Amber Archive Aug 2020: by date

Friday, 31 July 2020
- Re: [AMBER] Error in Gausian file preparation using MCPB.py gagandeep singh
- Re: [AMBER] Problems with MC barostat Gomez, Yessica
Saturday, 1 August 2020
- Re: [AMBER] Error in Gausian file preparation using MCPB.py gagandeep singh
Sunday, 2 August 2020
- [AMBER] how to calculate net charge of "molecule" using the command "netCharge" Billiot, Eugene
- Re: [AMBER] how to calculate net charge of "molecule" using the command "netCharge" Bill Ross
- [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. 李奕言
- Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." (???) 辛志宏
- [AMBER] Regarding the backup of amber nc files Jenny 148
- Re: [AMBER] Regarding the backup of amber nc files Bill Ross
Monday, 3 August 2020
- Re: [AMBER] how to calculate net charge of "molecule" using the command "netCharge" David A Case
- Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." (???) David A Case
- Re: [AMBER] Regarding the backup of amber nc files David A Case
- Re: [AMBER] how to calculate net charge of "molecule" using the command "netCharge" Billiot, Eugene
- Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." (???) 辛志宏
- [AMBER] Are Amber program can running using AMD processor? Setyanto Md
- Re: [AMBER] Are Amber program can running using AMD processor? Bill Ross
- Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. David Cerutti
- Re: [AMBER] Are Amber program can running using AMD processor? Bill Ross
- Re: [AMBER] Are Amber program can running using AMD processor? Setyanto Md
Tuesday, 4 August 2020
- Re: [AMBER] Structure Artifact After Autoimage Daniel Roe
- Re: [AMBER] Tracking lifetime distance by closest of specific water IDs? Daniel Roe
- Re: [AMBER] Problem installing AmberMD with MPI support on Cray XC40 Daniel Roe
- Re: [AMBER] fixatomorder Daniel Roe
- Re: [AMBER] Lipid bilayer imaging problem Daniel Roe
- [AMBER] open valence problem Ayesha Fatima
- Re: [AMBER] Regarding RMSD calculation and Clustering Daniel Roe
- Re: [AMBER] Usage of the Density Peaks Algorithm. Daniel Roe
- [AMBER] conversion of tripose mol2 to amber type Nikhil Maroli
- Re: [AMBER] conversion of tripose mol2 to amber type David A Case
- Re: [AMBER] open valence problem David A Case
Wednesday, 5 August 2020
- [AMBER] How to make amber/antechamber type mol2 from syble mol2 Nikhil Maroli
- [AMBER] gnuplot MYRIAN TORRES RICO
- Re: [AMBER] gnuplot Dr. Anselm Horn
- Re: [AMBER] gnuplot MYRIAN TORRES RICO
- [AMBER] weird energy histograms with REMD Diego Morone
- Re: [AMBER] weird energy histograms with REMD koushik kasavajhala
- Re: [AMBER] weird energy histograms with REMD Diego Morone
- Re: [AMBER] weird energy histograms with REMD Daniel Roe
- Re: [AMBER] weird energy histograms with REMD Christina Bergonzo
- Re: [AMBER] gnuplot Rodrigo Galindo-Murillo
- Re: [AMBER] conversion of tripose mol2 to amber type Nikhil Maroli
- Re: [AMBER] conversion of tripose mol2 to amber type David A Case
- [AMBER] implicit solvent calculations with calcium ion Piotr Fajer
- Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. 李奕言
- Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. David Cerutti
- Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. 李奕言
- Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. Bill Ross
Thursday, 6 August 2020
- Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. David Cerutti
- Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. David Cerutti
- Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. Bill Ross
- Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. David Cerutti
- Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. Bill Ross
- Re: [AMBER] open valence problem Ayesha Fatima
- Re: [AMBER] implicit solvent calculations with calcium ion David A Case
- Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. David A Case
