- Re: [AMBER] acdoctor: Warning: There are no hydrogen and halogens in this molecule, it is highly possible that this molecule has open valence Andreas Tosstorff
- Re: [AMBER] pka of CYS Adrian Roitberg
- Re: [AMBER] REMD with pressure coupling Adrian Roitberg
- [AMBER] Re_Re: Editing residue in PDB file Nikolay N. Kuzmich
- Re: [AMBER] acdoctor: Warning: There are no hydrogen and halogens in this molecule, it is highly possible that this molecule has open valence Bruno Falcone
- Re: [AMBER] acdoctor: Warning: There are no hydrogen and halogens in this molecule, it is highly possible that this molecule has open valence Andreas Tosstorff
- Re: [AMBER] HMR with ParmEd for PSF/PDB inputs? Jason Swails
- Re: [AMBER] pka of CYS Sowmya Indrakumar
- Re: [AMBER] pka of CYS Andreas Tosstorff
- Re: [AMBER] Re_Re: Editing residue in PDB file David A Case
- Re: [AMBER] Zinc Oxide and protein simulation with AMBER David A Case
- Re: [AMBER] pka of CYS Sowmya Indrakumar
- [AMBER] The right character for logical AND in mask definition in MMPBSA ? Marek Maly
- Re: [AMBER] pka of CYS Jason Swails
- Re: [AMBER] The right character for logical AND in mask definition in MMPBSA ? Jason Swails
- Re: [AMBER] Zinc Oxide and protein simulation with AMBER vivek m
- Re: [AMBER] pka of CYS Carlos Simmerling
- Re: [AMBER] pka of CYS Jason Swails
- Re: [AMBER] pka of CYS Carlos Simmerling
- Re: [AMBER] Zinc Oxide and protein simulation with AMBER Pengfei Li
- [AMBER] Fwd: AmberTools 16: IBM XL Compiler Support James Ostrander
- Re: [AMBER] The right character for logical AND in mask definition in MMPBSA ? Marek Maly
- Re: [AMBER] Fwd: AmberTools 16: IBM XL Compiler Support Jason Swails
- [AMBER] Hydrogen bond calculataion richa anand
Wednesday, 14 December 2016
- [AMBER] mmpbsa snapshots Mary Varughese
- Re: [AMBER] mmpbsa snapshots Elvis Martis
- Re: [AMBER] mmpbsa snapshots Mary Varughese
- Re: [AMBER] clustering doubt Mary Varughese
- Re: [AMBER] mmpbsa snapshots Elvis Martis
- Re: [AMBER] mmpbsa snapshots Mary Varughese
- [AMBER] Frequencies in AMBER, obtaining the hessian Stregone
- Re: [AMBER] Frequencies in AMBER, obtaining the hessian David A Case
- [AMBER] Uridine diphosphate rhamnose (UDP-Rha) Imma Speciale
- [AMBER] sviol script error ? Benjamin Chagot
- [AMBER] cpptraj cluster -representative structure Thomas Pochapsky
- Re: [AMBER] Uridine diphosphate rhamnose (UDP-Rha) David A Case
- Re: [AMBER] cpptraj cluster -representative structure Elvis Martis
- Re: [AMBER] cpptraj cluster -representative structure Thomas Cheatham
- Re: [AMBER] Hydrogen bond calculataion Daniel Roe
- Re: [AMBER] clustering doubt Daniel Roe
- Re: [AMBER] cpptraj cluster -representative structure Thomas Pochapsky
- Re: [AMBER] REMD with pressure coupling Neale, Christopher Andrew
- [AMBER] Constant pH across membrane Fabrício Bracht
- [AMBER] About Constant pH Molecular Dynamics 上海科技大学吴萌
- [AMBER] Two different graphics cards in the same PC for pmemd.cuda Anton Perera
- Re: [AMBER] Two different graphics cards in the same PC for pmemd.cuda Elvis Martis
- Re: [AMBER] Constant pH across membrane Jason Swails
