Amber Archive Mar 2022: by date

Monday, 28 February 2022
- Re: [AMBER] Clarification in 3DRISM Alexis Azucena
Tuesday, 1 March 2022
- Re: [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces Állan Ferrari
- Re: [AMBER] CPPTRAJ, Dipole autocorrelation? David A Case
- [AMBER] Error in using multiple distance restraints in a single RST file Prathit Chatterjee
Wednesday, 2 March 2022
- Re: [AMBER] Error in using multiple distance restraints in a single RST file David A Case
- Re: [AMBER] CUDART lib not found during install Charlotta Lebedenko
Thursday, 3 March 2022
- Re: [AMBER] CUDART lib not found during install Daniel Roe
- Re: [AMBER] CUDART lib not found during install Charlotta Lebedenko
- Re: [AMBER] Cpptraj - Density Action Command Units Gerardo Zerbetto De Palma
Friday, 4 March 2022
- [AMBER] Asking MMPBSA.PY Purnawan pontana putra
- [AMBER] How to use artificial covariance matrix in PCA analysis of cpptraj? wangjianing_mail
- Re: [AMBER] How to use artificial covariance matrix in PCA analysis of cpptraj? Daniel Roe
- Re: [AMBER] error preparing ligand parameters Vaibhav Dixit
Saturday, 5 March 2022
- Re: [AMBER] Asking MMPBSA.PY David A Case
Sunday, 6 March 2022
- Re: [AMBER] CUDART lib not found during install Charlotta Lebedenko
- Re: [AMBER] CUDART lib not found during install Alexis Azucena
Monday, 7 March 2022
- Re: [AMBER] CUDART lib not found during install Daniel Roe
- [AMBER] Watershell like command for lipids Vic De Roo
- Re: [AMBER] Watershell like command for lipids Daniel Roe
- [AMBER] TLEAP error when adding Ag+ Alysia Mandato
- Re: [AMBER] TLEAP error when adding Ag+ David A Case
- [AMBER] glibc causing amber install error Bruno Cramer
- [AMBER] Failed to generate rst file in partially deleted structure Yen Nguyen
- Re: [AMBER] Failed to generate rst file in partially deleted structure Daniel Roe
- Re: [AMBER] CUDART lib not found during install Daniel Roe
- [AMBER] Constant pH MD Simulations for General Organic Compounds Nathan Black
- Re: [AMBER] Constant pH MD Simulations for General Organic Compounds Vinicius Wilian Cruzeiro
- [AMBER] [Amber]Not able to generate eq_density.cpptraj file while doing QM/MM calculations Anita Meena
- [AMBER] EZAFF force field Elisa Frezza
Tuesday, 8 March 2022
- Re: [AMBER] glibc causing amber install error David A Case
- Re: [AMBER] [Amber]Not able to generate eq_density.cpptraj file while doing QM/MM calculations David A Case
- [AMBER] Entropy calculations in GIST Daniella Hares
- [AMBER] Penalty Scores for Amino Acid Dihedral Parameters Nathan Black
- Re: [AMBER] [Amber]Not able to generate eq_density.cpptraj file while doing QM/MM calculations Anita Meena
Wednesday, 9 March 2022
- Re: [AMBER] Calculate Lipid Surface Pressure/Tension from Lipid-Water Interface Mirza Ahmed Hammad
- Re: [AMBER] Penalty Scores for Amino Acid Dihedral Parameters David A Case
- Re: [AMBER] [Amber]Not able to generate eq_density.cpptraj file while doing QM/MM calculations Daniel Roe
- Re: [AMBER] [Amber]Not able to generate eq_density.cpptraj file while doing QM/MM calculations Anita Meena
- [AMBER] Unit cell size changed and coords overlap problems chanyann06.stu.scu.edu.cn
Thursday, 10 March 2022
- Re: [AMBER] Unit cell size changed and coords overlap problems Dr. Anselm Horn
- Re: [AMBER] [Amber]Not able to generate eq_density.cpptraj file while doing QM/MM calculations Daniel Roe
- Re: [AMBER] Unit cell size changed and coords overlap problems Daniel Roe
- Re: [AMBER] Failed to generate rst file in partially deleted structure Yen Nguyen
- Re: [AMBER] CUDART lib not found during install Charlotta Lebedenko
- [AMBER] tleap: keep crystallographic waters? Daniel Konstantinovsky
- Re: [AMBER] tleap: keep crystallographic waters? Carlos Simmerling
- Re: [AMBER] tleap: keep crystallographic waters? David A Case
- [AMBER] Unit cell size changed and coords overlap problems chanyann06.stu.scu.edu.cn
- [AMBER] calculate entropy using MMPBSA.py Ming Tang
- Re: [AMBER] calculate entropy using MMPBSA.py Thomas Cheatham
- [AMBER] Convergence issue in rism1d angad sharma
