Amber Archive Jan 2023: by thread

Re: [AMBER] H100 & RTX4090 Benchmarks Adrian Roitberg via AMBER (Sun Jan 01 2023 - 18:41:58 PST)
Re: [AMBER] error with titration curve in Constant pH tutorial Vaibhav Dixit via AMBER (Sun Jan 01 2023 - 20:31:36 PST)
- [AMBER] PM6-DH+ Parameters for dispersion correction not found James Kress via AMBER (Sun Jan 01 2023 - 20:50:32 PST)
  - Re: [AMBER] PM6-DH+ Parameters for dispersion correction not found David A Case via AMBER (Wed Jan 04 2023 - 06:19:41 PST)
- Re: [AMBER] error with titration curve in Constant pH tutorial Vaibhav Dixit via AMBER (Mon Jan 02 2023 - 01:24:56 PST)
- Re: [AMBER] error with titration curve in Constant pH tutorial Vaibhav Dixit via AMBER (Thu Jan 05 2023 - 05:14:57 PST)
[AMBER] Announcement about upcoming changes to Amber license fees David A Case via AMBER (Mon Jan 02 2023 - 05:48:27 PST)
- Re: [AMBER] Announcement about upcoming changes to Amber license fees James Kress via AMBER (Mon Jan 02 2023 - 09:47:34 PST)
  - Re: [AMBER] Announcement about upcoming changes to Amber license fees Suchetana Gupta via AMBER (Mon Jan 02 2023 - 10:26:10 PST)
- Re: [AMBER] Announcement about upcoming changes to Amber license fees Pablo Arantes via AMBER (Mon Jan 02 2023 - 10:28:46 PST)
- Re: [AMBER] Announcement about upcoming changes to Amber license fees Kshatresh Dutta Dubey via AMBER (Mon Jan 02 2023 - 12:04:01 PST)
- Re: [AMBER] Announcement about upcoming changes to Amber license fees Dr. Vaibhav Anil Dixit via AMBER (Mon Jan 02 2023 - 20:55:13 PST)
[AMBER] About the pthread error of installing the amber22(CUDA) Yeng-Tseng Wang via AMBER (Mon Jan 02 2023 - 19:33:17 PST)
[AMBER] CPPTRAJ native contact analysis output Prithviraj Nandigrami via AMBER (Tue Jan 03 2023 - 11:16:02 PST)
- Re: [AMBER] CPPTRAJ native contact analysis output Prithviraj Nandigrami via AMBER (Thu Jan 12 2023 - 15:01:24 PST)
[AMBER] amber20 installation error in ROCKY 8.5 with RTX A6000 GPU Md Fulbabu Sk via AMBER (Tue Jan 03 2023 - 20:17:24 PST)
- Re: [AMBER] amber20 installation error in ROCKY 8.5 with RTX A6000 GPU David A Case via AMBER (Wed Jan 04 2023 - 06:13:40 PST)
  - Re: [AMBER] amber20 installation error in ROCKY 8.5 with RTX A6000 GPU Md Fulbabu Sk via AMBER (Wed Jan 04 2023 - 07:44:38 PST)
    - Re: [AMBER] amber20 installation error in ROCKY 8.5 with RTX A6000 GPU Ross Walker via AMBER (Wed Jan 04 2023 - 07:47:38 PST)
Re: [AMBER] Determination of percentage population David A Case via AMBER (Wed Jan 04 2023 - 06:27:12 PST)
[AMBER] Non-standard KCX residue with missing hydrogen on carbamate and charge -1 Barbara Herlah via AMBER (Wed Jan 04 2023 - 21:35:33 PST)
- Re: [AMBER] Non-standard KCX residue with missing hydrogen on carbamate and charge -1 Dr. Anselm Horn via AMBER (Thu Jan 05 2023 - 05:20:18 PST)
- Re: [AMBER] Non-standard KCX residue with missing hydrogen on carbamate and charge -1 David A Case via AMBER (Thu Jan 05 2023 - 06:28:38 PST)
- Re: [AMBER] Non-standard KCX residue with missing hydrogen on carbamate and charge -1 Kenneth Huang via AMBER (Fri Jan 06 2023 - 16:22:13 PST)
