Amber Archive Mar 2023: by date

Wednesday, 1 March 2023
- Re: [AMBER] Terminal phosphates with RNA Piia Bartos via AMBER
- [AMBER] steered MD of anion transporters through membrane Jordi Bujons via AMBER
- Re: [AMBER] pmemd.cuda test possible failure Freddy Bernal via AMBER
- [AMBER] Adding organic molecules to the water box Dhanush Ramesh Anitha via AMBER
- Re: [AMBER] Adding organic molecules to the water box Carlos Simmerling via AMBER
- Re: [AMBER] MMPBSA problem Bill Miller III via AMBER
- Re: [AMBER] MMPBSA problem Bill Miller III via AMBER
Thursday, 2 March 2023
- [AMBER] Electrostatic Energy ! angad sharma via AMBER
- Re: [AMBER] Distance between residues: Too many iteration in routine He, Amy via AMBER
- [AMBER] Distance between residues: Too many iteration in routine Hocine EL KHAOUDI ENYOURY via AMBER
- Re: [AMBER] Distance between residues: Too many iteration in routine Hocine EL KHAOUDI ENYOURY via AMBER
- Re: [AMBER] Distance between residues: Too many iteration in routine He, Amy via AMBER
- [AMBER] RuntimeError in Pytraj maryam ghorbaninia via AMBER
- Re: [AMBER] RuntimeError in Pytraj Hai Nguyen via AMBER
- [AMBER] Free energy simulation with the MMPBSA ABDELATIF MESSAOUDI via AMBER
- Re: [AMBER] Free energy simulation with the MMPBSA SATYAJIT KHATUA via AMBER
- [AMBER] 回复: Free energy simulation with the MMPBSA Huang ZiJian via AMBER
- [AMBER] 回复: 回复: Electrostatic Energy ! Huang ZiJian via AMBER
Friday, 3 March 2023
- [AMBER] Error on tiMerge in parmed Osman, Roman via AMBER
- [AMBER] Is it Ok to upgrade NVidia driver Broto Santoso via AMBER
- [AMBER] amber22 installation error cusparse_LinearSolvers.cu Madhavan Jayaraman via AMBER
Saturday, 4 March 2023
- [AMBER] Distance matrix Dulal Mondal via AMBER
- [AMBER] Error when running Amber on GPU: cudaIpcOpenMemHandle failed on gpu->pbPeerAccumulator Handle invalid argument Siwakorn Sukharom via AMBER
Monday, 6 March 2023
- [AMBER] Problem with Zn ion in pdb file Siavoush Dastmalchi via AMBER
- [AMBER] ATP parameters for simulation compatible with Amber19SB force field? Gustavo Seabra via AMBER
- Re: [AMBER] Is it Ok to upgrade NVidia driver David A Case via AMBER
- Re: [AMBER] amber22 installation error cusparse_LinearSolvers.cu David A Case via AMBER
- [AMBER] Problem with Zn ion a protein-ligand complex Siavoush Dastmalchi via AMBER
- Re: [AMBER] amber22 installation error cusparse_LinearSolvers.cu ABDELATIF MESSAOUDI via AMBER
- [AMBER] Fwd: Distance matrix Dulal Mondal via AMBER
- [AMBER] Problem with Zn ion a protein-ligand complex Siavoush Dastmalchi via AMBER
Tuesday, 7 March 2023
- [AMBER] Problem with Zn2+ ion in a pdb file for a receptor-ligand complex Siavoush Dastmalchi via AMBER
- Re: [AMBER] [Sender Not Verified] Problem with Zn2+ ion in a pdb file for a receptor-ligand complex Steinbrecher, Thomas via AMBER
- Re: [AMBER] Fwd: Distance matrix Carlos Simmerling via AMBER
- [AMBER] CIC Annual Meeting during WiFo 2023 – Call for Papers – Deadline extended to 16.03. Guessregen, Stefan /DE via AMBER
- [AMBER] Constant pH MD simulation of non-protein systems MADHUSMITA DEVI via AMBER
- Re: [AMBER] Constant pH MD simulation of non-protein systems Vinicius Wilian Cruzeiro via AMBER
- [AMBER] How to shield charged side chain from ion binding / would you transform a counterion in TI simulations? He, Amy via AMBER
- Re: [AMBER] How to shield charged side chain from ion binding / would you transform a counterion in TI simulations? Carlos Simmerling via AMBER
- Re: [AMBER] How to shield charged side chain from ion binding / would you transform a counterion in TI simulations? Carlos Simmerling via AMBER
