Amber Archive May 2020: by date

Thursday, 30 April 2020
- [AMBER] SHAKE ALgorithm and frcmod file Elif Çiğdem Calvin
- Re: [AMBER] TI simulations Song, Lin
Friday, 1 May 2020
- [AMBER] timestep dt for higher temperatures Liao
- Re: [AMBER] wrong geometry amide nitrogen Arnaud Bondon
- Re: [AMBER] SHAKE ALgorithm and frcmod file Elif Çiğdem Calvin
- Re: [AMBER] SHAKE ALgorithm and frcmod file Carlos Simmerling
- Re: [AMBER] TI simulations Debarati DasGupta
- Re: [AMBER] SHAKE ALgorithm and frcmod file Elif Çiğdem Calvin
- Re: [AMBER] SHAKE ALgorithm and frcmod file David A Case
- Re: [AMBER] timestep dt for higher temperatures David A Case
- Re: [AMBER] SHAKE ALgorithm and frcmod file Elif Çiğdem Calvin
- [AMBER] QM/MM with finite temperature string Pratul Agarwal
- Re: [AMBER] wrong geometry amide nitrogen Junmei Wang
Saturday, 2 May 2020
- [AMBER] Leaprc error janardhanan c
- [AMBER] Simulation stops during NPT Sunita Patel
- Re: [AMBER] Simulation stops during NPT Carlos Simmerling
- Re: [AMBER] Leaprc error Daniel Roe
- Re: [AMBER] wrong geometry amide nitrogen Arnaud Bondon
- [AMBER] NPT 2 ns of equilibration Debarati DasGupta
- Re: [AMBER] NPT 2 ns of equilibration Carlos Simmerling
- [AMBER] Free energy calculation and system crash Sadaf Rani
- Re: [AMBER] Free energy calculation and system crash Carlos Simmerling
- Re: [AMBER] Free energy calculation and system crash Sadaf Rani
- Re: [AMBER] Simulation stops during NPT Sunita Patel
Sunday, 3 May 2020
- Re: [AMBER] Leaprc error janardhanan c
- Re: [AMBER] Simulation stops during NPT Carlos Simmerling
- Re: [AMBER] Simulation stops during NPT Sunita Patel
- Re: [AMBER] Simulation stops during NPT Sunita Patel
Monday, 4 May 2020
- [AMBER] CPPTRAJ: distance between atoms emanuele falbo
- Re: [AMBER] CPPTRAJ: distance between atoms Daniel Roe
- [AMBER] Release of Amber20 and AmberTools20 David A Case
- Re: [AMBER] Simulation stops during NPT David A Case
- [AMBER] Abasic Site and Errant OH Group on Sugar Robert Molt
- Re: [AMBER] Release of Amber20 and AmberTools20 Robert Molt
- Re: [AMBER] Free energy calculation and system crash Sadaf Rani
- Re: [AMBER] Free energy calculation and system crash Carlos Simmerling
- Re: [AMBER] Abasic Site and Errant OH Group on Sugar Christina Bergonzo
- [AMBER] Mass-weighted RMSD one-liner with cpptraj - possible? Martin Mielke
- Re: [AMBER] Release of Amber20 and AmberTools20 David A Case
- Re: [AMBER] Abasic Site and Errant OH Group on Sugar David A Case
- [AMBER] creating parameters for a thioglycoside rosaester.forgione.unina.it
- Re: [AMBER] creating parameters for a thioglycoside Karl Kirschner
- [AMBER] cpptraj PCA PC-mode pseudo traj Schröder, David Christopher
- Re: [AMBER] cpptraj PCA PC-mode pseudo traj Daniel Roe
- Re: [AMBER] cpptraj PCA PC-mode pseudo traj Schröder, David Christopher
Tuesday, 5 May 2020
- [AMBER] AmberTools20 comilation on macOS Gustaf Olsson