- Re: [AMBER] Two different graphics cards in the same PC for pmemd.cuda Elvis Martis
Thursday, 15 December 2016
- Re: [AMBER] REMD with pressure coupling Giovanni Bussi
- [AMBER] difference between %occupied and lifetime in hydrogen bond analysis Andrew Bostick
- Re: [AMBER] clustering doubt Mary Varughese
- Re: [AMBER] Constant pH across membrane Fabrício Bracht
- Re: [AMBER] clustering doubt Nhai
- Re: [AMBER] Constant pH across membrane Adrian Roitberg
- Re: [AMBER] sviol script error ? David A Case
- Re: [AMBER] Constant pH across membrane Fabrício Bracht
- [AMBER] pmemd.cuda incomplete output file Andreas Tosstorff
- Re: [AMBER] clustering doubt Daniel Roe
- Re: [AMBER] difference between %occupied and lifetime in hydrogen bond analysis Daniel Roe
- Re: [AMBER] Uridine diphosphate rhamnose (UDP-Rha) FyD
- [AMBER] Remove water from mdvel file The Cromicus Productions
- Re: [AMBER] pmemd.cuda incomplete output file Andreas Tosstorff
- Re: [AMBER] Remove water from mdvel file Nhai
- Re: [AMBER] pmemd.cuda incomplete output file Niel Henriksen
- Re: [AMBER] Remove water from mdvel file The Cromicus Productions
- Re: [AMBER] REMD with pressure coupling Jason Swails
- Re: [AMBER] pmemd.cuda incomplete output file Andreas Tosstorff
- Re: [AMBER] pmemd.cuda incomplete output file Hai Nguyen
- Re: [AMBER] pmemd.cuda incomplete output file Andreas Tosstorff
Friday, 16 December 2016
- Re: [AMBER] REMD with pressure coupling Giovanni Bussi
- Re: [AMBER] pmemd.cuda incomplete output file Niel Henriksen
- Re: [AMBER] pmemd.cuda incomplete output file David A Case
- [AMBER] Specify Grid Origin in 3D-RISM - Is it possible? Lucia Fusani
- Re: [AMBER] Specify Grid Origin in 3D-RISM - Is it possible? George Giambasu
- Re: [AMBER] pka of CYS Sowmya Indrakumar
- Re: [AMBER] pka of CYS Eric Lang
- [AMBER] ensuring lack of non-equilibrium jolt on restart Neale, Christopher Andrew
Saturday, 17 December 2016
- [AMBER] Unknown atom type EP A kS
- Re: [AMBER] Unknown atom type EP David Case
Sunday, 18 December 2016
- Re: [AMBER] pmemd.cuda incomplete output file Andreas Tosstorff
- Re: [AMBER] pmemd.cuda incomplete output file David Case
- Re: [AMBER] ensuring lack of non-equilibrium jolt on restart David Case
- Re: [AMBER] Unknown atom type EP A kS
- [AMBER] Constant pH Molecular Dynamics for membrane protein 上海科技大学吴萌
- Re: [AMBER] Constant pH Molecular Dynamics for membrane protein Jason Swails
- [AMBER] TI calculation problem in pmemd cuiyinglukitty
- Re: [AMBER] TI calculation problem in pmemd Hannes Loeffler
Monday, 19 December 2016
- Re: [AMBER] 10. QM/MM/MD g09 interface issues, now tleap David Case
- Re: [AMBER] Issue with the gaff parameters for "nh" atom type David Case
- [AMBER] parmchk2 multiple parameters Andreas Gavrielides
- [AMBER] Error in rst file Mohaddeseh Habibzadeh
- Re: [AMBER] Error in rst file Nhai
- Re: [AMBER] Error in rst file Mohaddeseh Habibzadeh
- Re: [AMBER] Error in rst file Nhai
- Re: [AMBER] REMD with pressure coupling Neale, Christopher Andrew
- Re: [AMBER] Error in rst file Mohaddeseh Habibzadeh
- Re: [AMBER] parmchk2 multiple parameters David Case
