Amber Archive Nov 2019: by date

Friday, 1 November 2019
- Re: [AMBER] Calculate MMGBSA keeping water in binding site Rosellen, Martin
- [AMBER] reinstallation of amber 14 Sruthi Sudhakar
Sunday, 3 November 2019
- [AMBER] Parameter file not saved student_cbc_1 nnlab
- Re: [AMBER] Parameter file not saved Bill Ross
- Re: [AMBER] Parameter file not saved Carlos Simmerling
- Re: [AMBER] Parameter file not saved David Case
- [AMBER] Problem with ABMD simulation Federico Iacovelli
- [AMBER] cpptraj.MPI query Debarati DasGupta
- [AMBER] velocity autocorrelation Ajeet Kumar Yadav
- Re: [AMBER] Problem with ABMD simulation Feng Pan
- Re: [AMBER] Problem in Leap PDB Reading Robert Molt
- Re: [AMBER] Problem in Leap PDB Reading Yong Duan
- Re: [AMBER] Problem in Leap PDB Reading Robert Molt
- Re: [AMBER] cpptraj.MPI query Daniel Roe
Monday, 4 November 2019
- [AMBER] Parameter file GTP or GMP containing tRNA student_cbc_1 nnlab
- Re: [AMBER] Parameter file GTP or GMP containing tRNA David A Case
- Re: [AMBER] cpptraj.MPI query Debarati DasGupta
- Re: [AMBER] cpptraj.MPI query Daniel Roe
- Re: [AMBER] cpptraj.MPI query Debarati DasGupta
- Re: [AMBER] cpptraj.MPI query Daniel Roe
- Re: [AMBER] velocity autocorrelation Daniel Roe
- Re: [AMBER] cpptraj.MPI query Debarati DasGupta
- Re: [AMBER] cpptraj.MPI query Daniel Roe
- Re: [AMBER] cpptraj.MPI query Debarati DasGupta
- Re: [AMBER] cpptraj.MPI query Daniel Roe
- Re: [AMBER] cpptraj.MPI query Debarati DasGupta
- [AMBER] Open Scientific Computing Roles at GSK. Ross Walker
- Re: [AMBER] cpptraj.MPI query Debarati DasGupta
Tuesday, 5 November 2019
- [AMBER] problem with MM/PB(GB)SA (Geng Dong) 东庚
- [AMBER] md simulation with GPU （Geng Dong）东庚
- [AMBER] Large GPU performance difference for umbrella sampling methods: (infe=1 and &pmd) vs (nmropt=1 and disang-rst) Åsmund Røhr Kjendseth
- Re: [AMBER] Large GPU performance difference for umbrella sampling methods: (infe=1 and &pmd) vs (nmropt=1 and disang-rst) accuratefreeenergy.gmail.com
- [AMBER] error in namelist Debarati DasGupta
- Re: [AMBER] md simulation with GPU （Geng Dong） Gerardo Zerbetto De Palma
- Re: [AMBER] error in namelist David A Case
- [AMBER] mmbpsa.py error Alen Ahmetovic
- Re: [AMBER] mmbpsa.py error David Case
- [AMBER] md simulation with GPU -Geng Dong 东庚
- Re: [AMBER] md simulation with GPU -Geng Dong Ross Walker
- Re: [AMBER] Problem in Leap PDB Reading Yong Duan
Wednesday, 6 November 2019
- [AMBER] mac os catalina..... (oh my god) Fabian Glaser
- Re: [AMBER] mac os catalina..... (oh my god) Gustaf Olsson
- [AMBER] jump in monomer position Fabian Glaser
- Re: [AMBER] mac os catalina..... (oh my god) Fabian Glaser
- Re: [AMBER] problem with MM/PB(GB)SA (Geng Dong) Ray Luo
- Re: [AMBER] jump in monomer position Carlos Simmerling
- Re: [AMBER] Minimization of ethanol in water David Case
- Re: [AMBER] jump in monomer position Fabian Glaser
Thursday, 7 November 2019
- Re: [AMBER] compiling Amber with gcc 9.2 and intel mpi 2019 Vlad Cojocaru
- Re: [AMBER] compiling Amber with gcc 9.2 and intel mpi 2019 David A Case