- Re: [AMBER] How to shield charged side chain from ion binding / would you transform a counterion in TI simulations? Carlos Simmerling via AMBER
- [AMBER] Implicit solvent MD for membrane proteins Ravi Abrol via AMBER
Wednesday, 8 March 2023
- [AMBER] Running QM/MM in parallel; multi-sander Vilhelm Ekberg via AMBER
- [AMBER] The latest version of miniconda3-py3.10 cannot successfully install amber20 with cmake wangjianing_mail via AMBER
- Re: [AMBER] RuntimeError in Pytraj Hai Nguyen via AMBER
- [AMBER] Extended ZN force field (EZAFF)? Kenneth Huang via AMBER
Thursday, 9 March 2023
- [AMBER] CPPTRAJ, mindset xyz components Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] CPPTRAJ, mindset xyz components Daniel Roe via AMBER
Friday, 10 March 2023
- Re: [AMBER] [Sender Not Verified] CPPTRAJ, mindset xyz components Steinbrecher, Thomas via AMBER
- Re: [AMBER] {SPAM?} Re: CPPTRAJ, mindist xyz components Daniel Roe via AMBER
- [AMBER] Amber22 installation on Ubuntu 22.04 Bansal, Prateek Dinesh via AMBER
- [AMBER] Request for Assistance with AMBER Output File for RMSF Analysis Roy, Rajarshi via AMBER
- Re: [AMBER] Request for Assistance with AMBER Output File for RMSF Analysis Daniel Roe via AMBER
- [AMBER] Water Survival Probability ABDUL BASIT via AMBER
- Re: [AMBER] [Sender Not Verified] Problem with Zn2+ ion in a pdb file for a receptor-ligand complex Siavoush Dastmalchi via AMBER
Saturday, 11 March 2023
- [AMBER] ambpdb -c flag is unknown Siavoush Dastmalchi via AMBER
- Re: [AMBER] ambpdb -c flag is unknown SATYAJIT KHATUA via AMBER
- Re: [AMBER] ambpdb -c flag is unknown David Case via AMBER
- [AMBER] auto-correlation using cpptraj Dulal Mondal via AMBER
Sunday, 12 March 2023
- Re: [AMBER] Request for Assistance with AMBER Output File for RMSF Analysis Daniel Roe via AMBER
- Re: [AMBER] auto-correlation using cpptraj Daniel Roe via AMBER
- Re: [AMBER] Water Survival Probability Daniel Roe via AMBER
Monday, 13 March 2023
- [AMBER] Constant pH pair list overflow. Increase MAX_TITR_RES in constantph.F90; recompile X
- [AMBER] Net charge of a POPC molecule is not zero Kosuke Tachibana via AMBER
Tuesday, 14 March 2023
- [AMBER] Wrong distance calculation with cpptraj Azurmendi, Hugo via AMBER
- Re: [AMBER] Wrong distance calculation with cpptraj Daniel Roe via AMBER
- [AMBER] Address the nonphysical coordination bond between Zn and the other atoms in the active site while using MCPB.py Deepthi Jose via AMBER
Wednesday, 15 March 2023
- [AMBER] problem with MMPBSA.py Siavoush Dastmalchi via AMBER
- Re: [AMBER] problem with MMPBSA.py Siavoush Dastmalchi via AMBER
- [AMBER] PCA warning Sayan Poddar via AMBER
- Re: [AMBER] PCA warning Daniel Roe via AMBER
- Re: [AMBER] Request for Assistance with AMBER Output File for RMSF Analysis Daniel Roe via AMBER
- [AMBER] [MicrosoftExchange329e71ec88ae4615bbc36ab6ce41109e@rutgersconnect.onmicrosoft.com: Re: Running QM/MM in parallel; multi-sander David A Case via AMBER
- Re: [AMBER] Amber22 installation on Ubuntu 22.04 David A Case via AMBER
- Re: [AMBER] Net charge of a POPC molecule is not zero Dickson, Callum via AMBER
- [AMBER] AMBER Parameters for LYS-GLY Isopeptide bond Shah, Tejas V. via AMBER
- Re: [AMBER] AMBER Parameters for LYS-GLY Isopeptide bond Robin Betz via AMBER
Thursday, 16 March 2023
- [AMBER] Help needed with thermodynamic integration: Collision of cations in binding energy calculation Mei Kevin via AMBER
- Re: [AMBER] Help needed with thermodynamic integration: Collision of cations in binding energy calculation He, Amy via AMBER
- [AMBER] Significant slow down with NMR restraints Ava Waggett via AMBER
- Re: [AMBER] Significant slow down with NMR restraints Carlos Simmerling via AMBER
