Amber Archive Jan 2023: by date

Sunday, 1 January 2023
- Re: [AMBER] H100 & RTX4090 Benchmarks Adrian Roitberg via AMBER
- Re: [AMBER] error with titration curve in Constant pH tutorial Vaibhav Dixit via AMBER
- [AMBER] PM6-DH+ Parameters for dispersion correction not found James Kress via AMBER
Monday, 2 January 2023
- Re: [AMBER] error with titration curve in Constant pH tutorial Vaibhav Dixit via AMBER
- [AMBER] Announcement about upcoming changes to Amber license fees David A Case via AMBER
- Re: [AMBER] Announcement about upcoming changes to Amber license fees James Kress via AMBER
- Re: [AMBER] Announcement about upcoming changes to Amber license fees Suchetana Gupta via AMBER
- Re: [AMBER] Announcement about upcoming changes to Amber license fees Pablo Arantes via AMBER
- Re: [AMBER] Announcement about upcoming changes to Amber license fees Kshatresh Dutta Dubey via AMBER
- [AMBER] About the pthread error of installing the amber22(CUDA) Yeng-Tseng Wang via AMBER
- Re: [AMBER] Announcement about upcoming changes to Amber license fees Dr. Vaibhav Anil Dixit via AMBER
Tuesday, 3 January 2023
- [AMBER] CPPTRAJ native contact analysis output Prithviraj Nandigrami via AMBER
- [AMBER] amber20 installation error in ROCKY 8.5 with RTX A6000 GPU Md Fulbabu Sk via AMBER
Wednesday, 4 January 2023
- Re: [AMBER] amber20 installation error in ROCKY 8.5 with RTX A6000 GPU David A Case via AMBER
- Re: [AMBER] PM6-DH+ Parameters for dispersion correction not found David A Case via AMBER
- Re: [AMBER] Determination of percentage population David A Case via AMBER
- Re: [AMBER] amber20 installation error in ROCKY 8.5 with RTX A6000 GPU Md Fulbabu Sk via AMBER
- Re: [AMBER] amber20 installation error in ROCKY 8.5 with RTX A6000 GPU Ross Walker via AMBER
- [AMBER] Non-standard KCX residue with missing hydrogen on carbamate and charge -1 Barbara Herlah via AMBER
Thursday, 5 January 2023
- Re: [AMBER] error with titration curve in Constant pH tutorial Vaibhav Dixit via AMBER
- Re: [AMBER] Non-standard KCX residue with missing hydrogen on carbamate and charge -1 Dr. Anselm Horn via AMBER
- Re: [AMBER] Non-standard KCX residue with missing hydrogen on carbamate and charge -1 David A Case via AMBER
- [AMBER] Thermodynamic integration for charge-changing mutations Skanda Sastry via AMBER
Friday, 6 January 2023
- [AMBER] Calculation of dG for dimeric system Enrico Martinez via AMBER
- [AMBER] broken installation of amber18 Adam Jarmula via AMBER
- [AMBER] External electric field in Amber Ignacio J. General via AMBER
- Re: [AMBER] Calculation of dG for dimeric system Enrico Martinez via AMBER
- [AMBER] How do I simulate D-amino acids? Suchetana Gupta via AMBER
- Re: [AMBER] How do I simulate D-amino acids? Suchetana Gupta via AMBER
- Re: [AMBER] Non-standard KCX residue with missing hydrogen on carbamate and charge -1 Kenneth Huang via AMBER
- Re: [AMBER] broken installation of amber18 David A Case via AMBER
- Re: [AMBER] How do I simulate D-amino acids? Suchetana Gupta via AMBER
Saturday, 7 January 2023
- Re: [AMBER] broken installation of amber18 Adam Jarmula via AMBER
- [AMBER] amber 22 installation on ubuntu 18 Dulal Mondal via AMBER
- Re: [AMBER] amber 22 installation on ubuntu 18 David A Case via AMBER
Sunday, 8 January 2023
- [AMBER] Aligning of ions and DNA angad sharma via AMBER
- [AMBER] Questions regarding the installation process Elahi, Pascal \(Pawsey, Kensington WA\) via AMBER
- [AMBER] Can imin=5 of sander treat NPT trajectories properly? Mei Kevin via AMBER
- Re: [AMBER] Can imin=5 of sander treat NPT trajectories properly? Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] Can imin=5 of sander treat NPT trajectories properly? Thomas Cheatham via AMBER
- Re: [AMBER] Can imin=5 of sander treat NPT trajectories properly? Mei Kevin via AMBER
Monday, 9 January 2023
- Re: [AMBER] Calculation of dG for dimeric system Téletchéa Stéphane via AMBER
