Amber Archive Mar 2024: by subject

[AMBER] (UNKNOWN ATOM TYPE: c5)
- David A Case via AMBER (Sat Mar 16 2024 - 11:36:44 PDT)
- Trevor Kramer via AMBER (Fri Mar 15 2024 - 12:43:41 PDT)
[AMBER] [Sender Not Verified] Modelling missing residues
- Steinbrecher, Thomas via AMBER (Wed Mar 13 2024 - 01:57:31 PDT)
[AMBER] Adding extra solvent molecules to a membrane-protein system
- Todd Minehardt via AMBER (Fri Mar 08 2024 - 08:57:36 PST)
- Stephan Schott via AMBER (Fri Mar 08 2024 - 07:25:50 PST)
- Bhattacharjee, Sinjini via AMBER (Fri Mar 08 2024 - 06:05:35 PST)
[AMBER] AMBER error vlimit exceed for step
- Téletchéa Stéphane via AMBER (Thu Mar 21 2024 - 11:22:44 PDT)
- David A Case via AMBER (Wed Mar 13 2024 - 09:04:36 PDT)
- He, Amy via AMBER (Fri Mar 08 2024 - 18:26:42 PST)
- VERONICA MARTIN HERNANDEZ via AMBER (Fri Mar 08 2024 - 08:20:24 PST)
[AMBER] Amber FF simulations with lipids not in LIPID21
- Derek M Shore via AMBER (Thu Mar 14 2024 - 16:30:17 PDT)
- Stephan Schott via AMBER (Thu Mar 14 2024 - 15:38:27 PDT)
- Derek M Shore via AMBER (Thu Mar 14 2024 - 15:15:53 PDT)
[AMBER] amber18 compilation for cuda.MPI
- David A Case via AMBER (Wed Mar 13 2024 - 08:56:37 PDT)
- Dulal Mondal via AMBER (Mon Mar 04 2024 - 21:20:11 PST)
- Hector A. Baldoni via AMBER (Sun Mar 03 2024 - 06:00:01 PST)
- Dulal Mondal via AMBER (Sun Mar 03 2024 - 00:16:14 PST)
- Dulal Mondal via AMBER (Fri Mar 01 2024 - 22:59:15 PST)
[AMBER] amber20 installation issue
- David A Case via AMBER (Sun Mar 24 2024 - 08:29:48 PDT)
- David A Case via AMBER (Sun Mar 24 2024 - 07:20:23 PDT)
- Sayan Poddar via AMBER (Sat Mar 23 2024 - 23:00:49 PDT)
[AMBER] Antechamber Error
- David A Case via AMBER (Sun Mar 17 2024 - 19:11:10 PDT)
- SUBHASMITA MAHAPATRA MAHAPATRA via AMBER (Sun Mar 17 2024 - 03:32:14 PDT)
[AMBER] Any news on AMBER24 release?
- Cenk Andac via AMBER (Sat Mar 09 2024 - 14:38:59 PST)
[AMBER] Boost Error in MoFT - metatwist
- Stephan Schott via AMBER (Fri Mar 15 2024 - 09:07:55 PDT)
- Lorenzo Cupellini via AMBER (Fri Mar 15 2024 - 09:05:54 PDT)
- Stephan Schott via AMBER (Thu Mar 14 2024 - 08:51:44 PDT)
- Lorenzo Cupellini via AMBER (Thu Mar 14 2024 - 07:19:30 PDT)
[AMBER] Compressing/Expanding Monolayer Systems
- Amanda Ferrante via AMBER (Tue Mar 19 2024 - 16:02:53 PDT)
[AMBER] Constant pH replica exchange
- Carlos Simmerling via AMBER (Fri Mar 01 2024 - 08:26:46 PST)
- Carlos Simmerling via AMBER (Fri Mar 01 2024 - 04:43:14 PST)
- Dulal Mondal via AMBER (Thu Feb 29 2024 - 23:08:16 PST)
[AMBER] cpptraj error with Test_SPAM
- Daniel Roe via AMBER (Fri Mar 15 2024 - 05:36:00 PDT)