Friday, 11 March 2022
- [AMBER] problems installing Amber20 + AmberTools21 parallel version with open-mpi Antonija Tomić
- Re: [AMBER] Convergence issue in rism1d David A Case
- Re: [AMBER] problems installing Amber20 + AmberTools21 parallel version with open-mpi David A Case
- Re: [AMBER] problems installing Amber20 + AmberTools21 parallel version with open-mpi Antonija Tomić
- Re: [AMBER] tleap: keep crystallographic waters? Daniel Konstantinovsky
- Re: [AMBER] problems installing Amber20 + AmberTools21 parallel version with open-mpi David A Case
- Re: [AMBER] tleap: keep crystallographic waters? David A Case
- Re: [AMBER] Unit cell size changed and coords overlap problems Daniel Roe
- [AMBER] Request help modifying a force field russ.brown.yahoo.com
- Re: [AMBER] CUDART lib not found during install Daniel Roe
- Re: [AMBER] calculate entropy using MMPBSA.py Ming Tang
- [AMBER] Stripping waters from trajectory except those forming bridged H-bond between Protein and Ligand Rakesh Srivastava
Sunday, 13 March 2022
- [AMBER] Error when using mmpbsa_py_nabnmode in parallel Ming Tang
- Re: [AMBER] Request help modifying a force field Dr. Anselm Horn
- Re: [AMBER] Request help modifying a force field Carlos Simmerling
- [AMBER] Non-Integer Charge for Systems Comprised of Large Number of Residues Nathan Black
- Re: [AMBER] Non-Integer Charge for Systems Comprised of Large Number of Residues David A Case
- [AMBER] How to read netcdf files on VMD Windows version? Suchetana Gupta
- Re: [AMBER] How to read netcdf files on VMD Windows version? Elvis Martis
Monday, 14 March 2022
- Re: [AMBER] problems installing Amber20 + AmberTools21 parallel version with open-mpi Antonija Tomić
- Re: [AMBER] How to read netcdf files on VMD Windows version? Carlos Simmerling
- [AMBER] Modeling cis-amide bonds in diketopiperazines Christian Schafmeister
- Re: [AMBER] Stripping waters from trajectory except those forming bridged H-bond between Protein and Ligand Daniel Roe
- Re: [AMBER] problems installing Amber20 + AmberTools21 parallel version with open-mpi David A Case
- Re: [AMBER] Convergence issue in rism1d tluchko
- [AMBER] NFE-Error Tanmoy Paul
- Re: [AMBER] How to read netcdf files on VMD Windows version? Suchetana Gupta
- Re: [AMBER] How to read netcdf files on VMD Windows version? Carlos Simmerling
- Re: [AMBER] How to read netcdf files on VMD Windows version? Suchetana Gupta
- Re: [AMBER] tleap error: "expected 'default'" Scott Brozell
- Re: [AMBER] Stripping waters from trajectory except those forming bridged H-bond between Protein and Ligand Rakesh Srivastava
- [AMBER] I cannot find NAB in AmberTools 21 russ.brown.yahoo.com
- Re: [AMBER] problems installing Amber20 + AmberTools21 parallel version with open-mpi Antonija Tomić
Tuesday, 15 March 2022
- Re: [AMBER] I cannot find NAB in AmberTools 21 David A Case
- Re: [AMBER] problems installing Amber20 + AmberTools21 parallel version with open-mpi David A Case
- Re: [AMBER] problems installing Amber20 + AmberTools21 parallel version with open-mpi Antonija Tomić
Wednesday, 16 March 2022
- [AMBER] Regarding treating ligand with QM level of theory Soumyajit Karmakar
- Re: [AMBER] problems installing Amber20 + AmberTools21 parallel version with open-mpi David A Case
- [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Matthew Guberman-Pfeffer
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Kenneth Huang
- Re: [AMBER] Regarding treating ligand with QM level of theory David A Case
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Matthew Guberman-Pfeffer
- [AMBER] question about ATP-Mg2+ binding system liu kai
- Re: [AMBER] question about ATP-Mg2+ binding system Carlos Simmerling
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Kenneth Huang
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Matthew Guberman-Pfeffer
- Re: [AMBER] question about ATP-Mg2+ binding system David A Case
- [AMBER] A way to stop simulations when certain criteria are met? Chris Lee
- Re: [AMBER] Regarding treating ligand with QM level of theory Soumyajit Karmakar