- Re: [AMBER] implicit solvent calculations with calcium ion Bill Ross
- Re: [AMBER] open valence problem Ayesha Fatima
- Re: [AMBER] open valence problem Ayesha Fatima
- [AMBER] Fatal error on running GAMESS for parameters of FE ion gagandeep singh
- [AMBER] asking about "timlim" in accelerated MD Setyanto Md
- [AMBER] tleap.in error Ayesha Fatima
- Re: [AMBER] Issue heating system in equilibration step Samuel A. Ratliff
- [AMBER] Parmed: Residues cannot be part of 2 molecules! Molecule section will not be correctly set. Samuel A. Ratliff
- Re: [AMBER] asking about "timlim" in accelerated MD David A Case
- Re: [AMBER] tleap.in error David A Case
- Re: [AMBER] tleap.in error Scott Brozell
- Re: [AMBER] Parmed: Residues cannot be part of 2 molecules! Molecule section will not be correctly set. David A Case
- Re: [AMBER] asking about "timlim" in accelerated MD Setyanto Md
- Re: [AMBER] Caping error mohamed marzouk
Friday, 7 August 2020
- Re: [AMBER] tleap.in error Matias Machado
- Re: [AMBER] tleap.in error Ayesha Fatima
- Re: [AMBER] tleap.in error Matias Machado
- [AMBER] problem in 3DRISM angad sharma
- Re: [AMBER] problem in 3DRISM ATUL KUMAR
- Re: [AMBER] problem in 3DRISM David A Case
- Re: [AMBER] Parmed: Residues cannot be part of 2 molecules! Molecule section will not be correctly set. Samuel A. Ratliff
- Re: [AMBER] Amber20 Performance on RTX (Turing): known problems, with a patch forthcoming David A Case
- [AMBER] Help with MDCRD file for calculating binding energy Ram Koganti
Saturday, 8 August 2020
- [AMBER] CALL FOR PAPER - 16th German Conference on Cheminformatics (GCC) and the SAMPL satellite workshop Guessregen, Stefan /DE
- [AMBER] Problem about ADP-Protein complex simulation neildancer.sina.com
Sunday, 9 August 2020
- [AMBER] Assigning new velocities from Maxwell-Boltzmann distribution (ntx = 1) German P. Barletta
- [AMBER] Amber20 with PLUMED not working with multiple CPUs Amanda Buyan
- [AMBER] about pressure calculation in Amber18 Li, Min
- Re: [AMBER] Assigning new velocities from Maxwell-Boltzmann distribution (ntx = 1) Bill Ross
Monday, 10 August 2020
- Re: [AMBER] Amber20 with PLUMED not working with multiple CPUs viktor drobot
- [AMBER] Defining/Selecting BLAS with cmake Gustaf Olsson
- Re: [AMBER] Assigning new velocities from Maxwell-Boltzmann distribution (ntx = 1) David A Case
- Re: [AMBER] Amber20 with PLUMED not working with multiple CPUs Amanda Buyan
Tuesday, 11 August 2020
- Re: [AMBER] Amber20 with PLUMED not working with multiple CPUs viktor drobot
- [AMBER] Using cpptraj to generate rst7 files from trajectory Liao
- Re: [AMBER] Amber20 with PLUMED not working with multiple CPUs Amanda Buyan
- Re: [AMBER] Assigning new velocities from Maxwell-Boltzmann distribution (ntx = 1) German P. Barletta
- Re: [AMBER] Using cpptraj to generate rst7 files from trajectory Gustaf Olsson
Wednesday, 12 August 2020
- Re: [AMBER] Problem installing AmberMD with MPI support on Cray XC40 Jakub Jalowiec
- [AMBER] Amazon Cloud services and Amber Debarati DasGupta
- Re: [AMBER] Amazon Cloud services and Amber Gustaf Olsson
- Re: [AMBER] Amazon Cloud services and Amber Raman Preet Singh
- Re: [AMBER] Amazon Cloud services and Amber Luca Codutti
- Re: [AMBER] Assigning new velocities from Maxwell-Boltzmann distribution (ntx = 1) Daniel Roe
- Re: [AMBER] Using cpptraj to generate rst7 files from trajectory Daniel Roe
- [AMBER] Compiling AmberTools on macOS Gustaf Olsson
- Re: [AMBER] Using cpptraj to generate rst7 files from trajectory Liao
- Re: [AMBER] Using cpptraj to generate rst7 files from trajectory Daniel Roe
- [AMBER] tleap error ankita mehta
- Re: [AMBER] Using cpptraj to generate rst7 files from trajectory Liao
- Re: [AMBER] Assigning new velocities from Maxwell-Boltzmann distribution German P. Barletta
- Re: [AMBER] tleap error David A Case
