Amber Archive Sep 2023: by date

Friday, 1 September 2023
- [AMBER] Coulomb energy in MMPBSA Richard Kullmann via AMBER
- Re: [AMBER] Coulomb energy in MMPBSA Ray Luo via AMBER
Saturday, 2 September 2023
- Re: [AMBER] Pressure controlling keyword: Nikolay N. Kuzmich via AMBER
Monday, 4 September 2023
- Re: [AMBER] Pressure controlling keyword: Dr. Anselm Horn via AMBER
- Re: [AMBER] Pressure controlling keyword: Kankana Bhattacharjee via AMBER
- Re: [AMBER] Pressure controlling keyword: Carlos Simmerling via AMBER
- [AMBER] Problem with water molecules angle in MD simulation Zafar,Muhammad Saqlain via AMBER
Tuesday, 5 September 2023
- [AMBER] Regarding atom types while using antechamber for modified DNA bases Sruthi Sudhakar via AMBER
- [AMBER] Clarification on attempted TMD run Malcolm Lim via AMBER
- Re: [AMBER] Clarification on attempted TMD run Carlos Simmerling via AMBER
- Re: [AMBER] Clarification on attempted TMD run Adrian Roitberg via AMBER
- Re: [AMBER] Clarification on attempted TMD run Carlos Simmerling via AMBER
- Re: [AMBER] Clarification on attempted TMD run Carlos Simmerling via AMBER
- [AMBER] Chirality flipped for 2 identical molecules Todd Minehardt via AMBER
- Re: [AMBER] Chirality flipped for 2 identical molecules Carlos Simmerling via AMBER
- Re: [AMBER] Chirality flipped for 2 identical molecules Carlos Simmerling via AMBER
- [AMBER] Visualizing amber MD trajectory in vmd: Kankana Bhattacharjee via AMBER
- Re: [AMBER] Visualizing amber MD trajectory in vmd: SATYAJIT KHATUA via AMBER
- Re: [AMBER] Visualizing amber MD trajectory in vmd: SATYAJIT KHATUA via AMBER
- Re: [AMBER] Visualizing amber MD trajectory in vmd: SATYAJIT KHATUA via AMBER
Wednesday, 6 September 2023
- [AMBER] Errors with .dcd files using MMPBSA VERONICA MARTIN HERNANDEZ via AMBER
- Re: [AMBER] Problem with water molecules angle in MD simulation Carlos Simmerling via AMBER
- [AMBER] Issue with MMPBSA calculation Enrico Martinez via AMBER
- Re: [AMBER] Issue with MMPBSA calculation Enrico Martinez via AMBER
- Re: [AMBER] Errors with .dcd files using MMPBSA Ray Luo via AMBER
- [AMBER] Strategies to run MMPBSA.py for multimeric systems yunshi11 via AMBER
Thursday, 7 September 2023
- [AMBER] Regarding issue in the minimization output KAJAL ABROL via AMBER
- Re: [AMBER] Issue with MMPBSA calculation Enrico Martinez via AMBER
- [AMBER] MMPBSA issue: Kankana Bhattacharjee via AMBER
- Re: [AMBER] Errors with .dcd files using MMPBSA Daniel Roe via AMBER
- Re: [AMBER] Regarding issue in the minimization output Daniel Roe via AMBER
- Re: [AMBER] MMPBSA issue: Bill Miller III via AMBER
Friday, 8 September 2023
- [AMBER] test message David A Case via AMBER
- [AMBER] Installing on Ubuntu 22.04/CUDA 12.2 John McDonnell via AMBER
- [AMBER] What is the best way to do triplicate runs Romero, Maria via AMBER
- [AMBER] Umbrella Sampling Jing Qu via AMBER
- Re: [AMBER] What is the best way to do triplicate runs Carlos Simmerling via AMBER
- Re: [AMBER] Umbrella Sampling Carlos Simmerling via AMBER
- Re: [AMBER] Umbrella Sampling Carlos Simmerling via AMBER
Saturday, 9 September 2023
- Re: [AMBER] Regarding issue in the minimization output David A Case via AMBER
- Re: [AMBER] Regarding issue in the minimization output David A Case via AMBER
- Re: [AMBER] Installing on Ubuntu 22.04/CUDA 12.2 David A Case via AMBER
Sunday, 10 September 2023
- [AMBER] extracting a frame from trajectory at a specific time James Kress via AMBER
- [AMBER] 回复: extracting a frame from trajectory at a specific time Huang ZiJian via AMBER
- Re: [AMBER] extracting a frame from trajectory at a specific time SATYAJIT KHATUA via AMBER
- [AMBER] MMPBSA PBRadii: Kankana Bhattacharjee via AMBER
Monday, 11 September 2023
- Re: [AMBER] MMPBSA issue: VERONICA MARTIN HERNANDEZ via AMBER