- Re: [AMBER] Stripping waters from trajectory except those forming bridged H-bond between Protein and Ligand Daniel Roe
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Kenneth Huang
- Re: [AMBER] question about ATP-Mg2+ binding system liu kai
- Re: [AMBER] question about ATP-Mg2+ binding system Thomas Cheatham
Thursday, 17 March 2022
- Re: [AMBER] Stripping waters from trajectory except those forming bridged H-bond between Protein and Ligand Rakesh Srivastava
- [AMBER] Query regarding AMBER meta dynamics Sruthi Sudhakar
- [AMBER] Hubbard derivative not found and element Na not supported for a QM/MM system Pau Mayorga Delgado
- Re: [AMBER] Hubbard derivative not found and element Na not supported for a QM/MM system David A Case
- Re: [AMBER] A way to stop simulations when certain criteria are met? Hai Nguyen
- [AMBER] CPPTRAJ, Conflicting H-Bonding Results Matthew Guberman-Pfeffer
- Re: [AMBER] A way to stop simulations when certain criteria are met? Dr. Anselm Horn
- Re: [AMBER] A way to stop simulations when certain criteria are met? Carlos Simmerling
- Re: [AMBER] AMBER Digest, Vol 3660, Issue 1 liu kai
Friday, 18 March 2022
- [AMBER] T-REMD Juliette Newell
- Re: [AMBER] T-REMD Carlos Simmerling
- Re: [AMBER] T-REMD Juliette Newell
- Re: [AMBER] T-REMD Carlos Simmerling
- [AMBER] PySander availability in PyTraj David Poole
- Re: [AMBER] PySander availability in PyTraj David A Case
- Re: [AMBER] CPPTRAJ, Conflicting H-Bonding Results Daniel Roe
- Re: [AMBER] CPPTRAJ, Conflicting H-Bonding Results Matthew Guberman-Pfeffer
- Re: [AMBER] PySander availability in PyTraj Hai Nguyen
Saturday, 19 March 2022
- Re: [AMBER] PySander availability in PyTraj David Poole
Sunday, 20 March 2022
- [AMBER] Installation errors of AmberTools 21 on Ubuntu 20.04 WSL2 M. Reza Ganjalikhany
- [AMBER] Cannot install AmberTools 21 due to errors in getline.c file Сергей Горелов
Monday, 21 March 2022
- [AMBER] Problems with DFTB3 and Na in Amber Pau Mayorga Delgado
- [AMBER] Small Cutoffs Not Supported for Implicit Solvent GPU Simulation Runs Nathan Black
- Re: [AMBER] Small Cutoffs Not Supported for Implicit Solvent GPU Simulation Runs David A Case
- Re: [AMBER] Small Cutoffs Not Supported for Implicit Solvent GPU Simulation Runs Carlos Simmerling
- Re: [AMBER] Cannot install AmberTools 21 due to errors in getline.c file Scott Brozell
- Re: [AMBER] Cannot install AmberTools 21 due to errors in getline.c file Сергей Горелов
- [AMBER] Problem with production run of cyclic peptide Suchetana Gupta
- [AMBER] Query related to TIMD SATYAJIT KHATUA
Tuesday, 22 March 2022
- [AMBER] 1D-RISM with 4-Point water models Grunewald, Lukas
- Re: [AMBER] Query related to TIMD Carlos Simmerling
- Re: [AMBER] Problem with production run of cyclic peptide Carlos Simmerling
- Re: [AMBER] Small Cutoffs Not Supported for Implicit Solvent GPU Simulation Runs Nathan Black
- Re: [AMBER] Error - corrupted size vs. prev_size saranya.cbmm.lodz.pl
- [AMBER] MMPBSA.py.MPI and pytraj bugs David Poole
- Re: [AMBER] Error - corrupted size vs. prev_size Maria Nagan
- Re: [AMBER] 1D-RISM with 4-Point water models tluchko
- Re: [AMBER] Small Cutoffs Not Supported for Implicit Solvent GPU Simulation Runs Nathan Black
- Re: [AMBER] Small Cutoffs Not Supported for Implicit Solvent GPU Simulation Runs David A Case
- Re: [AMBER] The tutorial 6.8 Westpa Tutorials Maria Nagan
Wednesday, 23 March 2022
- [AMBER] D-amino acids Daniel Konstantinovsky
- Re: [AMBER] D-amino acids Carlos Simmerling
- Re: [AMBER] D-amino acids Daniel Konstantinovsky
- [AMBER] ** NFE-Error ** : Selection weight overflows, try smaller selection constant Sruthi Sudhakar
- [AMBER] [AMBER ] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered. Anita Meena
- Re: [AMBER] [AMBER ] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered. Thomas Cheatham
Thursday, 24 March 2022
- [AMBER] How to visualize the results generated from the analysis of MD trajectory using Cpptraj in AMBER16 ? priya murugan