[AMBER] Thermodynamic integration for charge-changing mutations Skanda Sastry via AMBER (Thu Jan 05 2023 - 17:22:18 PST)
[AMBER] Calculation of dG for dimeric system Enrico Martinez via AMBER (Fri Jan 06 2023 - 01:29:00 PST)
- Re: [AMBER] Calculation of dG for dimeric system Enrico Martinez via AMBER (Fri Jan 06 2023 - 08:08:40 PST)
  - Re: [AMBER] Calculation of dG for dimeric system Téletchéa Stéphane via AMBER (Mon Jan 09 2023 - 03:57:53 PST)
[AMBER] broken installation of amber18 Adam Jarmula via AMBER (Fri Jan 06 2023 - 07:16:10 PST)
- Re: [AMBER] broken installation of amber18 David A Case via AMBER (Fri Jan 06 2023 - 18:32:29 PST)
  - Re: [AMBER] broken installation of amber18 Adam Jarmula via AMBER (Sat Jan 07 2023 - 05:26:30 PST)
[AMBER] External electric field in Amber Ignacio J. General via AMBER (Fri Jan 06 2023 - 07:48:49 PST)
[AMBER] How do I simulate D-amino acids? Suchetana Gupta via AMBER (Fri Jan 06 2023 - 09:22:22 PST)
- Re: [AMBER] How do I simulate D-amino acids? Suchetana Gupta via AMBER (Fri Jan 06 2023 - 10:18:11 PST)
- Re: [AMBER] How do I simulate D-amino acids? Suchetana Gupta via AMBER (Fri Jan 06 2023 - 19:01:38 PST)
[AMBER] amber 22 installation on ubuntu 18 Dulal Mondal via AMBER (Sat Jan 07 2023 - 06:54:18 PST)
- Re: [AMBER] amber 22 installation on ubuntu 18 David A Case via AMBER (Sat Jan 07 2023 - 18:05:48 PST)
[AMBER] Aligning of ions and DNA angad sharma via AMBER (Sun Jan 08 2023 - 01:00:11 PST)
[AMBER] Questions regarding the installation process Elahi, Pascal \(Pawsey, Kensington WA\) via AMBER (Sun Jan 08 2023 - 18:28:48 PST)
- Re: [AMBER] Questions regarding the installation process David A Case via AMBER (Mon Jan 09 2023 - 11:08:39 PST)
[AMBER] Can imin=5 of sander treat NPT trajectories properly? Mei Kevin via AMBER (Sun Jan 08 2023 - 19:22:24 PST)
- Re: [AMBER] Can imin=5 of sander treat NPT trajectories properly? Matthew Guberman-Pfeffer via AMBER (Sun Jan 08 2023 - 19:26:57 PST)
  - Re: [AMBER] Can imin=5 of sander treat NPT trajectories properly? Mei Kevin via AMBER (Sun Jan 08 2023 - 19:55:07 PST)
    - Re: [AMBER] Can imin=5 of sander treat NPT trajectories properly? Carlos Simmerling via AMBER (Mon Jan 09 2023 - 05:45:23 PST)
- Re: [AMBER] Can imin=5 of sander treat NPT trajectories properly? Thomas Cheatham via AMBER (Sun Jan 08 2023 - 19:37:07 PST)
- Re: [AMBER] Can imin=5 of sander treat NPT trajectories properly? Petr Kulhanek via AMBER (Mon Jan 09 2023 - 23:20:00 PST)
[AMBER] Distance restraints Juliette Newell via AMBER (Tue Jan 10 2023 - 00:58:16 PST)
- Re: [AMBER] Distance restraints Carlos Simmerling via AMBER (Tue Jan 10 2023 - 04:58:09 PST)
[AMBER] Amber Install Error Tacey, Sean A via AMBER (Tue Jan 10 2023 - 11:02:20 PST)
- Re: [AMBER] Amber Install Error David A Case via AMBER (Mon Jan 16 2023 - 10:50:26 PST)
  - Re: [AMBER] [EXTERNAL] Re: Amber Install Error Tacey, Sean A via AMBER (Wed Jan 18 2023 - 11:17:42 PST)
[AMBER] Increase maximum of atoms in COM distance restraint Javier Carmona Garcia via AMBER (Wed Jan 11 2023 - 06:56:22 PST)
