Amber Archive Aug 2023: by date

Tuesday, 1 August 2023
- [AMBER] Extract energy change contribution for specific mutation from TI simulation. Fanyu Zhao via AMBER
- [AMBER] The conversion between V and kcal/(mol*A*e) in external electric field. 郭家藩 via AMBER
Wednesday, 2 August 2023
- Re: [AMBER] Aligning MD snapshots excluding loops Daniel Roe via AMBER
- [AMBER] Parallel AmberTools Build Error: mpi4py.MPI fails to build Meyer, Olivia \(meyerok\) via AMBER
- [AMBER] Local structure index )LSI) help Zafar,Muhammad Saqlain via AMBER
Thursday, 3 August 2023
- [AMBER] constant pH MD constant pressure ERROR Amber 22 Mahdi Hassankalhori via AMBER
- Re: [AMBER] Parallel AmberTools Build Error: mpi4py.MPI fails to build Hai Nguyen via AMBER
- Re: [AMBER] Parallel AmberTools Build Error: mpi4py.MPI fails to build Hai Nguyen via AMBER
- [AMBER] Probability density with respect to Local structure index (LSI) Zafar,Muhammad Saqlain via AMBER
- [AMBER] Scientific Question_Debugging Maryam Foroozmehr via AMBER
- Re: [AMBER] Scientific Question_Debugging Adrian Roitberg via AMBER
- Re: [AMBER] Probability density with respect to Local structure index (LSI) Adrian Roitberg via AMBER
- Re: [AMBER] Probability density with respect to Local structure index (LSI) Zafar,Muhammad Saqlain via AMBER
- Re: [AMBER] Scientific Question_Debugging Adrian Roitberg via AMBER
- Re: [AMBER] Scientific Question_Debugging Maryam Foroozmehr via AMBER
- [AMBER] Amber problem looking for help leveen via AMBER
- [AMBER] weird simulation behavior when iwrap=1 Delwakkada Liyanage, Senal Dinuka via AMBER
Friday, 4 August 2023
- Re: [AMBER] Problem with time records in cpout- files in REMD CpHMD simulation Elvira Tarasova via AMBER
- [AMBER] CpHMD, membrane proteins Matthew Guberman-Pfeffer via AMBER
- [AMBER] Question about Zinc ions Sayan Poddar via AMBER
Saturday, 5 August 2023
- Re: [AMBER] Question about Zinc ions Ramachandran, Balajee via AMBER
- Re: [AMBER] Question about Zinc ions Sayan Poddar via AMBER
- [AMBER] DNA with two ligand molecules for MD maya nair via AMBER
- [AMBER] Input file for Curve+ angad sharma via AMBER
- [AMBER] sqm/mm FEP problem with lambda setting leveen via AMBER
Sunday, 6 August 2023
- Re: [AMBER] Scientific Question_Debugging Dr. Anselm Horn via AMBER
Monday, 7 August 2023
- [AMBER] Wrong results when using 4070Ti GPU Wang, Yin via AMBER
- [AMBER] Error running minimization Ritwika Chatterjee via AMBER
Tuesday, 8 August 2023
- [AMBER] Issue with deprecated np.float when using packmol-memgen Damas Joao CHST via AMBER
- Re: [AMBER] Issue with deprecated np.float when using packmol-memgen Stephan Schott via AMBER
- Re: [AMBER] Issue with deprecated np.float when using packmol-memgen Damas Joao CHST via AMBER
- Re: [AMBER] Problem with time records in cpout- files in REMD CpHMD simulation Elvira Tarasova via AMBER
- [AMBER] QMMM-FEP with sander.MPI 东庚 via AMBER
- [AMBER] QMMM-FEP with sander.MPI 东庚 via AMBER
Wednesday, 9 August 2023
- [AMBER] Regarding dU Force Field Priyasha Majee via AMBER
- [AMBER] questions about AmberTools installation from source Damas Joao CHST via AMBER
- Re: [AMBER] questions about AmberTools installation from source Stephan Schott via AMBER
- Re: [AMBER] Regarding dU Force Field Christina Bergonzo via AMBER
- [AMBER] SHAKE cannot be accomplished? Debarati DasGupta via AMBER
- Re: [AMBER] SHAKE cannot be accomplished? Carlos Simmerling via AMBER
- [AMBER] Regarding the compatibility of OL15 with protein-RNA-DNA complexes Sruthi Sudhakar via AMBER
Thursday, 10 August 2023