- Re: [AMBER] AmberTools20 comilation on macOS Gustaf Olsson
- Re: [AMBER] AmberTools20 comilation on macOS Gustaf Olsson
- Re: [AMBER] AmberTools20 comilation on macOS Gustaf Olsson
- [AMBER] The lipid section in the 2020 manual require updating Zhiyi Wu
- [AMBER] C4 parameters for Au0 from INTERFACE FF sbojarowski.chem.uw.edu.pl
- Re: [AMBER] AmberTools20 comilation on macOS David A Case
- Re: [AMBER] Mass-weighted RMSD one-liner with cpptraj - possible? Daniel Roe
- Re: [AMBER] The lipid section in the 2020 manual require updating David A Case
- Re: [AMBER] The lipid section in the 2020 manual require updating Stephan Schott
- Re: [AMBER] The lipid section in the 2020 manual require updating Gould, Ian R
- Re: [AMBER] The lipid section in the 2020 manual require updating Ross Walker
- Re: [AMBER] The lipid section in the 2020 manual require updating Stephan Schott
- Re: [AMBER] AmberTools20 comilation on macOS Gustaf Olsson
- Re: [AMBER] AmberTools20 comilation on macOS Gustaf Olsson
- [AMBER] CO atom type missing in PARMCHK.DAT Casalini Tommaso
- Re: [AMBER] AmberTools20 comilation on macOS David A Case
- Re: [AMBER] Mass-weighted RMSD one-liner with cpptraj - possible? Martin Mielke
- [AMBER] FRCMOD FILE DATABASE Jenny 148
- Re: [AMBER] AmberTools20 comilation on macOS Gustaf Olsson
- Re: [AMBER] FRCMOD FILE DATABASE Gustaf Olsson
Wednesday, 6 May 2020
- [AMBER] MM-PBSA calculation error Serena Vittorio
- [AMBER] Flags to Turn off Charges in pmemd Sharif Nada
- [AMBER] MMGBSA-DECOM calculation Renato Araujo
- [AMBER] Amber20 sander speed difference between cmake and old configure method Charo del Genio
- Re: [AMBER] FRCMOD FILE DATABASE Brent Krueger
- Re: [AMBER] MMGBSA-DECOM calculation Elvis Martis
- Re: [AMBER] AmberTools20 comilation on macOS David A Case
- Re: [AMBER] MM-PBSA calculation error David A Case
- Re: [AMBER] MMGBSA-DECOM calculation Renato Araujo
- [AMBER] can i analysis number of water molecules in protein by watershell 石娜
- Re: [AMBER] MMGBSA-DECOM calculation Renato Araujo
- Re: [AMBER] Mass-weighted RMSD one-liner with cpptraj - possible? Martin Mielke
- Re: [AMBER] MMGBSA-DECOM calculation Elvis Martis
- [AMBER] Amber20 sander speed difference between cmake and old configure method (addendum) Charo del Genio
- Re: [AMBER] AmberTools20 comilation on macOS Gustaf Olsson
- Re: [AMBER] Mass-weighted RMSD one-liner with cpptraj - possible? Daniel Roe
- Re: [AMBER] [BULK] Re: MM-PBSA calculation error Serena Vittorio
- [AMBER] addions Jisha B
- [AMBER] RMSD discontinuity between NPT and NVT with restraints Thomas Gaillard
- Re: [AMBER] addions Christina Bergonzo
- Re: [AMBER] Amber20 sander speed difference between cmake and old configure method David A Case
- [AMBER] about charmmgen Francesco Pietra
- Re: [AMBER] [BULK] Re: MM-PBSA calculation error David A Case
- Re: [AMBER] [EXTERNAL] addions Smith, Micholas D.