- Re: [AMBER] Significant slow down with NMR restraints Kenneth Huang via AMBER
- Re: [AMBER] Help needed with thermodynamic integration: Collision of cations in binding energy calculation Kevin Mei via AMBER
Friday, 17 March 2023
- [AMBER] Amber 22 Nvidia GPU Benchmarks Vincenzo D'Amore via AMBER
- [AMBER] ParmEd problem: LJ12_6_4 +pTYR. Error: Could not find parameters for ATOM_TYPE CG Paiardi, Giulia via AMBER
- [AMBER] Nonphysical coordination bond between Zn and the other atoms in the active site while using MCPB.py SHAHID P via AMBER
- Re: [AMBER] Amber 22 Nvidia GPU Benchmarks Ross Walker via AMBER
- [AMBER] Problem loading pdb4amber in Amber 20 Joanna Michelle E. Chua via AMBER
- Re: [AMBER] Problem loading pdb4amber in Amber 20 Hai Nguyen via AMBER
- Re: [AMBER] Problem loading pdb4amber in Amber 20 Hai Nguyen via AMBER
Saturday, 18 March 2023
- Re: [AMBER] Net charge of a POPC molecule is not zero Kosuke Tachibana via AMBER
Sunday, 19 March 2023
- Re: [AMBER] Help needed with thermodynamic integration: Collision of cations in binding energy calculation He, Amy via AMBER
Monday, 20 March 2023
- Re: [AMBER] Help needed with thermodynamic integration: Collision of cations in binding energy calculation David A Case via AMBER
- [AMBER] life time calculation Dulal Mondal via AMBER
- Re: [AMBER] life time calculation Daniel Roe via AMBER
- Re: [AMBER] ParmEd problem: LJ12_6_4 +pTYR. Error: Could not find parameters for ATOM_TYPE CG Jason Swails via AMBER
- [AMBER] Problem with running production with pmemd.cuda Joanna Michelle E. Chua via AMBER
- Re: [AMBER] Problem with running production with pmemd.cuda Carlos Simmerling via AMBER
- [AMBER] time correlation Dulal Mondal via AMBER
Tuesday, 21 March 2023
- Re: [AMBER] time correlation David A Case via AMBER
- Re: [AMBER] Problem loading pdb4amber in Amber 20 David A Case via AMBER
- Re: [AMBER] Problem loading pdb4amber in Amber 20 Joanna Michelle E. Chua via AMBER
- [AMBER] Antechamber preparation of the system docked to two identical ligands Enrico Martinez via AMBER
- [AMBER] Query regarding distance calculation Saikat Pal via AMBER
- Re: [AMBER] Antechamber preparation of the system docked to two identical ligands Dr. Anselm Horn via AMBER
- [AMBER] Implementing string method in AMBER Souvik Dey via AMBER
- [AMBER] Updates for sander python interface? Brian Radak via AMBER
- [AMBER] Half-harmonic restraint Jose Luis Guerra via AMBER
- Re: [AMBER] Half-harmonic restraint Carlos Simmerling via AMBER
- Re: [AMBER] Amber 22 Nvidia GPU Benchmarks Ross Walker via AMBER
- [AMBER] RTX6000-ADA Benchmarks Ross Walker via AMBER
- Re: [AMBER] Amber 22 Nvidia GPU Benchmarks Vincenzo Maria D'Amore via AMBER
- Re: [AMBER] Half-harmonic restraint Carlos Simmerling via AMBER
- [AMBER] Amber21 help! Ramírez, Gustavo via AMBER
- [AMBER] Issues with simulating 5'-phosphorylated RNA strands Harvey Dale via AMBER
- Re: [AMBER] Issues with simulating 5'-phosphorylated RNA strands Maria Nagan via AMBER
- Re: [AMBER] Amber21 help! Monsurat M. Lawal via AMBER
- Re: [AMBER] Query regarding distance calculation Daniel Roe via AMBER
Wednesday, 22 March 2023
- [AMBER] Query regarding restarting the replica exchange molecular dynamics simulation Munazzah Fatima Ansari via AMBER
- Re: [AMBER] Implementing string method in AMBER David A Case via AMBER
- Re: [AMBER] Amber21 help! David A Case via AMBER
- Re: [AMBER] [Sender Not Verified] Re: Issues with simulating 5'-phosphorylated RNA strands David A Case via AMBER
- [AMBER] Is Potential ABMD Memory Leak Fixed In AMBER22? Owen O'Reilly via AMBER
Thursday, 23 March 2023
- [AMBER] Thermodynamic Integration DV/DL output Songyan Xia \(LHS, 118010341\) via AMBER
