Amber Archive Feb 2020: by date

Saturday, 1 February 2020
- Re: [AMBER] cpptraj_clucster Lod King
- Re: [AMBER] cpptraj_clucster Daniel Roe
- [AMBER] ante-MMPBSA.py Rui Chen
- Re: [AMBER] ante-MMPBSA.py Elvis Martis
- Re: [AMBER] ante-MMPBSA.py Rui Chen
- [AMBER] installation of amber 18 failed - CUDA_HOME not set (although not true) Bisignano, Paola
- Re: [AMBER] ante-MMPBSA.py Elvis Martis
- Re: [AMBER] ante-MMPBSA.py Elvis Martis
- Re: [AMBER] installation of amber 18 failed - CUDA_HOME not set (although not true) Elvis Martis
- Re: [AMBER] installation of amber 18 failed - CUDA_HOME not set (although not true) Bisignano, Paola
- Re: [AMBER] ante-MMPBSA.py Rui Chen
- Re: [AMBER] installation of amber 18 failed - CUDA_HOME not set (although not true) Gerardo Zerbetto De Palma
Sunday, 2 February 2020
- Re: [AMBER] installation of amber 18 failed - CUDA_HOME not set (although not true) David Case
- [AMBER] "Bad inpcrd file!" when running pmemd.MPI but not pmemd Johannes Blaschke
Monday, 3 February 2020
- [AMBER] .crd error MYRIAN TORRES RICO
- Re: [AMBER] .crd error Daniel Roe
- Re: [AMBER] "Bad inpcrd file!" when running pmemd.MPI but not pmemd Daniel Roe
- Re: [AMBER] "Bad inpcrd file!" when running pmemd.MPI but not pmemd David A Case
- Re: [AMBER] .crd error David A Case
- Re: [AMBER] sulfonamide parameters for correct geometry Junmei Wang
- [AMBER] Reading Frames from Trajectory File Catherine Jenifer Rajam Rajendran
- Re: [AMBER] Reading Frames from Trajectory File Carlos Simmerling
- Re: [AMBER] [External] Re: Reading Frames from Trajectory File Catherine Jenifer Rajam Rajendran
- Re: [AMBER] [External] Re: Reading Frames from Trajectory File Carlos Simmerling
- Re: [AMBER] [External] Re: Reading Frames from Trajectory File Catherine Jenifer Rajam Rajendran
- Re: [AMBER] Reading Frames from Trajectory File Daniel Roe
- Re: [AMBER] [External] Re: Reading Frames from Trajectory File Catherine Jenifer Rajam Rajendran
- Re: [AMBER] Help building a model of a 2F-2S protein with MDPB.py Gustavo Seabra
- Re: [AMBER] Help building a model of a 2F-2S protein with MDPB.py Pengfei Li
- Re: [AMBER] About utilities to convert Amber input files for MD into the Tinker, NAMD, Genesis, or Desmond input files Pengfei Li
- Re: [AMBER] parameters for Si3N4 Pengfei Li
- [AMBER] heme B parameter by mcpb PRAGYA PRIYADARSHINI
Tuesday, 4 February 2020
- Re: [AMBER] .crd error MYRIAN TORRES RICO
- Re: [AMBER] .crd error Gustaf Olsson
- [AMBER] pdb4amber strips atoms Petro
- Re: [AMBER] Resolving overlapping atoms. Petro
- Re: [AMBER] .crd error MYRIAN TORRES RICO
- Re: [AMBER] pdb4amber strips atoms Petro
- Re: [AMBER] .crd error David A Case
- Re: [AMBER] .crd error MYRIAN TORRES RICO
- Re: [AMBER] .crd error Gustaf Olsson
- Re: [AMBER] .crd error Carlos Simmerling
- [AMBER] CPPTRAJ hydrogen bond analysis Rui Chen
- Re: [AMBER] .crd error MYRIAN TORRES RICO
- Re: [AMBER] .crd error Daniel Roe
- Re: [AMBER] CPPTRAJ hydrogen bond analysis Daniel Roe
- Re: [AMBER] CalcError: /truba/sw/centos6.4/app/amber/amber14/bin/sander failed with prmtop gas.complex.prmtop! Rana Rehan Khalid
- Re: [AMBER] CPPTRAJ hydrogen bond analysis Rui Chen
Wednesday, 5 February 2020
- [AMBER] Gas phase simulation for heat of vaporization calculation wijaya.t.aa.m.titech.ac.jp
- [AMBER] Reg. Periodic Boundary Conditions DHEERAJ CHITARA
- Re: [AMBER] Reg. Periodic Boundary Conditions Carlos Simmerling
- Re: [AMBER] Reg. Periodic Boundary Conditions David A Case
- Re: [AMBER] (no subject) mirzo
- [AMBER] counterions present in topology files for the MMPSA calculation Shilpa Gupta
- Re: [AMBER] counterions present in topology files for the MMPSA calculation Elvis Martis