- Hirosuke Hotta \(Fujitsu\) via AMBER (Thu Mar 14 2024 - 23:13:44 PDT)
[AMBER] cpptraj nastruct defined base-pairing
- David A Case via AMBER (Sat Mar 16 2024 - 11:33:49 PDT)
- Slavnikova Pavlina via AMBER (Fri Mar 15 2024 - 08:07:11 PDT)
[AMBER] cpptraj.mpi for multi-frame pdb trajectory
- Enrico Martinez via AMBER (Fri Mar 08 2024 - 00:59:02 PST)
[AMBER] CUDA version installation error: undefined reference to 'gpu_aoint_'
- Goetz, Andreas via AMBER (Sat Mar 02 2024 - 15:06:34 PST)
- Abdelaty, Mohamed via AMBER (Sat Mar 02 2024 - 11:28:59 PST)
[AMBER] Dpeaks Clustering Algorithm
- Daniel Roe via AMBER (Wed Mar 27 2024 - 08:47:00 PDT)
- Joshi, Keya via AMBER (Tue Mar 26 2024 - 11:00:01 PDT)
[AMBER] Error - Amber 22 Installation
- David A Case via AMBER (Sun Mar 24 2024 - 11:34:14 PDT)
[AMBER] Error building Amber22 with cuda
- Dhariwal, Rohit via AMBER (Wed Mar 13 2024 - 08:26:08 PDT)
- Goetz, Andreas via AMBER (Sat Mar 02 2024 - 15:00:40 PST)
- Dhariwal, Rohit via AMBER (Fri Mar 01 2024 - 08:35:06 PST)
[AMBER] Error with Amber22 test.serial
- Todd Minehardt via AMBER (Fri Mar 29 2024 - 14:59:11 PDT)
- David A Case via AMBER (Fri Mar 29 2024 - 14:06:53 PDT)
- David A Case via AMBER (Fri Mar 29 2024 - 09:02:57 PDT)
- Sayan Poddar via AMBER (Tue Mar 26 2024 - 10:55:45 PDT)
[AMBER] Error_install_run_cmake_Amber22
- David A Case via AMBER (Mon Mar 25 2024 - 11:39:41 PDT)
- ABDELATIF MESSAOUDI via AMBER (Mon Mar 25 2024 - 11:07:07 PDT)
- David A Case via AMBER (Mon Mar 25 2024 - 07:54:03 PDT)
- David A Case via AMBER (Sun Mar 24 2024 - 11:38:08 PDT)
- Daniel Roe via AMBER (Sun Mar 24 2024 - 10:59:30 PDT)
- ABDELATIF MESSAOUDI via AMBER (Sun Mar 24 2024 - 10:35:59 PDT)
[AMBER] ESANDER output question
- Carlos Simmerling via AMBER (Wed Mar 06 2024 - 13:57:40 PST)
- Matthew Guberman-Pfeffer via AMBER (Wed Mar 06 2024 - 13:48:54 PST)
[AMBER] GAMESS QM optimization protocols
- Debarati DasGupta via AMBER (Thu Mar 21 2024 - 12:43:42 PDT)
- James Kress via AMBER (Thu Mar 21 2024 - 12:36:51 PDT)
[AMBER] Gaussian imput error in QM/MM with external user template
- Claire Claire via AMBER (Thu Mar 07 2024 - 05:24:53 PST)
[AMBER] generate prmtop and inpcrd file
- David A Case via AMBER (Sun Mar 24 2024 - 07:22:38 PDT)
- Dulal Mondal via AMBER (Sun Mar 24 2024 - 06:39:24 PDT)
[AMBER] Generate prmtop file using parmed.
- He, Amy via AMBER (Thu Mar 07 2024 - 12:55:05 PST)
- Dulal Mondal via AMBER (Thu Mar 07 2024 - 07:21:16 PST)
[AMBER] Hamiltonian REMD simulation
- He, Amy via AMBER (Wed Mar 13 2024 - 08:55:23 PDT)
- Dulal Mondal via AMBER (Wed Mar 13 2024 - 01:58:07 PDT)
[AMBER] How to add KCl cellular concentration.