- Re: [AMBER] compiling Amber with gcc 9.2 and intel mpi 2019 Vlad Cojocaru
- Re: [AMBER] steered md at constant force Wesley Michael Botello-Smith
Friday, 8 November 2019
- [AMBER] tleap error MYRIAN TORRES RICO
- [AMBER] tleap error MYRIAN TORRES RICO
- Re: [AMBER] tleap error Akinpelu Olayinka
- [AMBER] tleap error MYRIAN TORRES RICO
- Re: [AMBER] tleap error Bill Ross
- [AMBER] building openMP cpptraj with intel compiler Vlad Cojocaru
- Re: [AMBER] tleap error David A Case
- Re: [AMBER] building openMP cpptraj with intel compiler Vlad Cojocaru
Saturday, 9 November 2019
- [AMBER] Metal ion parameterization using MCPB.py Abhilash J
Monday, 11 November 2019
- Re: [AMBER] How to check the convergence of NEB calculation? Charles-Alexandre Mattelaer
- [AMBER] How can I calculate dihedral distribution through CPPTRAJ 조준범
- Re: [AMBER] How to check the convergence of NEB calculation? Bill Ross
- Re: [AMBER] How to check the convergence of NEB calculation? Charles-Alexandre Mattelaer
- Re: [AMBER] How can I calculate dihedral distribution through CPPTRAJ David A Case
- [AMBER] Making ParmEd play nice with OpenEye? Brian Radak
- [AMBER] how to cluster by cpptraj 石娜
- [AMBER] cpptraj msd of center -of-mass motion 조준범
- Re: [AMBER] How can I calculate dihedral distribution through CPPTRAJ 조준범
- Re: [AMBER] How can I calculate dihedral distribution through CPPTRAJ Elvis Martis
Tuesday, 12 November 2019
- Re: [AMBER] How can I calculate dihedral distribution through CPPTRAJ 조준범
- Re: [AMBER] How can I calculate dihedral distribution through CPPTRAJ Elvis Martis
- [AMBER] AMBER18/16 12-6-4LJ Sander TI problem Paulius Kantakevicius
- Re: [AMBER] cpptraj msd of center -of-mass motion David A Case
- Re: [AMBER] strip problem in cpptraj Daniel Roe
- Re: [AMBER] building openMP cpptraj with intel compiler Daniel Roe
- Re: [AMBER] building openMP cpptraj with intel compiler Vlad Cojocaru
- Re: [AMBER] building openMP cpptraj with intel compiler Daniel Roe
- Re: [AMBER] how to cluster by cpptraj Daniel Roe
- Re: [AMBER] How can I calculate dihedral distribution through CPPTRAJ Daniel Roe
- Re: [AMBER] cpptraj msd of center -of-mass motion Daniel Roe
- [AMBER] NMR refined MD maya nair
- Re: [AMBER] building openMP cpptraj with intel compiler Vlad Cojocaru
- Re: [AMBER] NMR refined MD Christina Bergonzo
- Re: [AMBER] building openMP cpptraj with intel compiler Daniel Roe
- Re: [AMBER] NMR refined MD David A Case
- [AMBER] Using the polarizable FF GolP Lucas Bandeira
- [AMBER] Modification of gaff 조준범
- Re: [AMBER] NMR refined MD maya nair
- Re: [AMBER] NMR refined MD maya nair
Wednesday, 13 November 2019
- Re: [AMBER] Modification of gaff David A Case
- [AMBER] 2D graphic visualisation Giulia Paiardi
Thursday, 14 November 2019
- [AMBER] question about prmtop file 조준범
- [AMBER] Workshop on Free Energy calculations in Muenster March 11-13 2020 Vlad Cojocaru
- Re: [AMBER] question about prmtop file David A Case
- [AMBER] Charge neutrality in QM/MM system James Kress
- [AMBER] Calculation Tetrahedral Order Parameter of Water Ajeet Kumar Yadav
- [AMBER] different radii sets and GB models Neha Gandhi