- Re: [AMBER] Amazon Cloud services and Amber Thomas Cheatham
Thursday, 13 August 2020
- [AMBER] GlycoTools Webinar tomorrow Lachele Foley
Friday, 14 August 2020
- [AMBER] Running Paramfit with 300 + structures Samuel Himes
- Re: [AMBER] Running Paramfit with 300 + structures Robin Betz
- Re: [AMBER] Running Paramfit with 300 + structures David Cerutti
Saturday, 15 August 2020
- [AMBER] Time numbering problem with constant-pH simulations Jonee Lillard
- [AMBER] Error searching for compatible GPU Camila Clemente
- [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value 李奕言
- Re: [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value Bill Ross
Sunday, 16 August 2020
- Re: [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value 李奕言
- Re: [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value Bill Ross
- Re: [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value Bill Ross
- Re: [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value Qinghua Liao
- Re: [AMBER] Error searching for compatible GPU David A Case
- Re: [AMBER] Error searching for compatible GPU Camila Clemente
Monday, 17 August 2020
- [AMBER] AMBER18 pmemd.MPI installation error Shubhandra Tripathi
- [AMBER] preparing complexes Ayesha Fatima
- [AMBER] no collective variables output for infe=1 and abfqmmm FLORA, JOSEPH
- Re: [AMBER] preparing complexes neildancer
Tuesday, 18 August 2020
- Re: [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value 李奕言
- Re: [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value Bill Ross
- Re: [AMBER] preparing complexes David A Case
- Re: [AMBER] AMBER18 pmemd.MPI installation error David A Case
- Re: [AMBER] Time numbering problem with constant-pH simulations Daniel Roe
- [AMBER] Few workflow-LIE Neha Gandhi
- Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Mohamed M. Aboelnga
- [AMBER] 转发: Amber20 install problem （Geng Dong）东庚
- Re: [AMBER] 转发: Amber20 install problem （Geng Dong） David A Case
- Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Vaibhav Dixit
Wednesday, 19 August 2020
- Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Mohamed M. Aboelnga
- Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Vaibhav Dixit
- Re: [AMBER] 转发: Amber20 install problem （Geng Dong） David A Case
Thursday, 20 August 2020
- Re: [AMBER] Amber20 install problem （Geng Dong） Gustaf Olsson
- [AMBER] Antechamber and parmchk2 problem in case of processing mol2 input files Marek Maly
- [AMBER] converting prmtop to psf with improper and cross-term info stripped off Lod King
- Re: [AMBER] Antechamber and parmchk2 problem in case of processing mol2 input files Scott Brozell
Friday, 21 August 2020
- [AMBER] Force Field ankita mehta
- Re: [AMBER] Force Field Bowleg, Jerrano
- [AMBER] trouble with pdb4amber Mattia Cavallaro
- Re: [AMBER] Force Field Bill Ross
- Re: [AMBER] trouble with pdb4amber Bill Ross
- Re: [AMBER] trouble with pdb4amber viktor drobot
- Re: [AMBER] Force Field David A Case
- Re: [AMBER] trouble with pdb4amber David A Case
- [AMBER] Questions (and a small bug report) about SIRAH in Amber Charo del Genio
- Re: [AMBER] converting prmtop to psf with improper and cross-term info stripped off Daniel Roe
- Re: [AMBER] Antechamber and parmchk2 problem in case of processing mol2 input files Scott Brozell
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber Scott Brozell
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber David A Case
- Re: [AMBER] trouble with pdb4amber Hai Nguyen
Saturday, 22 August 2020
- Re: [AMBER] trouble with pdb4amber Mattia Cavallaro
- Re: [AMBER] Time numbering problem with constant-pH simulations Jonee Lillard
- [AMBER] Missing (ATTN, need revision) and poor parameters (high penalty score) for small molecule parameters and hard time with paramfit Állan Ferrari
- [AMBER] amber14 cuda code does not work Carlos