- Re: [AMBER] Can imin=5 of sander treat NPT trajectories properly? Carlos Simmerling via AMBER
- Re: [AMBER] Questions regarding the installation process David A Case via AMBER
- Re: [AMBER] Can imin=5 of sander treat NPT trajectories properly? Petr Kulhanek via AMBER
Tuesday, 10 January 2023
- [AMBER] Distance restraints Juliette Newell via AMBER
- Re: [AMBER] Distance restraints Carlos Simmerling via AMBER
- [AMBER] Amber Install Error Tacey, Sean A via AMBER
Wednesday, 11 January 2023
- [AMBER] Increase maximum of atoms in COM distance restraint Javier Carmona Garcia via AMBER
- [AMBER] Segmentation fault while using xtalsymm in cpptraj Thorben Poburski via AMBER
- [AMBER] no decomposition output for amber22 MMGBSA Adam Jarmula via AMBER
- [AMBER] Error due to unfilled valence in antechamber MADHUSMITA DEVI via AMBER
Thursday, 12 January 2023
- [AMBER] AmberTools22 installation problem - CondaFileIOError, run_cmake error Nikolay Kuzmich via AMBER
- Re: [AMBER] AmberTools22 installation problem - CondaFileIOError, run_cmake error David Case via AMBER
- Re: [AMBER] AmberTools22 installation problem - CondaFileIOError, run_cmake error Nikolay Kuzmich via AMBER
- Re: [AMBER] AmberTools22 installation problem - CondaFileIOError, run_cmake error Clay Berkley via AMBER
- Re: [AMBER] CPPTRAJ native contact analysis output Prithviraj Nandigrami via AMBER
Friday, 13 January 2023
- [AMBER] Strip based on distance to point Pietro ARONICA via AMBER
- Re: [AMBER] amber installation on linux mint nahoum a via AMBER
Saturday, 14 January 2023
- [AMBER] Amber 22 installation error Kshatresh Dutta Dubey via AMBER
- [AMBER] Use of nscm=0 with MC barostat Ramdhan,Peter A via AMBER
Sunday, 15 January 2023
- [AMBER] Center of mass, velocity, Momentum calculation Dulal Mondal via AMBER
Monday, 16 January 2023
- Re: [AMBER] ?==?utf-8?q? Increase maximum of atoms in COM distance restraint Javier Carmona Garcia via AMBER
- [AMBER] MMGBSA calculations - mbondi parameter Maria Bzówka via AMBER
- Re: [AMBER] MMGBSA calculations - mbondi parameter Carlos Simmerling via AMBER
- [AMBER] AMBER Free Energy Update Darrin York via AMBER
- Re: [AMBER] amber installation on linux mint David A Case via AMBER
- Re: [AMBER] Use of nscm=0 with MC barostat David A Case via AMBER
- Re: [AMBER] Center of mass, velocity, Momentum calculation David A Case via AMBER
- Re: [AMBER] MMGBSA calculations - mbondi parameter David A Case via AMBER
- Re: [AMBER] Amber Install Error David A Case via AMBER
- Re: [AMBER] Error due to unfilled valence in antechamber David A Case via AMBER
- Re: [AMBER] no decomposition output for amber22 MMGBSA David A Case via AMBER
- [AMBER] Question concerning the GLYCAM force field Jiang, Yaoyukun via AMBER
- Re: [AMBER] Center of mass, velocity, Momentum calculation Dulal Mondal via AMBER
Tuesday, 17 January 2023
- Re: [AMBER] Error due to unfilled valence in antechamber MADHUSMITA DEVI via AMBER
- Re: [AMBER] R: Reimaging issues Daniel Roe via AMBER
- Re: [AMBER] Segmentation fault while using xtalsymm in cpptraj Daniel Roe via AMBER
- [AMBER] TI Ignacio J. General via AMBER
- Re: [AMBER] Amber 22 installation error Kshatresh Dutta Dubey via AMBER
- Re: [AMBER] amber installation on linux mint nahoum a via AMBER
- Re: [AMBER] Center of mass, velocity, Momentum calculation Daniel Roe via AMBER
- [AMBER] the charge error in amber laura zhang via AMBER
- Re: [AMBER] the charge error in amber Carlos Simmerling via AMBER
- [AMBER] Multiple copies of simulation to check for reproducibility and convergence Suchetana Gupta via AMBER
Wednesday, 18 January 2023
- [AMBER] Fixing the rotation of the simulation box angad sharma via AMBER
- [AMBER] MMPBSA Pairwise Internal Energy Issue Pablo Arantes via AMBER
- Re: [AMBER] [EXTERNAL] Re: Amber Install Error Tacey, Sean A via AMBER
Thursday, 19 January 2023
- Re: [AMBER] MMGBSA calculations - mbondi parameter Maria Bzówka via AMBER