- Re: [AMBER] different radii sets and GB models Pietro Aronica
Friday, 15 November 2019
- [AMBER] Does amber work with NVIDIA RTX6000? Shenglong Wang
- [AMBER] Broken AmberTools19 cpptraj compilation for GNU, Intel and PGI on a Cray with -crayxt5 flag Victor Holanda Rusu
- Re: [AMBER] Broken AmberTools19 cpptraj compilation for GNU, Intel and PGI on a Cray with -crayxt5 flag Daniel Roe
- Re: [AMBER] AMBER18/16 12-6-4LJ Sander TI problem Pengfei Li
- Re: [AMBER] Does amber work with NVIDIA RTX6000? David Cerutti
- Re: [AMBER] Does amber work with NVIDIA RTX6000? Shenglong Wang
- [AMBER] decompose MMGBSA error Nisha Amarnath Jonniya
- Re: [AMBER] decompose MMGBSA error Elvis Martis
Saturday, 16 November 2019
- [AMBER] Problem running production run Airy Sanjeev
- Re: [AMBER] Problem running production run Bill Ross
- Re: [AMBER] Problem running production run Bill Ross
- Re: [AMBER] AMBER18/16 12-6-4LJ Sander TI problem Paulius Kantakevicius
- [AMBER] There is an bug in how Amber preserves charge neutrality in QM/MM system when ORCA is the targeted QM tool. James Kress
- Re: [AMBER] Does amber work with NVIDIA RTX6000? David Cerutti
- Re: [AMBER] AMBER18/16 12-6-4LJ Sander TI problem Pengfei Li
- Re: [AMBER] decompose MMGBSA error Nisha Amarnath Jonniya
- Re: [AMBER] Metal ion parameterization using MCPB.py Pengfei Li
Sunday, 17 November 2019
- [AMBER] Error in PMEMD installation with MPI Rahul Verma
- [AMBER] Simulation run issue Sayan Poddar
- Re: [AMBER] decompose MMGBSA error Elvis Martis
Monday, 18 November 2019
- Re: [AMBER] decompose MMGBSA error Nisha Amarnath Jonniya
- Re: [AMBER] decompose MMGBSA error Elvis Martis
- Re: [AMBER] Error in PMEMD installation with MPI David Case
- Re: [AMBER] Simulation run issue David Case
- Re: [AMBER] decompose MMGBSA error David Case
- [AMBER] Error in themodynamic integration with PMEMD.CUDA HOCHEOL LIM
- [AMBER] MD CYT C : heme bound emanuele falbo
- [AMBER] amber maillist Q Yu
- [AMBER] Conformation of NEB end states changing during 1HEAT Madhur Aggarwal
- Re: [AMBER] Conformation of NEB end states changing during 1HEAT Ghoreishi, Delaram
- Re: [AMBER] Conformation of NEB end states changing during 1HEAT Carlos Simmerling
- Re: [AMBER] amber15 cpptraj closest Q Yu
- Re: [AMBER] Conformation of NEB end states changing during 1HEAT Madhur Aggarwal
- [AMBER] Charge neutrality in QM/MM system James Kress
- Re: [AMBER] Charge neutrality in QM/MM system David Case
- [AMBER] PIMD restart error in Amber18 jinfeng liu
- Re: [AMBER] decompose MMGBSA error Nisha Amarnath Jonniya
- Re: [AMBER] Charge neutrality in QM/MM system James Kress
- [AMBER] Problem in generating the .rst file Airy Sanjeev
- [AMBER] Error with addIons 조준범
- Re: [AMBER] Error with addIons Bill Ross
- Re: [AMBER] Error with addIons 조준범
- Re: [AMBER] Error with addIons 조준범
- Re: [AMBER] Error with addIons Bill Ross
- Re: [AMBER] Conformation of NEB end states changing during 1HEAT Ghoreishi, Delaram
- Re: [AMBER] Error with addIons 조준범
- Re: [AMBER] Error with addIons 조준범
- Re: [AMBER] Error with addIons Bill Ross