Sunday, 23 August 2020
- Re: [AMBER] amber14 cuda code does not work David A Case
- Re: [AMBER] amber14 cuda code does not work Bill Ross
- [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme) using MCPB tool Mohamed M. Aboelnga
- [AMBER] error while running tutorial B5 Ayesha Fatima
- Re: [AMBER] amber14 cuda code does not work Carlos
- Re: [AMBER] Missing (ATTN, need revision) and poor parameters (high penalty score) for small molecule parameters and hard time with paramfit David Cerutti
- Re: [AMBER] error while running tutorial B5 David A Case
- [AMBER] Problem with MMPBSA.py Camila Clemente
- Re: [AMBER] Problem with MMPBSA.py Elvis Martis
- Re: [AMBER] Problem with MMPBSA.py Elvis Martis
- Re: [AMBER] error while running tutorial B5 Ayesha Fatima
Monday, 24 August 2020
- Re: [AMBER] error while running tutorial B5 Gustaf Olsson
- Re: [AMBER] Problem with MMPBSA.py David A Case
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber Matias Machado
- Re: [AMBER] amber14 cuda code does not work Daniel Roe
- [AMBER] Questions (and a small bug report) about SIRAH in Amber paraw
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber Matias Machado
- Re: [AMBER] error while running tutorial B5 Ayesha Fatima
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber paraw
- [AMBER] Request .nc to MMPBSA.py? Camila Mara Clemente
- Re: [AMBER] Request .nc to MMPBSA.py? Elvis Martis
- Re: [AMBER] Request .nc to MMPBSA.py? Camila Clemente
- Re: [AMBER] Request .nc to MMPBSA.py? Elvis Martis
- Re: [AMBER] Request .nc to MMPBSA.py? Camila Mara Clemente
- Re: [AMBER] Request .nc to MMPBSA.py? Elvis Martis
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber David A Case
- Re: [AMBER] Time numbering problem with constant-pH simulations Daniel Roe
- Re: [AMBER] Time numbering problem with constant-pH simulations Daniel Roe
Tuesday, 25 August 2020
- Re: [AMBER] error while running tutorial B5 Gustaf Olsson
- [AMBER] ANTECHAMBER error: Fatal Error! Weird atomic valence (5) for atom (ID: 7, Name: C5). Pooja Kesari
- Re: [AMBER] ANTECHAMBER error: Fatal Error! Weird atomic valence (5) for atom (ID: 7, Name: C5). Elvis Martis
- Re: [AMBER] ANTECHAMBER error: Fatal Error! Weird atomic valence (5) for atom (ID: 7, Name: C5). Carlos Simmerling
- [AMBER] novel residue from Glutamine alex rayevsky
- [AMBER] Fundamentals of LEaP Tutorial Gustaf Olsson
- Re: [AMBER] Fundamentals of LEaP Tutorial Maria Nagan
- Re: [AMBER] novel residue from Glutamine Dr. Anselm Horn
- Re: [AMBER] Time numbering problem with constant-pH simulations Jonee Lillard
- Re: [AMBER] amber14 cuda code does not work Carlos
- Re: [AMBER] Time numbering problem with constant-pH simulations Jonee Lillard
- Re: [AMBER] Antechamber and parmchk2 problem in case of processing mol2 input files Marek Maly
- Re: [AMBER] Request .nc to MMPBSA.py? Camila Clemente
- Re: [AMBER] Time numbering problem with constant-pH simulations Daniel Roe
- Re: [AMBER] Request .nc to MMPBSA.py? Elvis Martis
Wednesday, 26 August 2020
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber Charo del Genio
- Re: [AMBER] Time numbering problem with constant-pH simulations Jonee Lillard
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber Matias Machado
- Re: [AMBER] Time numbering problem with constant-pH simulations Daniel Roe
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber Charo del Genio
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber Matias Machado
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber Charo del Genio
- [AMBER] plumed does not work with pmemd.cuda but it works with sander Dmitry Karlov
- Re: [AMBER] plumed does not work with pmemd.cuda but it works with sander viktor drobot
- [AMBER] Change covar matrix precision when crdaction is used Guadalupe Alvarez