- [AMBER] Query regarding re-weighting in GaMD Munazzah Fatima Ansari via AMBER
- [AMBER] Position Announcement: Postdoctoral Scientist Opportunity accuratefreeenergy--- via AMBER
- Re: [AMBER] Problem with time records in cpout- files in REMD CpHMD simulation Elvira Tarasova via AMBER
Friday, 11 August 2023
- Re: [AMBER] Problem with time records in cpout- files in REMD CpHMD simulation Elvira Tarasova via AMBER
- Re: [AMBER] Problem with time records in cpout- files in REMD CpHMD simulation Elvira Tarasova via AMBER
- Re: [AMBER] Problem with time records in cpout- files in REMD CpHMD simulation Elvira Tarasova via AMBER
Saturday, 12 August 2023
- [AMBER] Problems with post-processing MD simulation with non-standard residues m.bzowka m.bzowka via AMBER
- Re: [AMBER] Problems with post-processing MD simulation with non-standard residues Daniel Roe via AMBER
- [AMBER] the charges and atom numbers are mismatch for the standard model! Emilie Gerard via AMBER
- Re: [AMBER] Problems with post-processing MD simulation with non-standard residues Daniel Roe via AMBER
Monday, 14 August 2023
- [AMBER] Warning in compilation: integer conversion resulted in change of sign Marcos Verissimo Alves via AMBER
Tuesday, 15 August 2023
- [AMBER] Error: Fast 3-point water residue, name and bond data incorrect! Derek M Shore via AMBER
Wednesday, 16 August 2023
- [AMBER] Tetrahedral Order Parameter Q Zafar,Muhammad Saqlain via AMBER
- Re: [AMBER] Tetrahedral Order Parameter Q SATYAJIT KHATUA via AMBER
- Re: [AMBER] Tetrahedral Order Parameter Q SATYAJIT KHATUA via AMBER
- [AMBER] Regarding-MMPBSA: Kankana Bhattacharjee via AMBER
- Re: [AMBER] Error: Fast 3-point water residue, name and bond data incorrect! Carlos Simmerling via AMBER
- Re: [AMBER] QMMM-FEP with sander.MPI King Wu via AMBER
Thursday, 17 August 2023
- [AMBER] MMPBSA-error: Kankana Bhattacharjee via AMBER
- Re: [AMBER] MMPBSA-error: SATYAJIT KHATUA via AMBER
- [AMBER] Blank frcmod file is generating KAJAL ABROL via AMBER
Friday, 18 August 2023
- Re: [AMBER] Blank frcmod file is generating Daniel Roe via AMBER
- [AMBER] LEaP scripting amber--- via AMBER
Saturday, 19 August 2023
- Re: [AMBER] LEaP scripting Dr. Anselm Horn via AMBER
- [AMBER] Regarding error in the tleap output file KAJAL ABROL via AMBER
Monday, 21 August 2023
- Re: [AMBER] questions about AmberTools installation from source Damas Joao CHST via AMBER
- Re: [AMBER] questions about AmberTools installation from source Stephan Schott via AMBER
- [AMBER] Simulation error when using pmemd.cuda Loftus, Alec via AMBER
- Re: [AMBER] Simulation error when using pmemd.cuda Rodrigo Galindo-Murillo via AMBER
Tuesday, 22 August 2023
- Re: [AMBER] [Sender Not Verified] Regarding error in the tleap output file Steinbrecher, Thomas via AMBER
- [AMBER] Trouble installing MPI version - ./configure_mpich not found Kovács Richárd Dezső via AMBER
- [AMBER] Benchmarks for new NVIDIA cards? Tucker Burgin via AMBER
- [AMBER] Zinc ions bonded with Glutamic acid Sayan Poddar via AMBER
Wednesday, 23 August 2023
- [AMBER] Applying external electric field in the simulation Markowska
- Re: [AMBER] Error: Fast 3-point water residue, name and bond data incorrect! Carlos Simmerling via AMBER
- [AMBER] Run problem in constant pH REMD in amber22 with pmemd.cuda.MPI in explicit solvent Dulal Mondal via AMBER
- Re: [AMBER] Run problem in constant pH REMD in amber22 with pmemd.cuda.MPI in explicit solvent Vinicius Wilian Cruzeiro via AMBER
- Re: [AMBER] Run problem in constant pH REMD in amber22 with pmemd.cuda.MPI in explicit solvent Dulal Mondal via AMBER