- Re: [AMBER] [EXTERNAL] addions Matias Machado
- [AMBER] Minimum recommended hardware specs for AmberTools20 and Amber20 Adrianne Lee
Thursday, 7 May 2020
- Re: [AMBER] Minimum recommended hardware specs for AmberTools20 and Amber20 Martin Mielke
- [AMBER] How to merge GLYCAM06 and lipid17 to generate force field for simple g; ycolipids? Vijay Achari
- Re: [AMBER] [BULK] Re: [BULK] Re: MM-PBSA calculation error Serena Vittorio
- [AMBER] Thermodynamic integration by parameter interpolation (PI-TI) Veenis, Andrew Jay
- Re: [AMBER] Mass-weighted RMSD one-liner with cpptraj - possible? Daniel Roe
Friday, 8 May 2020
- Re: [AMBER] Mass-weighted RMSD one-liner with cpptraj - possible? Martin Mielke
- [AMBER] MD and MD-tar restrictions MYRIAN TORRES RICO
- [AMBER] OHE residue and crashing Piia Kokkonen
- [AMBER] Xmin minimisation Athena N
- [AMBER] how to compute the protein interaction surface with the ligand Thomas Evangelidis
- Re: [AMBER] Xmin minimisation Scott Brozell
- [AMBER] Temperature and total energy keeps dropping with NVE ensemble Liao
Saturday, 9 May 2020
- [AMBER] GPU based TI runs Debarati DasGupta
- Re: [AMBER] Xmin minimisation David A Case
- Re: [AMBER] Temperature and total energy keeps dropping with NVE ensemble David A Case
- Re: [AMBER] GPU based TI runs David A Case
- Re: [AMBER] GPU based TI runs Debarati DasGupta
- Re: [AMBER] GPU based TI runs Song, Lin
- Re: [AMBER] Temperature and total energy keeps dropping with NVE ensemble Adrian Roitberg
- Re: [AMBER] GPU based TI runs Debarati DasGupta
- Re: [AMBER] GPU based TI runs Song, Lin
- Re: [AMBER] GPU based TI runs Debarati DasGupta
- Re: [AMBER] addions Robert Molt
- Re: [AMBER] addions James Kress
- Re: [AMBER] addions Robert Molt
- Re: [AMBER] addions Matias Machado
- Re: [AMBER] addions Robert Molt
- Re: [AMBER] addions James Kress
Sunday, 10 May 2020
- [AMBER] the error from make test.serial 谢信锐
- [AMBER] Neutralizing a system Jenny 148
- Re: [AMBER] the error from make test.serial David A Case
- Re: [AMBER] the error from make test.serial 谢信锐
- Re: [AMBER] tlea Lachele Foley
- Re: [AMBER] the error from make test.serial David A Case
- Re: [AMBER] Neutralizing a system David A Case
- Re: [AMBER] OHE residue and crashing David A Case
- Re: [AMBER] How to merge GLYCAM06 and lipid17 to generate force field for simple g; ycolipids? Lachele Foley
- Re: [AMBER] tlea David Cerutti
- [AMBER] Ewald grid size question Yuliana Bosken
- Re: [AMBER] Ewald grid size question David A Case
- Re: [AMBER] Ewald grid size question Yuliana Bosken
- Re: [AMBER] Ewald grid size question David Cerutti
- Re: [AMBER] Temperature and total energy keeps dropping with NVE ensemble David Cerutti
Monday, 11 May 2020
- [AMBER] error MMPBSA MYRIAN TORRES RICO
- Re: [AMBER] creating parameters for a thioglycoside rosaester.forgione.unina.it
- Re: [AMBER] error MMPBSA Elvis Martis
- [AMBER] MMPBSA - Ternary System = protein-ligand-1-ligand-2 Marcelo Andrade Chagas
- Re: [AMBER] error MMPBSA MYRIAN TORRES RICO
- Re: [AMBER] error MMPBSA David A Case
- Re: [AMBER] MMPBSA - Ternary System = protein-ligand-1-ligand-2 David A Case
- Re: [AMBER] OHE residue and crashing Christina Bergonzo
- Re: [AMBER] error MMPBSA Elvis Martis
- [AMBER] 2 aminpurine parameter from Bryce reference? Kenneth Huang
- [AMBER] 2 aminpurine parameter from Bryce reference? Kenneth Huang
- Re: [AMBER] 2 aminpurine parameter from Bryce reference? David A Case