[AMBER] Segmentation fault while using xtalsymm in cpptraj Thorben Poburski via AMBER (Wed Jan 11 2023 - 07:30:27 PST)
- Re: [AMBER] Segmentation fault while using xtalsymm in cpptraj Daniel Roe via AMBER (Tue Jan 17 2023 - 05:01:55 PST)
[AMBER] no decomposition output for amber22 MMGBSA Adam Jarmula via AMBER (Wed Jan 11 2023 - 12:24:29 PST)
- Re: [AMBER] no decomposition output for amber22 MMGBSA David A Case via AMBER (Mon Jan 16 2023 - 10:55:02 PST)
[AMBER] Error due to unfilled valence in antechamber MADHUSMITA DEVI via AMBER (Wed Jan 11 2023 - 23:38:02 PST)
- Re: [AMBER] Error due to unfilled valence in antechamber David A Case via AMBER (Mon Jan 16 2023 - 10:52:59 PST)
  - Re: [AMBER] Error due to unfilled valence in antechamber MADHUSMITA DEVI via AMBER (Tue Jan 17 2023 - 02:28:17 PST)
[AMBER] AmberTools22 installation problem - CondaFileIOError, run_cmake error Nikolay Kuzmich via AMBER (Thu Jan 12 2023 - 06:06:30 PST)
- Re: [AMBER] AmberTools22 installation problem - CondaFileIOError, run_cmake error David Case via AMBER (Thu Jan 12 2023 - 06:17:14 PST)
  - Re: [AMBER] AmberTools22 installation problem - CondaFileIOError, run_cmake error Nikolay Kuzmich via AMBER (Thu Jan 12 2023 - 07:41:04 PST)
    - Re: [AMBER] AmberTools22 installation problem - CondaFileIOError, run_cmake error Clay Berkley via AMBER (Thu Jan 12 2023 - 07:42:47 PST)
[AMBER] Strip based on distance to point Pietro ARONICA via AMBER (Fri Jan 13 2023 - 01:10:10 PST)
Re: [AMBER] amber installation on linux mint nahoum a via AMBER (Fri Jan 13 2023 - 03:22:44 PST)
- Re: [AMBER] amber installation on linux mint David A Case via AMBER (Mon Jan 16 2023 - 10:15:37 PST)
  - Re: [AMBER] amber installation on linux mint nahoum a via AMBER (Tue Jan 17 2023 - 09:05:30 PST)
[AMBER] Amber 22 installation error Kshatresh Dutta Dubey via AMBER (Sat Jan 14 2023 - 05:22:14 PST)
- Re: [AMBER] Amber 22 installation error Kshatresh Dutta Dubey via AMBER (Tue Jan 17 2023 - 08:59:23 PST)
[AMBER] Use of nscm=0 with MC barostat Ramdhan,Peter A via AMBER (Sat Jan 14 2023 - 12:04:27 PST)
- Re: [AMBER] Use of nscm=0 with MC barostat David A Case via AMBER (Mon Jan 16 2023 - 10:25:06 PST)
[AMBER] Center of mass, velocity, Momentum calculation Dulal Mondal via AMBER (Sun Jan 15 2023 - 05:01:08 PST)
- Re: [AMBER] Center of mass, velocity, Momentum calculation David A Case via AMBER (Mon Jan 16 2023 - 10:29:47 PST)
  - Re: [AMBER] Center of mass, velocity, Momentum calculation Dulal Mondal via AMBER (Mon Jan 16 2023 - 20:45:57 PST)
    - Re: [AMBER] Center of mass, velocity, Momentum calculation Daniel Roe via AMBER (Tue Jan 17 2023 - 10:05:17 PST)
Re: [AMBER] ?==?utf-8?q? Increase maximum of atoms in COM distance restraint Javier Carmona Garcia via AMBER (Mon Jan 16 2023 - 03:05:18 PST)
[AMBER] MMGBSA calculations - mbondi parameter Maria Bzówka via AMBER (Mon Jan 16 2023 - 06:16:20 PST)
- Re: [AMBER] MMGBSA calculations - mbondi parameter Carlos Simmerling via AMBER (Mon Jan 16 2023 - 06:21:46 PST)
- Re: [AMBER] MMGBSA calculations - mbondi parameter David A Case via AMBER (Mon Jan 16 2023 - 10:32:10 PST)