- Maria Nagan via AMBER (Thu Mar 07 2024 - 07:58:36 PST)
- Sayan Poddar via AMBER (Thu Mar 07 2024 - 07:50:31 PST)
[AMBER] How to reduce the standard deviation of MMPBSA
- David A Case via AMBER (Wed Mar 06 2024 - 19:46:03 PST)
- Todd Minehardt via AMBER (Wed Mar 06 2024 - 17:34:20 PST)
- Adrian Roitberg via AMBER (Wed Mar 06 2024 - 17:03:42 PST)
- Yang Wei via AMBER (Wed Mar 06 2024 - 16:13:45 PST)
[AMBER] imaging membrane system
- Daniel Roe via AMBER (Sun Mar 10 2024 - 09:46:06 PDT)
[AMBER] Information about number of water molecules found in .out files
- David A Case via AMBER (Tue Mar 26 2024 - 14:49:03 PDT)
- Maria Bzówka via AMBER (Tue Mar 26 2024 - 06:40:09 PDT)
[AMBER] Install Amber22 CUDA_12.0
- ABDELATIF MESSAOUDI via AMBER (Wed Mar 27 2024 - 02:53:49 PDT)
[AMBER] ir6 restraint with pmemd.cuda problem
- Niklas Halbwedl via AMBER (Fri Mar 08 2024 - 07:42:24 PST)
- Niklas Halbwedl via AMBER (Fri Mar 08 2024 - 03:38:20 PST)
- Niklas Halbwedl via AMBER (Mon Mar 04 2024 - 00:54:45 PST)
[AMBER] Issue with ANTECHAMBER library file generation
- David A Case via AMBER (Wed Mar 06 2024 - 19:34:56 PST)
- Sayan Poddar via AMBER (Tue Mar 05 2024 - 06:37:59 PST)
[AMBER] Issue with glycam nomenclature
- Daniel Roe via AMBER (Tue Mar 26 2024 - 09:43:59 PDT)
- Daniel Roe via AMBER (Fri Mar 22 2024 - 05:17:06 PDT)
- SUBHASMITA MAHAPATRA MAHAPATRA via AMBER (Fri Mar 22 2024 - 03:46:04 PDT)
[AMBER] LJ Energy Mismatch
- Carlos Simmerling via AMBER (Mon Mar 25 2024 - 15:06:02 PDT)
- Carlos Simmerling via AMBER (Mon Mar 25 2024 - 13:37:38 PDT)
- William Livernois via AMBER (Mon Mar 25 2024 - 13:24:20 PDT)
[AMBER] make install error related to pmemd xray & MKL
- David A Case via AMBER (Fri Mar 01 2024 - 17:36:08 PST)
[AMBER] make-install amber22_cuda
- David A Case via AMBER (Fri Mar 29 2024 - 08:58:11 PDT)
- David A Case via AMBER (Thu Mar 28 2024 - 13:29:21 PDT)
- ABDELATIF MESSAOUDI via AMBER (Thu Mar 28 2024 - 03:18:57 PDT)
[AMBER] Maximum coordination exceeded on metal ions
- 杨镇岳 via AMBER (Sun Mar 17 2024 - 04:03:37 PDT)
[AMBER] Metadynamics question
- Carlos Simmerling via AMBER (Mon Mar 04 2024 - 09:36:17 PST)
- Carlos Simmerling via AMBER (Fri Mar 01 2024 - 04:19:02 PST)
- Matthew Guberman-Pfeffer via AMBER (Fri Mar 01 2024 - 04:11:14 PST)
[AMBER] Minimization fails with a larger solvent box
- Carlos Simmerling via AMBER (Sun Mar 17 2024 - 13:53:47 PDT)
- Sasha Buzko via AMBER (Sat Mar 16 2024 - 19:54:34 PDT)
[AMBER] Minimization with pmemd.cuda
- Enrico Martinez via AMBER (Fri Mar 29 2024 - 09:05:55 PDT)
- Enrico Martinez via AMBER (Fri Mar 29 2024 - 07:33:48 PDT)
[AMBER] MM-GBSA Entropy Calculation Error
- Daniel Roe via AMBER (Sun Mar 10 2024 - 09:21:43 PDT)
- Robert Palmere via AMBER (Thu Mar 07 2024 - 06:59:03 PST)
[AMBER] MM-PBSA for membrane protein system
- Ray Luo via AMBER (Wed Mar 20 2024 - 08:07:10 PDT)
- Bhattacharjee, Sinjini via AMBER (Wed Mar 20 2024 - 05:45:31 PDT)
[AMBER] MMGBSA Analysis