- Re: [AMBER] OHE residue and crashing Piia Kokkonen
Tuesday, 12 May 2020
- Re: [AMBER] OHE residue and crashing David A Case
- Re: [AMBER] Amber20 sander speed difference between cmake and old configure method David A Case
- [AMBER] How to perameterize peptide like compound Rana Rehan Khalid
- Re: [AMBER] How to perameterize peptide like compound David Cerutti
- [AMBER] help MYRIAN TORRES RICO
- Re: [AMBER] 2 aminpurine parameter from Bryce reference? Kenneth Huang
- [AMBER] Topology and parameters for the T4 - Thyroxine Marcelo Andrade Chagas
- Re: [AMBER] help David A Case
- Re: [AMBER] 2 aminpurine parameter from Bryce reference? David A Case
- Re: [AMBER] Topology and parameters for the T4 - Thyroxine David A Case
- [AMBER] Open a hole into an equilibrated lipid bilayer Eduardo R. Almeida
- [AMBER] pmemd simulation Sofia Vasilakaki
- Re: [AMBER] pmemd simulation David Cerutti
Wednesday, 13 May 2020
- Re: [AMBER] How to perameterize peptide like compound Liao
- Re: [AMBER] OHE residue and crashing Piia Kokkonen
- Re: [AMBER] help MYRIAN TORRES RICO
- [AMBER] autoimage waters Hector A. Baldoni
- Re: [AMBER] OHE residue and crashing David A Case
- [AMBER] About having an auto-restart keyword for the amber/orca interface. Zhiyi Wu
- Re: [AMBER] autoimage waters Daniel Roe
- [AMBER] installation problem Arthur Glasfeld
- [AMBER] Steered MD with COM_ANGLE Amanda Buyan
- Re: [AMBER] Steered MD with COM_ANGLE Adrian Roitberg
- Re: [AMBER] autoimage waters Hector A. Baldoni
- Re: [AMBER] Steered MD with COM_ANGLE Amanda Buyan
- Re: [AMBER] Steered MD with COM_ANGLE Kellon Belfon
- Re: [AMBER] Steered MD with COM_ANGLE Amanda Buyan
Thursday, 14 May 2020
- Re: [AMBER] installation problem David A Case
- [AMBER] AMBER 18 GPU Renato Araujo
- Re: [AMBER] AMBER 18 GPU Liao
- Re: [AMBER] Steered MD with COM_ANGLE Kellon Belfon
- [AMBER] differences in EGB energies sander vs. pmemd Niransha Kumarachchi
- Re: [AMBER] differences in EGB energies sander vs. pmemd David A Case
- Re: [AMBER] help David A Case
- Re: [AMBER] Steered MD with COM_ANGLE Amanda Buyan
- [AMBER] Fwd: Fw: Amber18 - MPI version error on HPC Cluster Sivanandam Magudeeswaran
- [AMBER] Questions about PCA Kat G
- Re: [AMBER] Fwd: Fw: Amber18 - MPI version error on HPC Cluster Gustaf Olsson
- [AMBER] Query regarding calculating RMSF. DHEERAJ CHITARA
Friday, 15 May 2020
- Re: [AMBER] help MYRIAN TORRES RICO
- [AMBER] Installation error Hrishikesh Dhondge
- [AMBER] updating to ambertools 20 from version 19 Homeo Morphism
- Re: [AMBER] Query regarding calculating RMSF. Md Fulbabu Sk
- [AMBER] Installation Error while linking C executable xaLeap Hrishikesh Dhondge
- [AMBER] Similar RESP1 and RESP2 fitting outputs Kodituwakku,Dimuthu Nirmani
- Re: [AMBER] Installation error David A Case
- Re: [AMBER] updating to ambertools 20 from version 19 David A Case
- Re: [AMBER] Fwd: Fw: Amber18 - MPI version error on HPC Cluster David A Case
- [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer Lod King
- Re: [AMBER] cellulose chain Pinky Mazumder
- [AMBER] Query regarding force fields SHAUNAK BADANI
- Re: [AMBER] Query regarding force fields Carlos Simmerling
- [AMBER] upgrade to 19 Scott Brozell
- Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer Renato Araujo
- Re: [AMBER] cellulose chain Lachele Foley
- Re: [AMBER] cellulose chain Pinky Mazumder
- Re: [AMBER] cellulose chain Pinky Mazumder
- [AMBER] Amber20 MPIC location problem Filip Fratev
- Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer Lod King
Saturday, 16 May 2020
- Re: [AMBER] cellulose chain Lachele Foley
- Re: [AMBER] Amber20 MPICH location problem Filip Fratev
- Re: [AMBER] Installation error Hrishikesh Dhondge
- [AMBER] Could not find control namelist error Jisha B
- Re: [AMBER] Could not find control namelist error Carlos Simmerling
- Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer David A Case
- Re: [AMBER] upgrade to 19 David A Case
- Re: [AMBER] Amber20 MPIC location problem David A Case
- Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer Lod King
- [AMBER] Absolute free energy calculation-GitHub Sadaf Rani
- Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer David A Case
- Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer Lod King
- Re: [AMBER] Amber20 MPICH location problem fratev.biomed.bas.bg
Sunday, 17 May 2020
- Re: [AMBER] Amber20 MPICH location problem Filip Fratev
- [AMBER] Amber20 pmemd.cuda installation and performance problems Filip Fratev
- Re: [AMBER] Amber20 pmemd.cuda installation and performance problems viktor drobot
- Re: [AMBER] Amber20 MPICH location problem David A Case
- Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer Renato Araujo
- Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer Lod King
Thursday, 14 May 2020
- [AMBER] Galactosylation of 5-Hydroxylysine Harald Lanig
Sunday, 17 May 2020
- Re: [AMBER] Amber20 MPIC location problem Gerald Monard
- Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer Renato Araujo
- Re: [AMBER] Amber20 pmemd.cuda installation David A Case
Monday, 18 May 2020
- Re: [AMBER] Steered MD with COM_ANGLE Feng Pan
- Re: [AMBER] Query regarding calculating RMSF. Daniel Roe
- [AMBER] parameter for modified residue sangita kachhap
- Re: [AMBER] how to compute the protein interaction surface with the ligand Thomas Evangelidis
Tuesday, 19 May 2020
- [AMBER] COM position mohamed marzouk
- Re: [AMBER] COM position Daniel Roe
- Re: [AMBER] parameter for modified residue David A Case
- Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer David A Case
- Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer Lod King
- Re: [AMBER] Amber20 pmemd.cuda installation and performance problems David Cerutti
- Re: [AMBER] parameter for modified residue sangita kachhap
- Re: [AMBER] Galactosylation of 5-Hydroxylysine Lachele Foley
- Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer David A Case
Wednesday, 20 May 2020
- Re: [AMBER] how to compute the protein interaction surface with the ligand Daniel Roe
- Re: [AMBER] Questions about PCA Daniel Roe
- Re: [AMBER] can i analysis number of water molecules in protein by watershell Daniel Roe
- [AMBER] How to use set pert=true Dawid das
- Re: [AMBER] can i analysis number of water molecules in protein by watershell Wesley Michael Botello-Smith
- [AMBER] AMBER Tools 20: Bug in libraries of modified amino acids prevents force field load Matias Machado
- Re: [AMBER] how to compute the protein interaction surface with the ligand David A Case
- Re: [AMBER] How to use set pert=true David A Case
- Re: [AMBER] how to compute the protein interaction surface with the ligand Thomas Evangelidis
- Re: [AMBER] How to use set pert=true Dawid das
- Re: [AMBER] how to compute the protein interaction surface with the ligand Carlos Simmerling
- Re: [AMBER] AMBER Tools 20: Bug in libraries of modified amino acids prevents force field load Kellon Belfon