- Re: [AMBER] parmchk2 multiple parameters Andreas Gavrielides
- [AMBER] Amber16 on GPUs and speed differences between CUDA_VISIBLE_DEVICES=0, 1 or 0, 2 Neale, Christopher Andrew
- [AMBER] Amber16 on GPUs and speed differences between CUDA_VISIBLE_DEVICES=0, 1 or 0, 2 Neale, Christopher Andrew
- [AMBER] Amber16 on GPUs and speed differences between CUDA_VISIBLE_DEVICES=0, 1 or 0, 2 Neale, Christopher Andrew
- [AMBER] locating cpinutil.py file Tsibela German Tebello Mofokeng
- Re: [AMBER] locating cpinutil.py file Hai Nguyen
- Re: [AMBER] Amber16 on GPUs and speed differences between CUDA_VISIBLE_DEVICES=0, 1 or 0, 2 Andreas Tosstorff
- [AMBER] Benign typo for a constant in barostats.F90 Neale, Christopher Andrew
- [AMBER] ERROR no map function for HH12 ARG srinivas penumutchu
- Re: [AMBER] AmberTools16 installation problem a.jarmula.nencki.gov.pl
- [AMBER] Error: The system has extended beyond the extent of the virtual box. Taylor, Miles
- Re: [AMBER] Error: The system has extended beyond the extent of the virtual box. Nhai
Tuesday, 20 December 2016
- Re: [AMBER] Error in rst file Mohaddeseh Habibzadeh
- Re: [AMBER] ERROR no map function for HH12 ARG David Case
- Re: [AMBER] Error in rst file David Case
- [AMBER] bad atom type MN2+ ions in the binding free energy decomposition (Amber14) 袁浩亮
- Re: [AMBER] Error in rst file Mohaddeseh Habibzadeh
- [AMBER] How to have a certain number of water molecules? Azade Yazdan Yar
- Re: [AMBER] bad atom type MN2+ ions in the binding free energy decomposition (Amber14) Elvis Martis
- [AMBER] problem building Amber 16 with Intel compilers Susan Chacko
- Re: [AMBER] problem building Amber 16 with Intel compilers Hai Nguyen
- Re: [AMBER] problem building Amber 16 with Intel compilers Hai Nguyen
- [AMBER] van der Waals parameters GAFF UFF OPLS Bruno Falcone
- Re: [AMBER] problem building Amber 16 with Intel compilers Susan Chacko
- Re: [AMBER] REMD with pressure coupling Neale, Christopher Andrew
- Re: [AMBER] problem building Amber 16 with Intel compilers Susan Chacko
- Re: [AMBER] problem building Amber 16 with Intel compilers Hai Nguyen
- Re: [AMBER] How to have a certain number of water molecules? David Case
- [AMBER] addion issue Hirdesh Kumar
- Re: [AMBER] addion issue Hai Nguyen
- Re: [AMBER] addion issue Hirdesh Kumar
- Re: [AMBER] addion issue Hai Nguyen
- Re: [AMBER] van der Waals parameters GAFF UFF OPLS David Case
- Re: [AMBER] addion issue Hirdesh Kumar
- Re: [AMBER] problem building Amber 16 with Intel compilers Susan Chacko
- Re: [AMBER] problem building Amber 16 with Intel compilers Hai Nguyen
- Re: [AMBER] problem building Amber 16 with Intel compilers Daniel Roe
- Re: [AMBER] problem building Amber 16 with Intel compilers Yeng-Tseng Wang
- Re: [AMBER] Fwd: AmberTools 16: IBM XL Compiler Support James Ostrander
- Re: [AMBER] Fwd: AmberTools 16: IBM XL Compiler Support James Ostrander
- Re: [AMBER] 10. QM/MM/MD g09 interface issues, now tleap David Poole
- Re: [AMBER] problem building Amber 16 with Intel compilers Susan Chacko
- Re: [AMBER] problem building Amber 16 with Intel compilers Hai Nguyen
- Re: [AMBER] Fwd: AmberTools 16: IBM XL Compiler Support Hai Nguyen