- Re: [AMBER] Antechamber preparation of the system docked to two identical ligands Enrico Martinez via AMBER
- [AMBER] AMBER18 pmemd.cuda installation on NVIDIA 3080 Daniel Hall via AMBER
- Re: [AMBER] AMBER18 pmemd.cuda installation on NVIDIA 3080 Daniel Hall via AMBER
- Re: [AMBER] AMBER18 pmemd.cuda installation on NVIDIA 3080 Ross Walker via AMBER
- Re: [AMBER] AMBER18 pmemd.cuda installation on NVIDIA 3080 Ross Walker via AMBER
- Re: [AMBER] AMBER18 pmemd.cuda installation on NVIDIA 3080 Daniel Hall via AMBER
- Re: [AMBER] [Sender Not Verified] Re: Issues with simulating 5'-phosphorylated RNA strands Harvey Dale via AMBER
- Re: [AMBER] Implementing string method in AMBER Souvik Dey via AMBER
Friday, 24 March 2023
- Re: [AMBER] [Sender Not Verified] Re: Antechamber preparation of the system docked to two identical ligands Enrico Martinez via AMBER
- Re: [AMBER] [Sender Not Verified] Re: Antechamber preparation of the system docked to two identical ligands Enrico Martinez via AMBER
- Re: [AMBER] Thermodynamic Integration DV/DL output David A Case via AMBER
- Re: [AMBER] Thermodynamic Integration DV/DL output Songyan Xia \(LHS, 118010341\) via AMBER
- Re: [AMBER] Implicit solvent MD for membrane proteins Ravi Abrol via AMBER
Saturday, 25 March 2023
- [AMBER] H++ server got hacker attack. Setyanto Md via AMBER
- Re: [AMBER] Implementing string method in AMBER Jose Luis Guerra via AMBER
Sunday, 26 March 2023
- Re: [AMBER] Thermodynamic Integration DV/DL output David A Case via AMBER
- Re: [AMBER] Thermodynamic Integration DV/DL output Songyan Xia \(LHS, 118010341\) via AMBER
Monday, 27 March 2023
- [AMBER] TI calculation regarding charge change in TI region. Fanyu Zhao via AMBER
- Re: [AMBER] [Sender Not Verified] Re: Antechamber preparation of the system docked to two identical ligands Enrico Martinez via AMBER
- [AMBER] ff19SB + OPC3 water model Vlad Cojocaru via AMBER
- Re: [AMBER] ff19SB + OPC3 water model Carlos Simmerling via AMBER
- Re: [AMBER] [Sender Not Verified] Re: Antechamber preparation of the system docked to two identical ligands Enrico Martinez via AMBER
- Re: [AMBER] [Sender Not Verified] Re: Antechamber preparation of the system docked to two identical ligands Enrico Martinez via AMBER
- Re: [AMBER] [Sender Not Verified] Re: Antechamber preparation of the system docked to two identical ligands Enrico Martinez via AMBER
Tuesday, 28 March 2023
- Re: [AMBER] [Sender Not Verified] Re: Antechamber preparation of the system docked to two identical ligands Enrico Martinez via AMBER
- Re: [AMBER] [Sender Not Verified] Re: Antechamber preparation of the system docked to two identical ligands Enrico Martinez via AMBER
- [AMBER] MCPB.py step 2 KeyError with crystal water Jasmin Güven via AMBER
- Re: [AMBER] [Sender Not Verified] Re: Antechamber preparation of the system docked to two identical ligands Enrico Martinez via AMBER
- [AMBER] 回复: MCPB.py step 2 KeyError with crystal water Huang ZiJian via AMBER
Wednesday, 29 March 2023
- [AMBER] Segmentation fault when running pmemd.cuda.MPI in Amber22 with plumed 2.8.2 Tien Phan via AMBER
Friday, 31 March 2023
- [AMBER] Error in running nmode showing ZeroDivisionError: division by zero Nishad Ankita Rudal via AMBER
- [AMBER] An update on Folding at Work-From-Home and Fast AF MD Jason Swails via AMBER
- Re: [AMBER] Error in running nmode showing ZeroDivisionError: division by zero Jason Swails via AMBER
- [AMBER] Volmap using cpptraj Dulal Mondal via AMBER
- Re: [AMBER] Volmap using cpptraj Hai Nguyen via AMBER

Last message date: Fri Mar 31 2023 - 07:30:02 PDT
Archived on: Fri Apr 19 2024 - 05:56:00 PDT

Amber Archive Mar 2023 by date