- Re: [AMBER] MMPBSA Pairwise Internal Energy Issue Bill Miller III via AMBER
- Re: [AMBER] the charge error in amber David A Case via AMBER
Friday, 20 January 2023
- Re: [AMBER] Issues with nucleic acid simulations Prithviraj Nandigrami via AMBER
- [AMBER] tleap parameter file Mac Kevin Braza via AMBER
- Re: [AMBER] tleap parameter file Suchetana Gupta via AMBER
- [AMBER] problem setting up an amber simulation laura zhang via AMBER
- Re: [AMBER] problem setting up an amber simulation Carlos Simmerling via AMBER
Saturday, 21 January 2023
- [AMBER] Choosing GPU edition for building own system M. Reza Ganjalikhany via AMBER
- [AMBER] Can not install Amber with CUDA supported Broto Santoso via AMBER
- Re: [AMBER] Can not install Amber with CUDA supported Ross Walker via AMBER
Sunday, 22 January 2023
- [AMBER] Problem met in running GBn2 model Jiaan Zhu via AMBER
- Re: [AMBER] Problem met in running GBn2 model Carlos Simmerling via AMBER
- Re: [AMBER] problem setting up an amber simulation David A Case via AMBER
- Re: [AMBER] problem setting up an amber simulation Daniel Roe via AMBER
- Re: [AMBER] Problem met in running GBn2 model David A Case via AMBER
Tuesday, 24 January 2023
- [AMBER] Unit Dulal Mondal via AMBER
- [AMBER] MCPB.py error on first step. DE-SANTANA-PONTES, FREDERICO J. via AMBER
- Re: [AMBER] Unit David A Case via AMBER
- [AMBER] AMBER simulation heating step Prithviraj Nandigrami via AMBER
- [AMBER] Heating the soft core atoms in TI simulations He, Amy via AMBER
- Re: [AMBER] Heating the soft core atoms in TI simulations Steinbrecher, Thomas via AMBER
Wednesday, 25 January 2023
- Re: [AMBER] Heating the soft core atoms in TI simulations Darrin York via AMBER
- [AMBER] Segmentation fault when trying outputting MBAR data in vacuum Miroslav Suruzhon via AMBER
- [AMBER] MPICH configure failed, returning 1 ABDELATIF MESSAOUDI via AMBER
- Re: [AMBER] MPICH configure failed, returning 1 David Case via AMBER
- Re: [AMBER] Heating the soft core atoms in TI simulations He, Amy via AMBER
Friday, 27 January 2023
- [AMBER] Installation Amber22 failed Freddy Bernal via AMBER
- [AMBER] LEaP Issue Gonzalo R. Vazquez-Jimenez via AMBER
- [AMBER] idecomp = 1 for TI simulations: Energies not printed / cannot be calculated He, Amy via AMBER
- Re: [AMBER] idecomp = 1 for TI simulations: Energies not printed / cannot be calculated He, Amy via AMBER
- [AMBER] test message, per SRB David A Case via AMBER
- Re: [AMBER] Installation Amber22 failed (fwd) Scott Brozell via AMBER
- Re: [AMBER] LEaP Issue Scott Brozell via AMBER
- Re: [AMBER] LEaP Issue Stephan Schott via AMBER
Saturday, 28 January 2023
- [AMBER] Install Amber22 ABDELATIF MESSAOUDI via AMBER
Monday, 30 January 2023
- [AMBER] How restart md simulation with amber22 ABDELATIF MESSAOUDI via AMBER
- Re: [AMBER] How restart md simulation with amber22 SATYAJIT KHATUA via AMBER
- Re: [AMBER] How restart md simulation with amber22 SATYAJIT KHATUA via AMBER
- [AMBER] parmed: ff19SB to gromacs .top Patricio German Barletta via AMBER
- [AMBER] Random failure of parmchk2? Brian Radak via AMBER
- Re: [AMBER] Random failure of parmchk2? Brian Radak via AMBER
- Re: [AMBER] Random failure of parmchk2? Brian Radak via AMBER
- Re: [AMBER] Installation Amber22 failed David A Case via AMBER
- Re: [AMBER] Install Amber22 David A Case via AMBER
Tuesday, 31 January 2023
- [AMBER] Possible failures in test Freddy Bernal via AMBER
- [AMBER] Error while running finddgref.py script Akhil Sudarsan via AMBER
- [AMBER] CPPTRAJ, PCA, Effect of Mutation Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] Error while running finddgref.py script Vinicius Wilian Cruzeiro via AMBER
- Re: [AMBER] Distance calculation using cpptraj Carlos Simmerling via AMBER

Last message date: Tue Jan 31 2023 - 12:30:03 PST
Archived on: Mon Feb 03 2025 - 05:56:09 PST

Amber Archive Jan 2023 by date