- Re: [AMBER] MMPBSA PBRadii: Bill Miller III via AMBER
Tuesday, 12 September 2023
- [AMBER] MMPBSA calculation of multiple complex simulations: Kankana Bhattacharjee via AMBER
- Re: [AMBER] MMPBSA calculation of multiple complex simulations: Bill Miller III via AMBER
- [AMBER] Average RMSF calculation Hocine EL KHAOUDI ENYOURY via AMBER
- [AMBER] the parameter mctrdz in mmpbsa.in shiyu wang via AMBER
Wednesday, 13 September 2023
- [AMBER] high positive values for VDW interactions using LIE function Pirhadi, Somayeh via AMBER
- Re: [AMBER] the parameter mctrdz in mmpbsa.in Ray Luo via AMBER
Thursday, 14 September 2023
- [AMBER] Calculation of RMSD VERONICA MARTIN HERNANDEZ via AMBER
- Re: [AMBER] Calculation of RMSD Carlos Simmerling via AMBER
Friday, 15 September 2023
- Re: [AMBER] Umbrella Sampling Jing Qu via AMBER
- [AMBER] RNA simulation basics Debarati DasGupta via AMBER
- Re: [AMBER] Umbrella Sampling Carlos Simmerling via AMBER
- Re: [AMBER] RNA simulation basics Carlos Simmerling via AMBER
- [AMBER] Maestro PDB to Amber PDB Vinicius Cruzeiro $Vinny$ via AMBER
- Re: [AMBER] Maestro PDB to Amber PDB Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] Maestro PDB to Amber PDB He, Amy via AMBER
Saturday, 16 September 2023
- [AMBER] CpHMD in amber18 using cuda Dulal Mondal via AMBER
- [AMBER] Reagarding AMBER ff14SB-ildn Midhun K Madhu 1620103 via AMBER
- Re: [AMBER] Reagarding AMBER ff14SB-ildn Carlos Simmerling via AMBER
Monday, 18 September 2023
- [AMBER] AMBER error slurmstepd VERONICA MARTIN HERNANDEZ via AMBER
- Re: [AMBER] AMBER error slurmstepd SATYAJIT KHATUA via AMBER
- [AMBER] How to get the Z component of ions from the trajectory file? Markowska
- Re: [AMBER] AMBER error slurmstepd SATYAJIT KHATUA via AMBER
- Re: [AMBER] AMBER error slurmstepd Adrian Roitberg via AMBER
- [AMBER] PhD position at University Complutense of Madrid in biocondensate modelling Andres Tejedor Reyes via AMBER
- [AMBER] antechamber error: "This molecule may have more than one unit..." Yang, Li-Yen via AMBER
- Re: [AMBER] antechamber error: "This molecule may have more than one unit..." Rodrigo Galindo-Murillo via AMBER
- Re: [AMBER] Maestro PDB to Amber PDB Vinicius Cruzeiro $Vinny$ via AMBER
- [AMBER] Incomplete installation: "Fixing Miniconda script shebangs" Claire Harmange Magnani via AMBER
- Re: [AMBER] antechamber error: "This molecule may have more than one unit..." He, Amy via AMBER
- [AMBER] Issue with bond and angle parameters Koirala, Kushal via AMBER
Tuesday, 19 September 2023
- [AMBER] How can I resolve the issue of the 'NAB' command not being found in AmberTools23? Fadaei Fatemeh Mgr. via AMBER
- [AMBER] How to get Inherent structure (Minimization energy) Zafar,Muhammad Saqlain via AMBER
- Re: [AMBER] How can I resolve the issue of the 'NAB' command not being found in AmberTools23? Claire Harmange Magnani via AMBER
- Re: [AMBER] antechamber error: "This molecule may have more than one unit..." Yang, Li-Yen via AMBER
- [AMBER] Query regarding unusual atom Sourav Bhowmik via AMBER
- [AMBER] charge extract from cpin file Dulal Mondal via AMBER
- Re: [AMBER] [Sender Not Verified] Query regarding unusual atom Steinbrecher, Thomas via AMBER
Wednesday, 20 September 2023
- [AMBER] CUDA version of nabnmode? Cenk Andac via AMBER
- [AMBER] Installing on Ubuntu Question Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] Query regarding unusual atom Carlos Simmerling via AMBER
- Re: [AMBER] How can I resolve the issue of the 'NAB' command not being found in AmberTools23? David A Case via AMBER
- Re: [AMBER] How to get Inherent structure (Minimization energy) David A Case via AMBER
- Re: [AMBER] Installing on Ubuntu Question David A Case via AMBER
- [AMBER] attempting to run QUICK Andriy Kovalenko via AMBER