- Re: [AMBER] Fwd: AmberTools 16: IBM XL Compiler Support Jason Swails
- Re: [AMBER] 10. QM/MM/MD g09 interface issues, now tleap David Case
- [AMBER] Problem building FEW and mmpbsa.pl in Amber16 Tong Zhu
- Re: [AMBER] Problem building FEW and mmpbsa.pl in Amber16 Nhai
- Re: [AMBER] bad atom type MN2+ ions in the binding free energy decomposition (Amber14) 袁浩亮
- [AMBER] Possible conformations predicted by MD from NMR data (RDC, dihedral) Trang Nguyen
- Re: [AMBER] Problem building FEW and mmpbsa.pl in Amber16 Tong Zhu
Wednesday, 21 December 2016
- Re: [AMBER] addion issue Prajwal Nandekar
- [AMBER] rdf_with_center_in_cpptraj_16 JAIME RUBIO MARTINEZ
- Re: [AMBER] Possible conformations predicted by MD from NMR data (RDC, dihedral) David A Case
- [AMBER] Problem about one GPU & multiple CPUs 吴萌
- [AMBER] cpptraj LIE on a ghost-atom Elisa Pieri
- Re: [AMBER] Problem about one GPU & multiple CPUs Daniel Roe
- Re: [AMBER] rdf_with_center_in_cpptraj_16 Daniel Roe
- Re: [AMBER] addion issue Hirdesh Kumar
- Re: [AMBER] rdf_with_center_in_cpptraj_16 JAIME RUBIO MARTINEZ
- Re: [AMBER] Zinc Oxide and protein simulation with AMBER vivek m
- [AMBER] Force field modifications Jonathan Huihui
- Re: [AMBER] Force field modifications David Cerutti
Thursday, 22 December 2016
- [AMBER] solvatebox command Mohaddeseh Habibzadeh
- [AMBER] How to perform energy decomposition in Thermodynamic integration with Sander in Amber 14? Stefan Ivanov
- Re: [AMBER] Force field modifications Jonathan Huihui
- Re: [AMBER] solvatebox command David A Case
- Re: [AMBER] Force field modifications David A Case
- [AMBER] neutralization and Salt concentration for DNA simulations Muthukumaran R
- Re: [AMBER] How to perform energy decomposition in Thermodynamic integration with Sander in Amber 14? Dwight McGee
- Re: [AMBER] pmemd.cuda incomplete output file Andreas Tosstorff
- Re: [AMBER] pmemd.cuda incomplete output file Niel Henriksen
- Re: [AMBER] neutralization and Salt concentration for DNA simulations Rodrigo Galindo-Murillo
- Re: [AMBER] REMD with pressure coupling Feng Pan
- Re: [AMBER] Zinc Oxide and protein simulation with AMBER Pengfei Li
- Re: [AMBER] REMD with pressure coupling Chris Neale
- [AMBER] error in amber 16 mpi installation Michael Shokhen
- Re: [AMBER] error in amber 16 mpi installation Daniel Roe
- Re: [AMBER] error in amber 16 mpi installation Hai Nguyen
- Re: [AMBER] error in amber 16 mpi installation Michael Shokhen
- [AMBER] Amber16 configure: error: could not find mpi library for --enable-mpi Michael Shokhen
- Re: [AMBER] Amber16 configure: error: could not find mpi library for --enable-mpi Nhai
- Re: [AMBER] REMD with pressure coupling Jason Swails
- Re: [AMBER] cpptraj LIE on a ghost-atom Jason Swails
- Re: [AMBER] REMD with pressure coupling Feng Pan
- Re: [AMBER] REMD with pressure coupling Chris Neale
- Re: [AMBER] REMD with pressure coupling Chris Neale
- Re: [AMBER] REMD with pressure coupling Feng Pan
Friday, 23 December 2016
- Re: [AMBER] How to perform energy decomposition in Thermodynamic integration with Sander in Amber 14? Stefan Ivanov