- Re: [AMBER] How to visualize the results generated from the analysis of MD trajectory using Cpptraj in AMBER16 ? Daniel Roe
- Re: [AMBER] 1D-RISM with 4-Point water models Grunewald, Lukas
- Re: [AMBER] [AMBER ] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered. Daniel Roe
- Re: [AMBER] Entropy calculations in GIST Franz Waibl
- Re: [AMBER] 1D-RISM with 4-Point water models tluchko
- [AMBER] PMEMD does not support single H residues! Huimin Tian
- Re: [AMBER] PMEMD does not support single H residues! Carlos Simmerling
- Re: [AMBER] PMEMD does not support single H residues! Thomas Cheatham
- [AMBER] Atom coordinate disagreement error in running the TI calculation Bhakti Hirlekar
Friday, 25 March 2022
- [AMBER] mmpbsa divalent ion bug xiangyu
- [AMBER] Error while running minimization run while doing thermodynamic integration. Divya Rai
- [AMBER] Amber20 installation error Chen, Guoquan
- [AMBER] Is it possible to use less replicas by freezing some atoms of protein in which I'm not interested? 云之彼端
- Re: [AMBER] Amber20 installation error David A Case
Monday, 28 March 2022
- [AMBER] ** NFE-Error ** : Selection weight overflows, try smaller selection constant Sruthi Sudhakar
- Re: [AMBER] ** NFE-Error ** : Selection weight overflows, try smaller selection constant Feng Pan
- Re: [AMBER] ** NFE-Error ** : Selection weight overflows, try smaller selection constant Sruthi Sudhakar
- Re: [AMBER] ** NFE-Error ** : Selection weight overflows, try smaller selection constant Feng Pan
- [AMBER] Tyrosine anion simulation Пушкарев Сергей
Tuesday, 29 March 2022
- [AMBER] Error in parameter file preparation Debasish Mandal
- Re: [AMBER] Error in parameter file preparation Carlos Simmerling
- Re: [AMBER] Tyrosine anion simulation Dr. Anselm Horn
- Re: [AMBER] {SPAM?} Re: Tyrosine anion simulation Matthew Guberman-Pfeffer
- Re: [AMBER] Tyrosine anion simulation Kellon Belfon
- Re: [AMBER] Tyrosine anion simulation Kellon Belfon
- [AMBER] Distance Restraints and/or Periodic Boundaries for Implicit Solvent Nathan Black
- [AMBER] Is there a way to restart MMPBSA.py calculation? Ming Tang
- [AMBER] mmpbsa.py divalent ion issue xiangyu
- [AMBER] How to use GPU and GLYCAM force fields s.ohno.tohoku-mpu.ac.jp
Wednesday, 30 March 2022
- Re: [AMBER] How to use GPU and GLYCAM force fields Dr. Anselm Horn
- [AMBER] Entropy calculations upon covalent modification Aravind R
- Re: [AMBER] How to use GPU and GLYCAM force fields David A Case
- Re: [AMBER] Entropy calculations upon covalent modification David A Case
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Daniel Roe
- [AMBER] Toluene solvent box equilibration Pedro Miguel Reis Figueiredo
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Matthew Guberman-Pfeffer
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Daniel Roe
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Daniel Roe
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Matthew Guberman-Pfeffer
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Matthew Guberman-Pfeffer
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Daniel Roe
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Matthew Guberman-Pfeffer
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Daniel Roe
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Matthew Guberman-Pfeffer
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Daniel Roe
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Matthew Guberman-Pfeffer
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Daniel Roe
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Matthew Guberman-Pfeffer
- [AMBER] problem with using amber Feng Su
Thursday, 31 March 2022
- Re: [AMBER] Toluene solvent box equilibration David A Case
- Re: [AMBER] problem with using amber David A Case
- Re: [AMBER] Unit 9 Error on OPEN: inpcrd When Running GPU Simulation on PMEMD.CUDA Nathan Black
- Re: [AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding Matthew Guberman-Pfeffer

Last message date: Thu Mar 31 2022 - 10:30:02 PDT
Archived on: Fri Apr 19 2024 - 05:55:57 PDT

Amber Archive Mar 2022 by date