- [AMBER] simulated annealing of DNA-ligand complex using NMR restrain Anirban Ghosh via AMBER
- Re: [AMBER] simulated annealing of DNA-ligand complex using NMR restrain Carlos Simmerling via AMBER
- [AMBER] Question regarding PBC simulations with ions Prithviraj Nandigrami via AMBER
- Re: [AMBER] Question regarding PBC simulations with ions shiyu wang via AMBER
Thursday, 24 August 2023
- Re: [AMBER] Applying external electric field in the simulation Markowska
- [AMBER] minimisation with pmemd.cuda Enrico Martinez via AMBER
Friday, 25 August 2023
- [AMBER] Paths with spaces in cpptraj Mark Mackey via AMBER
- [AMBER] MMPBSA-Nonpolar-solvation-energy-parameters: Kankana Bhattacharjee via AMBER
- Re: [AMBER] Paths with spaces in cpptraj Carlos Simmerling via AMBER
Saturday, 26 August 2023
- [AMBER] gamma_ln in simulated annealing Anirban Ghosh via AMBER
- Re: [AMBER] MMPBSA-Nonpolar-solvation-energy-parameters: Ray Luo via AMBER
Sunday, 27 August 2023
- Re: [AMBER] MMPBSA-Nonpolar-solvation-energy-parameters: Ray Luo via AMBER
- Re: [AMBER] MMPBSA-Nonpolar-solvation-energy-parameters: Kankana Bhattacharjee via AMBER
- Re: [AMBER] MMPBSA-Nonpolar-solvation-energy-parameters: Ray Luo via AMBER
- Re: [AMBER] [Sender Not Verified] gamma_ln in simulated annealing Steinbrecher, Thomas via AMBER
Monday, 28 August 2023
- Re: [AMBER] MMPBSA-Nonpolar-solvation-energy-parameters: Kankana Bhattacharjee via AMBER
- [AMBER] Adding new atom type in PARMCHK.DAT Priyasha Majee via AMBER
- Re: [AMBER] MMPBSA-Nonpolar-solvation-energy-parameters: Ray Luo via AMBER
- Re: [AMBER] MMPBSA-Nonpolar-solvation-energy-parameters: Kankana Bhattacharjee via AMBER
- Re: [AMBER] MMPBSA-Nonpolar-solvation-energy-parameters: Ray Luo via AMBER
- Re: [AMBER] MMPBSA-Nonpolar-solvation-energy-parameters: Kankana Bhattacharjee via AMBER
- [AMBER] How to place extra point of charge to simulate sigma hole on halogens Friederike Leßmöllmann via AMBER
- [AMBER] Compiling AMBER23 Javier O Sanlley-hernandez via AMBER
- Re: [AMBER] Compiling AMBER23 SATYAJIT KHATUA via AMBER
- Re: [AMBER] MMPBSA-Nonpolar-solvation-energy-parameters: Kankana Bhattacharjee via AMBER
- [AMBER] CpHMD run in explicit solvent in cuda Dulal Mondal via AMBER
Tuesday, 29 August 2023
- Re: [AMBER] CpHMD run in explicit solvent in cuda Dulal Mondal via AMBER
- Re: [AMBER] Compiling AMBER23 accuratefreeenergy--- via AMBER
- Re: [AMBER] CpHMD run in explicit solvent in cuda Jason Swails via AMBER
- Re: [AMBER] Paths with spaces in cpptraj Carlos Simmerling via AMBER
- Re: [AMBER] MMPBSA-Nonpolar-solvation-energy-parameters: Ray Luo via AMBER
- [AMBER] H-bond analysis Neelanjana via AMBER
Wednesday, 30 August 2023
- Re: [AMBER] Adding new atom type in PARMCHK.DAT Dr. Anselm Horn via AMBER
- [AMBER] Fwd: H-bond analysis Neelanjana via AMBER
- [AMBER] cpptraj: offset option for trajout Enrico Martinez via AMBER
- [AMBER] ATTN, need revision Priyasha Majee via AMBER
- [AMBER] Error in energy minimization step KAJAL ABROL via AMBER
- Re: [AMBER] Error in energy minimization step Carlos Simmerling via AMBER
- Re: [AMBER] ATTN, need revision He, Amy via AMBER
Thursday, 31 August 2023
- Re: [AMBER] ATTN, need revision Priyasha Majee via AMBER
- [AMBER] Membrane protein tutorial: dimensions of the system Enrico Martinez via AMBER
- Re: [AMBER] ATTN, need revision He, Amy via AMBER
- [AMBER] Cross Correlation Analysis Shah, Tejas V. via AMBER

Last message date: Thu Aug 31 2023 - 13:30:02 PDT
Archived on: Wed May 08 2024 - 05:56:04 PDT

Amber Archive Aug 2023 by date