- [AMBER] Help for building cross linking polymer using graphic antechamber Pinky Mazumder
- Re: [AMBER] Help for building cross linking polymer using graphic antechamber Pinky Mazumder
Thursday, 27 August 2020
- [AMBER] Tutorial B0 Gustaf Olsson
- [AMBER] Confusion regarding Center of mass coordinates for protein, with CPPTRAJ Prathit Chatterjee
- Re: [AMBER] Help for building cross linking polymer using graphic antechamber David A Case
- [AMBER] Help for building two different salt concentration system using tLeap module Fulbabu Sk
- [AMBER] MMPBSA.py with saline environment Camila Clemente
- Re: [AMBER] Help for building two different salt concentration system using tLeap module Matias Machado
- Re: [AMBER] MMPBSA.py with saline environment Elvis Martis
- [AMBER] Unable to complete heating stage Ramanathan Rajesh
- Re: [AMBER] Unable to complete heating stage Adrian Roitberg
- Re: [AMBER] Unable to complete heating stage Ramanathan Rajesh
- Re: [AMBER] MMPBSA.py with saline environment Camila Clemente
- [AMBER] Fw: covalent molecule and modified residue parameters Sarah Jane
- [AMBER] Stripping Protocol in Cpptraj An Ta
- [AMBER] "Atom does not have a type" despite adding .frcmod parameters Erika Davidoff
- Re: [AMBER] Antechamber and parmchk2 problem in case of processing mol2 input files Scott Brozell
- Re: [AMBER] "Atom does not have a type" despite adding .frcmod parameters Ayesha Fatima
- Re: [AMBER] "Atom does not have a type" despite adding .frcmod parameters Maria Nagan
- Re: [AMBER] "Atom does not have a type" despite adding .frcmod parameters Ayesha Fatima
- Re: [AMBER] "Atom does not have a type" despite adding .frcmod parameters Maria Nagan
- Re: [AMBER] Fw: covalent molecule and modified residue parameters David A Case
- Re: [AMBER] MMPBSA.py with saline environment Elvis Martis
Friday, 28 August 2020
- Re: [AMBER] "Atom does not have a type" despite adding .frcmod parameters David A Case
- [AMBER] "After the fact" lifetime analysis with CPPTRAJ Gustaf Olsson
- [AMBER] facing problem in 3DRISM angad sharma
- Re: [AMBER] facing problem in 3DRISM Tyler Luchko (Lists)
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber Matias Machado
- Re: [AMBER] MMPBSA.py with saline environment Camila Clemente
- [AMBER] "FATAL: Atom *** does not have a type" Error Jatin Kashyap
- Re: [AMBER] "FATAL: Atom *** does not have a type" Error Elvis Martis
Saturday, 29 August 2020
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber Charo del Genio
- Re: [AMBER] "FATAL: Atom *** does not have a type" Error David A Case
- [AMBER] FATAL atom does not have a type crispr cas9 pdb Jisha B
- Re: [AMBER] "FATAL: Atom *** does not have a type" Error Kashyap, Jatin
Sunday, 30 August 2020
- Re: [AMBER] new to amber20 aishen
- [AMBER] How to select groups for energy calculations-CPPtraj Nikhil Maroli
- [AMBER] EXTENDED DEADLINE for Submissions - 16th German Conference on Cheminformatics (GCC) and the SAMPL satellite workshop Guessregen, Stefan /DE
Monday, 31 August 2020
- Re: [AMBER] "After the fact" lifetime analysis with CPPTRAJ Gustaf Olsson
- [AMBER] Fatal error atom type work around Ayesha Fatima
- [AMBER] azobenzene atoms name in amber format Aashish Bhatt
- Re: [AMBER] FATAL atom does not have a type crispr cas9 pdb David A Case
- Re: [AMBER] new to amber20 David A Case
- Re: [AMBER] "FATAL: Atom *** does not have a type" Error David A Case
- [AMBER] Attention: All CPPTRAJ Questions Daniel Roe
- [AMBER] Asking for Fe2-S2 cluster and Molybdopterin AMBER force field parameters Maghsoud, Yazdan
- Re: [AMBER] azobenzene atoms name in amber format David A Case
- Re: [AMBER] Attention: All CPPTRAJ Questions aishen
- Re: [AMBER] Fatal error atom type work around David A Case

Last message date: Mon Aug 31 2020 - 13:00:04 PDT
Archived on: Fri Nov 15 2024 - 05:56:04 PST

Amber Archive Aug 2020 by date