- [AMBER] Several FAILED tests for AmberTools19 and Amber18 zmatovic.kg.ac.rs
- [AMBER] AQUA-DUCT Summer School 22-25 June, Gliwice, Poland Markowska
- [AMBER] hiii ankita mehta
- Re: [AMBER] hiii David A Case
- Re: [AMBER] hiii ankita mehta
- Re: [AMBER] hiii ankita mehta
Thursday, 6 February 2020
- [AMBER] MMPBSA calculations Baptiste Legrand
- Re: [AMBER] hiii Daniel Roe
- Re: [AMBER] Shaw DE RNA ff in Amber format Josh Berryman
- [AMBER] Question about LSC-IVR keep running without any output information after PIMD sampling wangjianing_mail
- Re: [AMBER] sulfonamide parameters for correct geometry Annachiara TINIVELLA
- Re: [AMBER] Shaw DE RNA ff in Amber format Cavender, Chapin
- [AMBER] On QM/MM dummy atom and deprotonated TYR David Sáez
- [AMBER] tleap/xleap performance enhancement Himanshu Joshi
- Re: [AMBER] On QM/MM dummy atom and deprotonated TYR Clorice Reinhardt
- Re: [AMBER] On QM/MM dummy atom and deprotonated TYR David Sáez
- Re: [AMBER] MMPBSA calculations Elvis Martis
Friday, 7 February 2020
- Re: [AMBER] tleap/xleap performance enhancement David A Case
- [AMBER] [LEaP] Atom does not have a type Johannes Kalliauer
- Re: [AMBER] [LEaP] Atom does not have a type Gustavo Seabra
- Re: [AMBER] [LEaP] Atom does not have a type mirzo
- Re: [AMBER] tleap/xleap performance enhancement Himanshu Joshi
- Re: [AMBER] tleap/xleap performance enhancement Himanshu Joshi
- Re: [AMBER] [LEaP] Atom does not have a type David A Case
- [AMBER] question about pressure and sensible MD trajectories Gordon Richard Chalmers
- Re: [AMBER] question about pressure and sensible MD trajectories Gordon Richard Chalmers
Saturday, 8 February 2020
- [AMBER] query on a script called getdvdl.py in AMBER TI tutorial section Debarati DasGupta
- [AMBER] Regarding RMSD calculation and Clustering Manish Kumar Mohanty
Monday, 10 February 2020
- [AMBER] TI on pmemd CUDA, AMBER18 Hosein Geraili Daronkola
- [AMBER] DOCKED LIGAND CONFORMATION INTO AMBER MD Sruthi Sudhakar
- Re: [AMBER] DOCKED LIGAND CONFORMATION INTO AMBER MD Elvis Martis
- Re: [AMBER] tleap/xleap performance enhancement Matias Machado
- [AMBER] kindly guide me. ALAMGIR KHAN
Tuesday, 11 February 2020
- Re: [AMBER] kindly guide me. David A Case
- [AMBER] how to treat capped non-standard AA residue Vaibhav Dixit
- Re: [AMBER] TI on pmemd CUDA, AMBER18 Taisung Lee
- Re: [AMBER] On QM/MM dummy atom and deprotonated TYR David Sáez
- Re: [AMBER] On QM/MM dummy atom and deprotonated TYR Clorice Reinhardt
- Re: [AMBER] On QM/MM dummy atom and deprotonated TYR Clorice Reinhardt
- [AMBER] pmemd.cuda installation Bacaita Simona
- [AMBER] AMBER 18 installation issue Abhilash J
- [AMBER] Query regarding 3DRISM in Amber with CHARMM force field Rakesh Srivastava
Wednesday, 12 February 2020
- Re: [AMBER] pmemd.cuda installation David A Case
- Re: [AMBER] Amber install error David A Case
- Re: [AMBER] AMBER 18 installation issue David A Case
- Re: [AMBER] AMBER 18 installation issue Abhilash J
- Re: [AMBER] Query regarding 3DRISM in Amber with CHARMM force field Tyler Luchko (Lists)
- [AMBER] Simulation of an asymmetric membrane model Eduardo R. Almeida
- [AMBER] Representative structures from `clusterdihedral`? Gustavo Seabra
- [AMBER] BMRB Chemical shift values Lod King
- [AMBER] counter ions in TI calculations Maier, Sarah
- Re: [AMBER] counter ions in TI calculations Josh Berryman
Thursday, 13 February 2020
- [AMBER] QM/MM AMBER/ORCA: output emanuele falbo
- Re: [AMBER] Simulation of an asymmetric membrane model ABEL Stephane
- Re: [AMBER] QM/MM AMBER/ORCA: output Goetz, Andreas
- Re: [AMBER] BMRB Chemical shift values Christina Bergonzo
- Re: [AMBER] QM/MM AMBER/ORCA: output emanuele falbo