- Re: [AMBER] Problem building FEW and mmpbsa.pl in Amber16 David A Case
Sunday, 25 December 2016
- Re: [AMBER] rdf_with_center_in_cpptraj_16 JAIME RUBIO MARTINEZ
- [AMBER] failed testing cuda Michael Shokhen
Monday, 26 December 2016
- [AMBER] Problem in not defining the hybridization of a atomtype A kS
- [AMBER] 2D distance plots Abhilash J
- [AMBER] SEP non-standard phosphoserine issue. Saman Yousuf ali
- Re: [AMBER] SEP non-standard phosphoserine issue. Hai Nguyen
- Re: [AMBER] SEP non-standard phosphoserine issue. Hai Nguyen
- [AMBER] Distance diffusion calculation in ptraj and cpptraj wei
Tuesday, 27 December 2016
- Re: [AMBER] Distance diffusion calculation in ptraj and cpptraj Huang Jing
- Re: [AMBER] failed testing cuda David A Case
- Re: [AMBER] Problem in not defining the hybridization of a atomtype David A Case
- [AMBER] Water density near the protein suspiciously low I Lőrincz
- Re: [AMBER] Water density near the protein suspiciously low Hai Nguyen
- Re: [AMBER] Water density near the protein suspiciously low Bill Ross
- Re: [AMBER] Water density near the protein suspiciously low Chris Moth
- [AMBER] 回复：Re: Distance diffusion calculation in ptraj and cpptraj wei
- Re: [AMBER] Water density near the protein suspiciously low David Case
- [AMBER] Proplem about how to set substrate concentration Shanghaitech University WuMeng
- Re: [AMBER] Proplem about how to set substrate concentration Huang Jing
Wednesday, 28 December 2016
- Re: [AMBER] Water density near the protein suspiciously low I Lőrincz
- Re: [AMBER] Proplem about how to set substrate concentration Sérgio Marques
- Re: [AMBER] Distance diffusion calculation in ptraj and cpptraj Daniel Roe
- Re: [AMBER] 回复：Re: Distance diffusion calculation in ptraj and cpptraj Daniel Roe
- [AMBER] cuda.h: No such file or directory Elka Firmanda
- Re: [AMBER] cuda.h: No such file or directory David Case
Thursday, 29 December 2016
- [AMBER] help in restart file Robin Jain
- Re: [AMBER] help in restart file Hai Nguyen
- [AMBER] Should I image atoms when I calculate translational and rotational diffusion constants with cpptraj? wei
Friday, 30 December 2016
- Re: [AMBER] help in restart file David A Case
- Re: [AMBER] Should I image atoms when I calculate translational and rotational diffusion constants with cpptraj? David A Case
- [AMBER] Umbrella sampling (US) along RMSD-based coordinates using targeted MD script Tarsis
- [AMBER] Principal Component Analysis (PCA) query. Abhilash J
- Re: [AMBER] Principal Component Analysis (PCA) query. Daniel Roe
- Re: [AMBER] rdf_with_center_in_cpptraj_16 Daniel Roe
- Re: [AMBER] Principal Component Analysis (PCA) query. Abhilash J
- [AMBER] Remove motion of center of mass after obtaining trajectory The Cromicus Productions
- Re: [AMBER] Remove motion of center of mass after obtaining trajectory Hai Nguyen
- Re: [AMBER] Remove motion of center of mass after obtaining trajectory The Cromicus Productions
- Re: [AMBER] Remove motion of center of mass after obtaining trajectory The Cromicus Productions

Last message date: Sat Dec 31 2016 - 00:00:03 PST
Archived on: Wed Dec 25 2024 - 05:55:27 PST

Amber Archive Dec 2016 by date