Tuesday, 19 November 2019
- Re: [AMBER] Problem in generating the .rst file Carlos Simmerling
- [AMBER] amber 16 with nVIDIA Tesla T4 GPU Schröder, David Christopher
- Re: [AMBER] Error with addIons David Case
- Re: [AMBER] Conformation of NEB end states changing during 1HEAT Madhur Aggarwal
- Re: [AMBER] Conformation of NEB end states changing during 1HEAT Ghoreishi, Delaram
- Re: [AMBER] Conformation of NEB end states changing during 1HEAT Carlos Simmerling
- [AMBER] RROR: I could not understand line - during US Fabian Glaser
- [AMBER] Error parameterizing a heme using MCPB Mohamed M. Aboelnga
- Re: [AMBER] RROR: I could not understand line - during US David Case
- Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Charles-Alexandre Mattelaer
Wednesday, 20 November 2019
- Re: [AMBER] Conformation of NEB end states changing during 1HEAT Madhur Aggarwal
- [AMBER] Amber updates brings duplicate patch viktor drobot
- Re: [AMBER] decompose MMGBSA error Nisha Amarnath Jonniya
- Re: [AMBER] RROR: I could not understand line - during US Fabian Glaser
- Re: [AMBER] RROR: I could not understand line - during US Bill Ross
- Re: [AMBER] decompose MMGBSA error Elvis Martis
- Re: [AMBER] RROR: I could not understand line - during US Fabian Glaser
- Re: [AMBER] RROR: I could not understand line - during US David A Case
- Re: [AMBER] Amber updates brings duplicate patch David A Case
- Re: [AMBER] Amber updates brings duplicate patch viktor drobot
- Re: [AMBER] RROR: I could not understand line - during US Fabian Glaser
- [AMBER] Using NetCDF trajectory files as ParmEd structure Brian Radak
- Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Ross Walker
- Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Charles-Alexandre Mattelaer
- Re: [AMBER] RROR: I could not understand line - during US David A Case
- Re: [AMBER] Amber updates brings duplicate patch David A Case
- Re: [AMBER] Error parameterizing a heme using MCPB Pengfei Li
- [AMBER] Fwd: Error in PMEMD installation with MPI Rahul Verma
- [AMBER] antechamber QM calculation/qmcharge error Rui Chen
- Re: [AMBER] decompose MMGBSA error Nisha Amarnath Jonniya
Thursday, 21 November 2019
- [AMBER] Force-field with only Bond parameters Stefano Motta
- Re: [AMBER] Force-field with only Bond parameters Carlos Simmerling
- Re: [AMBER] Force-field with only Bond parameters Stefano Motta
- Re: [AMBER] Force-field with only Bond parameters Carlos Simmerling
- Re: [AMBER] Force-field with only Bond parameters Stefano Motta
- Re: [AMBER] Force-field with only Bond parameters Carlos Simmerling
- Re: [AMBER] Force-field with only Bond parameters Stefano Motta
- Re: [AMBER] Force-field with only Bond parameters Carlos Simmerling
- Re: [AMBER] Amber updates brings duplicate patch viktor drobot
- Re: [AMBER] Force-field with only Bond parameters Stefano Motta
- Re: [AMBER] Amber updates brings duplicate patch David A Case
- Re: [AMBER] antechamber QM calculation/qmcharge error David A Case
- Re: [AMBER] decompose MMGBSA error David A Case
- Re: [AMBER] Error parameterizing a heme using MCPB Mohamed M. Aboelnga