  - Re: [AMBER] MMGBSA calculations - mbondi parameter Maria Bzówka via AMBER (Thu Jan 19 2023 - 01:04:57 PST)
[AMBER] AMBER Free Energy Update Darrin York via AMBER (Mon Jan 16 2023 - 09:24:44 PST)
[AMBER] Question concerning the GLYCAM force field Jiang, Yaoyukun via AMBER (Mon Jan 16 2023 - 19:48:35 PST)
Re: [AMBER] R: Reimaging issues Daniel Roe via AMBER (Tue Jan 17 2023 - 04:30:29 PST)
[AMBER] TI Ignacio J. General via AMBER (Tue Jan 17 2023 - 06:44:27 PST)
[AMBER] the charge error in amber laura zhang via AMBER (Tue Jan 17 2023 - 10:16:20 PST)
- Re: [AMBER] the charge error in amber Carlos Simmerling via AMBER (Tue Jan 17 2023 - 13:06:25 PST)
- Re: [AMBER] the charge error in amber David A Case via AMBER (Thu Jan 19 2023 - 10:13:46 PST)
[AMBER] Multiple copies of simulation to check for reproducibility and convergence Suchetana Gupta via AMBER (Tue Jan 17 2023 - 13:37:16 PST)
[AMBER] Fixing the rotation of the simulation box angad sharma via AMBER (Wed Jan 18 2023 - 02:16:00 PST)
[AMBER] MMPBSA Pairwise Internal Energy Issue Pablo Arantes via AMBER (Wed Jan 18 2023 - 09:48:02 PST)
- Re: [AMBER] MMPBSA Pairwise Internal Energy Issue Bill Miller III via AMBER (Thu Jan 19 2023 - 09:53:23 PST)
Re: [AMBER] Issues with nucleic acid simulations Prithviraj Nandigrami via AMBER (Fri Jan 20 2023 - 12:47:03 PST)
[AMBER] tleap parameter file Mac Kevin Braza via AMBER (Fri Jan 20 2023 - 13:52:00 PST)
- Re: [AMBER] tleap parameter file Suchetana Gupta via AMBER (Fri Jan 20 2023 - 13:56:42 PST)
[AMBER] problem setting up an amber simulation laura zhang via AMBER (Fri Jan 20 2023 - 14:46:43 PST)
- Re: [AMBER] problem setting up an amber simulation Carlos Simmerling via AMBER (Fri Jan 20 2023 - 14:54:47 PST)
- Re: [AMBER] problem setting up an amber simulation David A Case via AMBER (Sun Jan 22 2023 - 09:45:29 PST)
  - Re: [AMBER] problem setting up an amber simulation Daniel Roe via AMBER (Sun Jan 22 2023 - 09:58:55 PST)
[AMBER] Choosing GPU edition for building own system M. Reza Ganjalikhany via AMBER (Sat Jan 21 2023 - 03:30:45 PST)
[AMBER] Can not install Amber with CUDA supported Broto Santoso via AMBER (Sat Jan 21 2023 - 05:54:26 PST)
- Re: [AMBER] Can not install Amber with CUDA supported Ross Walker via AMBER (Sat Jan 21 2023 - 08:45:16 PST)
[AMBER] Problem met in running GBn2 model Jiaan Zhu via AMBER (Sun Jan 22 2023 - 03:32:37 PST)
- Re: [AMBER] Problem met in running GBn2 model Carlos Simmerling via AMBER (Sun Jan 22 2023 - 05:29:38 PST)
- Re: [AMBER] Problem met in running GBn2 model David A Case via AMBER (Sun Jan 22 2023 - 09:59:17 PST)
[AMBER] Unit Dulal Mondal via AMBER (Tue Jan 24 2023 - 06:14:39 PST)
- Re: [AMBER] Unit David A Case via AMBER (Tue Jan 24 2023 - 09:21:26 PST)
[AMBER] MCPB.py error on first step. DE-SANTANA-PONTES, FREDERICO J. via AMBER (Tue Jan 24 2023 - 07:03:21 PST)
[AMBER] AMBER simulation heating step Prithviraj Nandigrami via AMBER (Tue Jan 24 2023 - 11:47:51 PST)
[AMBER] Heating the soft core atoms in TI simulations He, Amy via AMBER (Tue Jan 24 2023 - 17:01:20 PST)