- Re: [AMBER] BMRB Chemical shift values Gordon Richard Chalmers
- Re: [AMBER] BMRB Chemical shift values Lod King
- Re: [AMBER] BMRB Chemical shift values Adrian Roitberg
- Re: [AMBER] Simulation of an asymmetric membrane model Matias Machado
- [AMBER] Compatibility issue of Atom type naming in AMBER Lod King
- [AMBER] H++ processing non-standard amino acids: Atom does not have a type Wei-Tse Hsu
- Re: [AMBER] QM/MM AMBER/ORCA: output Goetz, Andreas
Friday, 14 February 2020
- [AMBER] combination of MD simulations with NMR Vlad Cojocaru
- [AMBER] Production run in NVT ensemble Baptiste Legrand
Thursday, 13 February 2020
- [AMBER] how to locate all parameters for specific AA in parm directory Vaibhav Dixit
Friday, 14 February 2020
- Re: [AMBER] how to locate all parameters for specific AA in parm directory Carlos Simmerling
- Re: [AMBER] Production run in NVT ensemble Carlos Simmerling
- Re: [AMBER] how to locate all parameters for specific AA in parm directory Vaibhav Dixit
- [AMBER] Dihedral restraint problems in AMBER16/18 Rebecca Twidale
- Re: [AMBER] Compatibility issue of Atom type naming in AMBER David A Case
- Re: [AMBER] H++ processing non-standard amino acids: Atom does not have a type Ramu Anandakrishnan
- Re: [AMBER] how to locate all parameters for specific AA in parm directory Vaibhav Dixit
- Re: [AMBER] how to locate all parameters for specific AA in parm directory Carlos Simmerling
- [AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin. Marcelo Andrade Chagas
- Re: [AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin. Lachele Foley
- Re: [AMBER] Dihedral restraint problems in AMBER16/18 Kellon Belfon
Saturday, 15 February 2020
- [AMBER] tLEaP error of the N-terminal OXT atom Wei-Tse Hsu
- Re: [AMBER] tLEaP error of the N-terminal OXT atom Carlos Simmerling
Sunday, 16 February 2020
- [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit
- Re: [AMBER] no bonds formed between AA and non-standard residue Clorice Reinhardt
- Re: [AMBER] no bonds formed between AA and non-standard residue Carlos Simmerling
- Re: [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit
- Re: [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit
- Re: [AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin. Marcelo Andrade Chagas
- Re: [AMBER] no bonds formed between AA and non-standard residue Busra Demir
- Re: [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit
Monday, 17 February 2020
- Re: [AMBER] no bonds formed between AA and non-standard residue Busra Demir
- [AMBER] MMPBSA.py error Sruthi Sudhakar
- Re: [AMBER] MMPBSA.py error Pietro Aronica
- Re: [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit
- Re: [AMBER] no bonds formed between AA and non-standard residue David A Case
- Re: [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit
- Re: [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit
- [AMBER] install amber Nicolas Feldman
- Re: [AMBER] install amber Elvis Martis
- Re: [AMBER] install amber Nicolas Feldman
- Re: [AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin. Oliver Grant
- Re: [AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin. Marcelo Andrade Chagas
- Re: [AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin. Karl Kirschner
- [AMBER] installing Nicolas Feldman
- Re: [AMBER] installing Gerardo Zerbetto De Palma
- Re: [AMBER] installing Nicolas Feldman
- Re: [AMBER] installing Gerardo Zerbetto De Palma
- Re: [AMBER] installing Gerardo Zerbetto De Palma
- Re: [AMBER] installing Nicolas Feldman
- Re: [AMBER] installing Gerardo Zerbetto De Palma
- Re: [AMBER] installing Nicolas Feldman
- Re: [AMBER] installing Nicolas Feldman
- Re: [AMBER] installing Gerardo Zerbetto De Palma