- [AMBER] Error in themodynamic integration with PMEMD.CUDA HOCHEOL LIM
- [AMBER] Error in themodynamic integration with PMEMD.CUDA HOCHEOL LIM
- Re: [AMBER] antechamber QM calculation/qmcharge error Rui Chen
- Re: [AMBER] amber15 cpptraj closest Daniel Roe
- Re: [AMBER] Force-field with only Bond parameters David A Case
- Re: [AMBER] Error in themodynamic integration with PMEMD.CUDA David A Case
- Re: [AMBER] PIMD restart error in Amber18 David A Case
- Re: [AMBER] decompose MMGBSA error Nisha Amarnath Jonniya
- Re: [AMBER] decompose MMGBSA error Elvis Martis
- [AMBER] Error in the namelist cntrl Airy Sanjeev
Friday, 22 November 2019
- Re: [AMBER] Force-field with only Bond parameters Stefano Motta
- Re: [AMBER] Error in the namelist cntrl David A Case
- Re: [AMBER] amber15 cpptraj closest Q Yu
- Re: [AMBER] amber15 cpptraj closest Daniel Roe
- [AMBER] ATP gamma phosphate distorted in MD Qing Lv
- Re: [AMBER] ATP gamma phosphate distorted in MD Zachary Fallon
- [AMBER] absolute binding free energy calculations Debarati DasGupta
- [AMBER] List of GAF2 atom types? Gustavo Seabra
- Re: [AMBER] List of GAF2 atom types? David Case
- Re: [AMBER] ATP gamma phosphate distorted in MD Qing Lv
Monday, 25 November 2019
- [AMBER] [Bug-Report] NAB: TER record need a serial number Johannes Kalliauer
- [AMBER] Finding radial distribution function using cpptraj Raghav Arora
- Re: [AMBER] Finding radial distribution function using cpptraj Daniel Roe
- Re: [AMBER] [Bug-Report] NAB: TER record need a serial number Daniel Roe
- Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Daniel Roe
- [AMBER] Citation for GAFF2 Gustaf Olsson
- Re: [AMBER] Error parameterizing a heme using MCPB Pengfei Li
Tuesday, 26 November 2019
- [AMBER] umbrella box size for protein-protein Fabian Glaser
- [AMBER] Regarding Amber16 installation dilrajl.bii.a-star.edu.sg
- Re: [AMBER] Regarding Amber16 installation David Case
- [AMBER] Tleap-complex PDB problem Rui Chen
- Re: [AMBER] Tleap-complex PDB problem Lachele Foley
Wednesday, 27 November 2019
- Re: [AMBER] Tleap-complex PDB problem Rui Chen
- Re: [AMBER] Tleap-complex PDB problem David A Case
- Re: [AMBER] Tleap-complex PDB problem Rui Chen
- Re: [AMBER] Using NetCDF trajectory files as ParmEd structure Jason Swails
- [AMBER] ff19SB inpcrd test file missing David Wang
- Re: [AMBER] Tleap-complex PDB problem Rui Chen
- Re: [AMBER] ff19SB inpcrd test file missing Chuan Tian
Thursday, 28 November 2019
- [AMBER] Obtaining excess molar volumes using Molecular Dynamics Raghav Arora
- Re: [AMBER] decompose MMGBSA error Nisha Amarnath Jonniya
- Re: [AMBER] decompose MMGBSA error Elvis Martis
- Re: [AMBER] ff19SB inpcrd test file missing David Case
Friday, 29 November 2019
- [AMBER] HTTP Error 500 - download Mattia Pini
- [AMBER] help on this error Debarati DasGupta
- Re: [AMBER] HTTP Error 500 - download Hai Nguyen
- Re: [AMBER] help on this error David Case
Saturday, 30 November 2019
- [AMBER] MMGBSA error RITUPARNA ROY

Last message date: Sat Nov 30 2019 - 09:00:01 PST
Archived on: Fri Dec 20 2024 - 05:55:55 PST

Amber Archive Nov 2019 by date