- Re: [AMBER] Heating the soft core atoms in TI simulations Steinbrecher, Thomas via AMBER (Tue Jan 24 2023 - 23:28:05 PST)
  - Re: [AMBER] Heating the soft core atoms in TI simulations Darrin York via AMBER (Wed Jan 25 2023 - 08:01:58 PST)
    - Re: [AMBER] Heating the soft core atoms in TI simulations He, Amy via AMBER (Wed Jan 25 2023 - 15:43:46 PST)
[AMBER] Segmentation fault when trying outputting MBAR data in vacuum Miroslav Suruzhon via AMBER (Wed Jan 25 2023 - 09:24:13 PST)
[AMBER] MPICH configure failed, returning 1 ABDELATIF MESSAOUDI via AMBER (Wed Jan 25 2023 - 12:50:59 PST)
- Re: [AMBER] MPICH configure failed, returning 1 David Case via AMBER (Wed Jan 25 2023 - 13:57:02 PST)
[AMBER] Installation Amber22 failed Freddy Bernal via AMBER (Fri Jan 27 2023 - 07:05:25 PST)
- Re: [AMBER] Installation Amber22 failed David A Case via AMBER (Mon Jan 30 2023 - 18:45:05 PST)
[AMBER] LEaP Issue Gonzalo R. Vazquez-Jimenez via AMBER (Fri Jan 27 2023 - 10:12:51 PST)
- Re: [AMBER] LEaP Issue Scott Brozell via AMBER (Fri Jan 27 2023 - 19:04:31 PST)
- Re: [AMBER] LEaP Issue Stephan Schott via AMBER (Fri Jan 27 2023 - 20:39:08 PST)
[AMBER] idecomp = 1 for TI simulations: Energies not printed / cannot be calculated He, Amy via AMBER (Fri Jan 27 2023 - 15:14:06 PST)
- Re: [AMBER] idecomp = 1 for TI simulations: Energies not printed / cannot be calculated He, Amy via AMBER (Fri Jan 27 2023 - 15:15:51 PST)
[AMBER] test message, per SRB David A Case via AMBER (Fri Jan 27 2023 - 18:30:27 PST)
Re: [AMBER] Installation Amber22 failed (fwd) Scott Brozell via AMBER (Fri Jan 27 2023 - 18:45:17 PST)
[AMBER] Install Amber22 ABDELATIF MESSAOUDI via AMBER (Sat Jan 28 2023 - 01:32:41 PST)
- Re: [AMBER] Install Amber22 David A Case via AMBER (Mon Jan 30 2023 - 18:57:57 PST)
[AMBER] How restart md simulation with amber22 ABDELATIF MESSAOUDI via AMBER (Mon Jan 30 2023 - 00:30:33 PST)
- Re: [AMBER] How restart md simulation with amber22 SATYAJIT KHATUA via AMBER (Mon Jan 30 2023 - 00:45:35 PST)
- Re: [AMBER] How restart md simulation with amber22 SATYAJIT KHATUA via AMBER (Mon Jan 30 2023 - 05:09:49 PST)
[AMBER] parmed: ff19SB to gromacs .top Patricio German Barletta via AMBER (Mon Jan 30 2023 - 07:24:18 PST)
[AMBER] Random failure of parmchk2? Brian Radak via AMBER (Mon Jan 30 2023 - 07:43:42 PST)
- Re: [AMBER] Random failure of parmchk2? Brian Radak via AMBER (Mon Jan 30 2023 - 08:23:17 PST)
  - Re: [AMBER] Random failure of parmchk2? Brian Radak via AMBER (Mon Jan 30 2023 - 08:35:04 PST)
[AMBER] Possible failures in test Freddy Bernal via AMBER (Tue Jan 31 2023 - 00:33:13 PST)
[AMBER] Error while running finddgref.py script Akhil Sudarsan via AMBER (Tue Jan 31 2023 - 08:23:38 PST)
- Re: [AMBER] Error while running finddgref.py script Vinicius Wilian Cruzeiro via AMBER (Tue Jan 31 2023 - 09:10:15 PST)
[AMBER] CPPTRAJ, PCA, Effect of Mutation Matthew Guberman-Pfeffer via AMBER (Tue Jan 31 2023 - 08:36:40 PST)
Re: [AMBER] Distance calculation using cpptraj Carlos Simmerling via AMBER (Tue Jan 31 2023 - 11:58:28 PST)

Amber Archive Jan 2023 by thread