- Re: [AMBER] installing Gustaf Olsson
- Re: [AMBER] installing Nicolas Feldman
- Re: [AMBER] installing Gustaf Olsson
- Re: [AMBER] installing Gerardo Zerbetto De Palma
- Re: [AMBER] installing Nicolas Feldman
- Re: [AMBER] installing Gerardo Zerbetto De Palma
- Re: [AMBER] installing Nicolas Feldman
- Re: [AMBER] installing Gerardo Zerbetto De Palma
- Re: [AMBER] installing Nicolas Feldman
- Re: [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit
- [AMBER] suggest an article for MD for covalent inhibitors ALAMGIR KHAN
- [AMBER] Force field for terminal phosphorylated residues Ming Tang
Tuesday, 18 February 2020
- [AMBER] What Can I do for Mixture of Solutions simulation and what should I assign epsilon value for this? Erdem Yeler
- [AMBER] mmpbsa.py Sruthi Sudhakar
- Re: [AMBER] Force field for terminal phosphorylated residues David A Case
- Re: [AMBER] mmpbsa.py David A Case
- Re: [AMBER] installing Daniel Roe
- Re: [AMBER] mmpbsa.py Sruthi Sudhakar
- Re: [AMBER] installing Nicolas Feldman
- Re: [AMBER] installing Gerardo Zerbetto De Palma
- Re: [AMBER] installing Nicolas Feldman
- Re: [AMBER] mmpbsa.py Ray Luo
- Re: [AMBER] installing Gerardo Zerbetto De Palma
- Re: [AMBER] mmpbsa.py Sruthi Sudhakar
- Re: [AMBER] installing Nicolas Feldman
- Re: [AMBER] installing Gerardo Zerbetto De Palma
- Re: [AMBER] What Can I do for Mixture of Solutions simulation and what should I assign epsilon value for this? David A Case
- Re: [AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin. Lachele Foley
- [AMBER] Shearing useful tips for adding ions to biomolecular simulations Matias Machado
- Re: [AMBER] Force field for terminal phosphorylated residues Ming Tang
- Re: [AMBER] Force field for terminal phosphorylated residues Ming Tang
- Re: [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit
Wednesday, 19 February 2020
- Re: [AMBER] Production run in NVT ensemble Baptiste Legrand
- [AMBER] kindly guide me ALAMGIR KHAN
- Re: [AMBER] kindly guide me Pietro Aronica
- [AMBER] Running Amber in a GPU cluster Aravind R
- Re: [AMBER] Running Amber in a GPU cluster Carlos Simmerling
- Re: [AMBER] no bonds formed between AA and non-standard residue David A Case
- Re: [AMBER] kindly guide me David A Case
- [AMBER] facing problem in installation of Amber18 with CUDA support SATYAJIT KHATUA
- [AMBER] Doubt in running mmpbsa Sruthi Sudhakar
- Re: [AMBER] Doubt in running mmpbsa Elvis Martis
- [AMBER] amber18 tests failures Antonio Bauzá Riera
- Re: [AMBER] amber18 tests failures David Cerutti
- Re: [AMBER] Doubt in running mmpbsa Sruthi Sudhakar
- Re: [AMBER] Doubt in running mmpbsa Elvis Martis
- Re: [AMBER] QM/MM AMBER/ORCA: output emanuele falbo
- Re: [AMBER] Doubt in running mmpbsa Sruthi Sudhakar
- Re: [AMBER] QM/MM AMBER/ORCA: output Goetz, Andreas
- [AMBER] Versions of AMBER Frederico Henrique
- Re: [AMBER] Versions of AMBER David A Case
- [AMBER] Unexpected reaction occurred in QM/MM umbrella sampling Qing Lv
- Re: [AMBER] Unexpected reaction occurred in QM/MM umbrella sampling Goetz, Andreas
- Re: [AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin. Lachele Foley
- Re: [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit
- [AMBER] facing problem in installation of Amber18 with CUDA support SATYAJIT KHATUA
- Re: [AMBER] facing problem in installation of Amber18 with CUDA support David Cerutti
Thursday, 20 February 2020
- [AMBER] amber18 tests failure Antonio Bauzá
- Re: [AMBER] Unexpected reaction occurred in QM/MM umbrella sampling Qing Lv
- Re: [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit
- Re: [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit
- Re: [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit
- [AMBER] facing problem in installation of Amber18 with CUDA SATYAJIT KHATUA
- [AMBER] Using cutoffs smaller than 8 A Abdullah Bin Faheem
Friday, 21 February 2020
- Re: [AMBER] TI on pmemd CUDA, AMBER18 Hosein Geraili Daronkola
Saturday, 22 February 2020
- [AMBER] Amber 16 or 20 Fabian Glaser
- [AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available? Pietro Amodeo
- Re: [AMBER] Amber 16 or 20 David A Case
- [AMBER] Regarding compatibility of PLUMED with the MPI and CUDA versions of pmemd SATYAJIT KHATUA
- Re: [AMBER] Amber 16 or 20 Vaibhav Dixit
Sunday, 23 February 2020
- [AMBER] vmd progress time Fabian Glaser
- Re: [AMBER] vmd progress time James Kress
- [AMBER] inquiry regarding minimum-image convention in cpptraj Akshay Prabhakant
Monday, 24 February 2020
- Re: [AMBER] inquiry regarding minimum-image convention in cpptraj Daniel Roe
- [AMBER] frcmod.urea Parameters for urea (or urea-water mixtures). Fabian Glaser
- [AMBER] Clustering logistics Debarati DasGupta
- Re: [AMBER] Clustering logistics Daniel Roe
Tuesday, 25 February 2020
- [AMBER] make test MPI don't continue Nicolas Feldman
- Re: [AMBER] vmd progress time Fabian Glaser
Wednesday, 26 February 2020
- Re: [AMBER] vmd progress time Gustaf Olsson
- Re: [AMBER] vmd progress time Fabian Glaser
- Re: [AMBER] vmd progress time Gustaf Olsson
- Re: [AMBER] vmd progress time Arun Srikanth
- Re: [AMBER] vmd progress time Fabian Glaser
- [AMBER] Single ion solvation free energy calculations. Akhilesh Paspureddi
- [AMBER] Weird error with antechamber for metal ion / MCPB tutorial Gustavo Seabra
- Re: [AMBER] Weird error with antechamber for metal ion / MCPB tutorial David A Case
- Re: [AMBER] Weird error with antechamber for metal ion / MCPB tutorial David A Case
Thursday, 27 February 2020
- Re: [AMBER] Weird error with antechamber for metal ion / MCPB tutorial Marcelo Andrade Chagas
- [AMBER] lack scripts for Continuous constant pH molecular dynamics Yingang Feng
- Re: [AMBER] make test MPI don't continue Gustaf Olsson
- Re: [AMBER] make test MPI don't continue Gustaf Olsson
- Re: [AMBER] Weird error with antechamber for metal ion / MCPB tutorial Gustavo Seabra
- Re: [AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available? Abhilash J
- Re: [AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available? Ross Walker
- Re: [AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available? Ross Walker
- Re: [AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available? Abhilash J
- Re: [AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available? Ross Walker
- Re: [AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available? Abhilash J
- Re: [AMBER] Single ion solvation free energy calculations. Tyler Luchko (Lists)
- [AMBER] MCPB.py with mixed valence di-iron system? Gustavo Seabra
- Re: [AMBER] MCPB.py with mixed valence di-iron system? Marcelo Andrade Chagas
Friday, 28 February 2020
- [AMBER] generate ligand frcmod and lib files Madhur Aggarwal
- Re: [AMBER] generate ligand frcmod and lib files Elvis Martis
- [AMBER] replica exchange with GPU bbalta.itu.edu.tr
- Re: [AMBER] replica exchange with GPU Carlos Simmerling
- [AMBER] Tutorial A08 Nicolas Feldman
- [AMBER] TI calculations in AMBER18 Debarati DasGupta
- [AMBER] G quadruplex simulation Sruthi Sudhakar
Saturday, 29 February 2020
- Re: [AMBER] G quadruplex simulation Sruthi Sudhakar
- [AMBER] Amber and Domains Conformational Dynamics mario
- Re: [AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available? Pietro Amodeo

Last message date: Sat Feb 29 2020 - 12:30:02 PST
Archived on: Wed Nov 20 2024 - 05:55:45 PST

Amber Archive Feb 2020 by date