- Re: [AMBER] How to use set pert=true David A Case
Thursday, 21 May 2020
- [AMBER] MMPBSA - per residue decomposition Prasanth G, Research Scholar
- [AMBER] paramfit - negative energy for 1 of the 2 term Erdem Yeler
- [AMBER] Amber20 serial make test FAILUREs on IBM Power9 Cong Liu
- [AMBER] TI production runs(20ns) NVT query Debarati DasGupta
- Re: [AMBER] Amber20 serial make test FAILUREs on IBM Power9 Cong Liu
- [AMBER] QM/MM MD: Error reading box emanuele falbo
- Re: [AMBER] Amber20 serial make test FAILUREs on IBM Power9 David A Case
- Re: [AMBER] QM/MM MD: Error reading box David A Case
- Re: [AMBER] Amber20 serial make test FAILUREs on IBM Power9 Cong Liu
- [AMBER] Free energy of solvation using polarizable force fields Carl Heroneme
- Re: [AMBER] paramfit - negative energy for 1 of the 2 term Robin Betz
Friday, 22 May 2020
- Re: [AMBER] QM/MM MD: Error reading box emanuele falbo
- Re: [AMBER] QM/MM MD: Error reading box Daniel Roe
- Re: [AMBER] QM/MM MD: Error reading box David A Case
- Re: [AMBER] QM/MM MD: Error reading box emanuele falbo
- Re: [AMBER] How to use set pert=true Dawid das
- Re: [AMBER] QM/MM MD: Error reading box Daniel Roe
- Re: [AMBER] QM/MM MD: Error reading box Daniel Roe
- Re: [AMBER] MMPBSA - per residue decomposition Prasanth G, Research Scholar
Saturday, 23 May 2020
- [AMBER] Different LJ parameters in .dat file and 'atominfo' output José Daniel Martinez
- [AMBER] Changing hydrogen atom radius to optimize saltbridge in GB-OBC model Sunita Patel
- [AMBER] Amber18 with AmberTools20 test.serial FAILURES and ERRORS Samanta M
- Re: [AMBER] Changing hydrogen atom radius to optimize saltbridge in GB-OBC model Carlos Simmerling
- Re: [AMBER] paramfit - negative energy for 1 of the 2 term Erdem Yeler
- Re: [AMBER] Amber18 with AmberTools20 test.serial FAILURES and ERRORS Josh Berryman
- Re: [AMBER] Amber18 with AmberTools20 test.serial FAILURES and ERRORS David A Case
- Re: [AMBER] Free energy of solvation using polarizable force fields David A Case
- Re: [AMBER] Amber18 with AmberTools20 test.serial FAILURES and ERRORS Samanta M
- Re: [AMBER] how to compute the protein interaction surface with the ligand Thomas Evangelidis
- Re: [AMBER] how to compute the protein interaction surface with the ligand Carlos Simmerling
- Re: [AMBER] how to compute the protein interaction surface with the ligand Thomas Evangelidis
- Re: [AMBER] Changing hydrogen atom radius to optimize saltbridge in GB-OBC model Sunita Patel
- Re: [AMBER] Changing hydrogen atom radius to optimize saltbridge in GB-OBC model Kellon Belfon
Sunday, 24 May 2020
- Re: [AMBER] QM/MM MD: Error reading box emanuele falbo
- Re: [AMBER] Changing hydrogen atom radius to optimize saltbridge in GB-OBC model Sunita Patel
- Re: [AMBER] QM/MM MD: Error reading box David A Case
- [AMBER] Help with Acpype on AMberTools19 Prapasiri Pongprayoon
- [AMBER] Help with Acpype in AmberTools19 Prapasiri Pongprayoon
Monday, 25 May 2020
- Re: [AMBER] Amber20 pmemd.cuda performance problems (especially on Turing-based GPUs) Thomas Zeiser
- Re: [AMBER] QM/MM MD: Error reading box emanuele falbo
- Re: [AMBER] Amber20 pmemd.cuda performance problems (especially on Turing-based GPUs) David Cerutti
- Re: [AMBER] Amber20 pmemd.cuda performance problems (especially on Turing-based GPUs) Brent Krueger
- [AMBER] Questions about QM Ignjat Filipović
- [AMBER] clustering parameter files Ranim Maaieh
Tuesday, 26 May 2020
- Re: [AMBER] clustering parameter files Daniel Roe