- [AMBER] Alternatives to NAB for building DNA Claire Harmange Magnani via AMBER
- [AMBER] Failed test cases in $AMBERHOME/test/nfe/bbmd in Amber22/Amber23 Vlad via AMBER
- [AMBER] Optimization and balancing steps for a membrane protein, small molecule and POPC bilayer membrane complex system 李美玲 via AMBER
- Re: [AMBER] Alternatives to NAB for building DNA David A Case via AMBER
- Re: [AMBER] attempting to run QUICK Goetz, Andreas via AMBER
Thursday, 21 September 2023
- [AMBER] Autocorrelation function : Kankana Bhattacharjee via AMBER
- Re: [AMBER] Alternatives to NAB for building DNA aishen via AMBER
- Re: [AMBER] Autocorrelation function : Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] attempting to run QUICK Andriy Kovalenko via AMBER
- Re: [AMBER] Autocorrelation function : Kankana Bhattacharjee via AMBER
- Re: [AMBER] error in amber22 installation Setyanto Md via AMBER
Friday, 22 September 2023
- [AMBER] How to designate the Bond type(Sodium) in amber 22 K A SIVASANKER via AMBER
- [AMBER] Differences between the same dynamic VERONICA MARTIN HERNANDEZ via AMBER
- Re: [AMBER] [Sender Not Verified] Differences between the same dynamic Steinbrecher, Thomas via AMBER
- Re: [AMBER] How to designate the Bond type(Sodium) in amber 22 Dr. Anselm Horn via AMBER
- Re: [AMBER] How to designate the Bond type(Sodium) in amber 22 K A SIVASANKER via AMBER
- Re: [AMBER] How to designate the Bond type(Sodium) in amber 22 Carlos Simmerling via AMBER
- [AMBER] Regarding periodic box dimentions Midhun K Madhu 1620103 via AMBER
- Re: [AMBER] Regarding periodic box dimentions Carlos Simmerling via AMBER
- [AMBER] Support or H100s Pieri, Elisa via AMBER
- Re: [AMBER] Regarding periodic box dimentions Cianna Calia via AMBER
- Re: [AMBER] Support or H100s Goetz, Andreas via AMBER
Saturday, 23 September 2023
- [AMBER] CPPTRAJ, protein width Matthew Guberman-Pfeffer via AMBER
Sunday, 24 September 2023
- [AMBER] amber unit Dulal Mondal via AMBER
Monday, 25 September 2023
- [AMBER] cpptraj nativecontacts Enrico Martinez via AMBER
- Re: [AMBER] amber unit Daniel Roe via AMBER
- Re: [AMBER] Chirality flipped for 2 identical molecules Todd Minehardt via AMBER
- [AMBER] Amber22 DDBoost Install Error Hantz, Eric via AMBER
- Re: [AMBER] Amber22 DDBoost Install Error David A Case via AMBER
- Re: [AMBER] Amber22 DDBoost Install Error Shi Zhang via AMBER
- Re: [AMBER] Amber22 DDBoost Install Error Hantz, Eric via AMBER
- [AMBER] SASA calculation: Kankana Bhattacharjee via AMBER
Tuesday, 26 September 2023
- [AMBER] Adding organic ligand in membrane system Enrico Martinez via AMBER
- Re: [AMBER] SASA calculation: Dr. Anselm Horn via AMBER
- Re: [AMBER] SASA calculation: Kankana Bhattacharjee via AMBER
- [AMBER] watershell cpptraj: Kankana Bhattacharjee via AMBER
- [AMBER] Error in equillibrium step of MD Shreeramesh via AMBER
- Re: [AMBER] cpptraj nativecontacts Enrico Martinez via AMBER
Wednesday, 27 September 2023
- [AMBER] AmberTools23 fails to build with python 3.11 - Reply Doležal Rafael via AMBER
- Re: [AMBER] AmberTools23 fails to build with python 3.11 - Reply Hai Nguyen via AMBER
Thursday, 28 September 2023
- [AMBER] Problem with adding new atoms in prep file Barbara Lech via AMBER
Friday, 29 September 2023
- [AMBER] Problem preparing structures VERONICA MARTIN HERNANDEZ via AMBER
- Re: [AMBER] Problem preparing structures Dr. Anselm Horn via AMBER
Saturday, 30 September 2023
- [AMBER] Query Regarding PDB2GMX Error with Amber Force Field Fadaei Fatemeh Mgr. via AMBER
- Re: [AMBER] ?==?utf-8?q? ?==?utf-8?q? ?= Alternatives to NAB for building DN Fadaei Fatemeh Mgr. via AMBER

Last message date: Sat Sep 30 2023 - 09:00:02 PDT
Archived on: Wed May 08 2024 - 05:56:04 PDT

Amber Archive Sep 2023 by date