- Re: [AMBER] Different LJ parameters in .dat file and 'atominfo' output Daniel Roe
- [AMBER] What would you like to see in visualization of chemical data? Jan Mičan
- [AMBER] installation failed libsanderles.dir amd plumed Andrew Waight
Wednesday, 27 May 2020
- Re: [AMBER] Different LJ parameters in .dat file and 'atominfo' output José Daniel Martinez
- Re: [AMBER] Amber20 pmemd.cuda installation and performance problems Filip Fratev
- Re: [AMBER] Amber20 pmemd.cuda installation and performance problems Filip Fratev
- [AMBER] Missing bond parameters after MCPB.py Oleksandr Kravchenko
- Re: [AMBER] Amber20 pmemd.cuda installation and performance problems David Cerutti
- Re: [AMBER] installation failed libsanderles.dir amd plumed David A Case
- Re: [AMBER] installation failed libsanderles.dir amd plumed Andrew Waight
- Re: [AMBER] Different LJ parameters in .dat file and 'atominfo' output Daniel Roe
- [AMBER] Tool to calculate CSP and NOE for DNA trajectory? Kenneth Huang
Thursday, 28 May 2020
- [AMBER] Installing latest ambertools (2020) with conda Alan
- Re: [AMBER] Tool to calculate CSP and NOE for DNA trajectory? Christina Bergonzo
- [AMBER] Small molecules paramters Athena N
- [AMBER] Amber99SB force field Seketoulie Keretsu
- Re: [AMBER] Installing latest ambertools (2020) with conda David A Case
- Re: [AMBER] Installing latest ambertools (2020) with conda Alan
- Re: [AMBER] Amber99SB force field Carlos Simmerling
- Re: [AMBER] Amber99SB force field Gustavo Seabra
- Re: [AMBER] Amber99SB force field Carlos Simmerling
- Re: [AMBER] Installing latest ambertools (2020) with conda David A Case
- Re: [AMBER] Amber20 pmemd.cuda performance problems (especially on Turing-based GPUs) David Cerutti
- [AMBER] AMBER 16 NFE MULTI_RMSD Question on the Output of reaction variable Xiaoyong Zhang
- [AMBER] Simulating pyridine in water TIP3P Debarati DasGupta
- Re: [AMBER] [EXTERNAL] Re: Amber99SB force field Smith, Micholas D.
- Re: [AMBER] Amber20 pmemd.cuda installation and performance problems David Cerutti
- Re: [AMBER] Simulating pyridine in water TIP3P David A Case
- Re: [AMBER] Tool to calculate CSP and NOE for DNA trajectory? Kenneth Huang
- Re: [AMBER] Small molecules paramters Gustaf Olsson
- Re: [AMBER] adding hydrogen to pdbqt ligand files Eduardo Mayo
- [AMBER] Amber20 Performance on RTX (Turing): known problems, with a patch forthcoming David Cerutti
Friday, 29 May 2020
- [AMBER] questions for mdgx-virtual site Gao J
- Re: [AMBER] questions for mdgx-virtual site David Cerutti
- Re: [AMBER] questions for mdgx-virtual site David Cerutti
- [AMBER] igb for non-aqueous solvent? Timothy Schutt
- Re: [AMBER] cellulose chain Pinky Mazumder
- Re: [AMBER] Small molecules paramters Gustavo Seabra
- Re: [AMBER] cellulose chain David A Case
- [AMBER] how to identify lipids around a protein Sally Pias
- Re: [AMBER] how to identify lipids around a protein Prajwal Nandekar
Saturday, 30 May 2020
- Re: [AMBER] Amber for help 马海川
- Re: [AMBER] AMBER Digest, Vol 3017, Issue 1 Gao J
- [AMBER] amber20 output header Baker, Joseph
- Re: [AMBER] amber20 output header David Cerutti
- Re: [AMBER] AMBER Digest, Vol 3017, Issue 1 David Cerutti
Sunday, 31 May 2020
- Re: [AMBER] Using pytraj with jupyter notebook Rangarajan, Amith
- Re: [AMBER] Using pytraj with jupyter notebook Hai Nguyen

Last message date: Sun May 31 2020 - 17:00:02 PDT
Archived on: Wed Apr 17 2024 - 05:55:50 PDT

Amber Archive May 2020 by date