- Todd Minehardt via AMBER (Mon Mar 04 2024 - 08:56:31 PST)
- Joshi, Keya via AMBER (Mon Mar 04 2024 - 07:35:25 PST)
[AMBER] MMGBSA Calculation Warning
- Bill Miller III via AMBER (Mon Mar 04 2024 - 09:48:55 PST)
- Robert Palmere via AMBER (Mon Mar 04 2024 - 06:07:39 PST)
[AMBER] Modelling missing residues
- Charo del Genio via AMBER (Wed Mar 13 2024 - 01:58:00 PDT)
- VERONICA MARTIN HERNANDEZ via AMBER (Wed Mar 13 2024 - 01:31:19 PDT)
[AMBER] mpirun error for thermodynamic integration
- David A Case via AMBER (Sat Mar 16 2024 - 11:31:22 PDT)
- Dulal Mondal via AMBER (Fri Mar 15 2024 - 06:31:01 PDT)
[AMBER] Multiple trajectory MMPBSA
- David A Case via AMBER (Sat Mar 16 2024 - 11:38:36 PDT)
- Yang Wei via AMBER (Fri Mar 15 2024 - 13:37:06 PDT)
[AMBER] native contacts calculation using cpptraj
- Prithviraj Nandigrami via AMBER (Wed Mar 27 2024 - 16:15:02 PDT)
[AMBER] New cpptraj processing issue with oligomeric system
- Enrico Martinez via AMBER (Mon Mar 11 2024 - 06:55:31 PDT)
[AMBER] No restraint defined when using torsional restraints
- Carlos Simmerling via AMBER (Fri Mar 08 2024 - 14:33:53 PST)
[AMBER] Non-Standard Parametrization Issue
- He, Amy via AMBER (Thu Mar 21 2024 - 23:40:50 PDT)
- Kavinda Kashi Juliyan Gunasinghe via AMBER (Thu Mar 21 2024 - 23:31:56 PDT)
- He, Amy via AMBER (Thu Mar 21 2024 - 23:05:52 PDT)
- Kavinda Kashi Juliyan Gunasinghe via AMBER (Thu Mar 21 2024 - 22:38:42 PDT)
[AMBER] NPT run prior to REMD
- Liyanage, Risi \(MU-Student\) via AMBER (Mon Mar 04 2024 - 13:36:17 PST)
[AMBER] Parametrization of a system with missed loop fragments
- Enrico Martinez via AMBER (Fri Mar 29 2024 - 04:13:36 PDT)
- Enrico Martinez via AMBER (Tue Mar 26 2024 - 00:50:54 PDT)
- Enrico Martinez via AMBER (Fri Mar 22 2024 - 08:31:09 PDT)
[AMBER] Partial charge calculation from gaussian ESP calculation
- Carlos Simmerling via AMBER (Fri Mar 08 2024 - 13:33:47 PST)
- Intravaia, Lauren E via AMBER (Fri Mar 08 2024 - 13:14:04 PST)
[AMBER] Peptide linked to a protein: force field limitations?
- Carlos Simmerling via AMBER (Wed Mar 13 2024 - 13:51:53 PDT)
- Carlos Simmerling via AMBER (Wed Mar 13 2024 - 09:46:23 PDT)
- Sasha Buzko via AMBER (Wed Mar 13 2024 - 07:56:27 PDT)
[AMBER] Please remove my email from mailing list. Thank you
- David A Case via AMBER (Fri Mar 01 2024 - 17:31:56 PST)
[AMBER] Possible bug in PMEMD (appearence of synchronization artifacts between parallel tasks)
- Adrian Roitberg via AMBER (Fri Mar 29 2024 - 08:09:37 PDT)
- Charo del Genio via AMBER (Wed Mar 20 2024 - 04:28:21 PDT)
[AMBER] Protein Binding Question
- Carlos Simmerling via AMBER (Mon Mar 25 2024 - 06:16:23 PDT)
- Matthew Guberman-Pfeffer via AMBER (Fri Mar 22 2024 - 06:53:54 PDT)
- Carlos Simmerling via AMBER (Fri Mar 22 2024 - 05:53:33 PDT)
- Matthew Guberman-Pfeffer via AMBER (Fri Mar 22 2024 - 05:40:07 PDT)
[AMBER] Query regarding amber20 ambertools23 installation
- David Case via AMBER (Sat Mar 23 2024 - 20:23:06 PDT)
- Sayan Poddar via AMBER (Sat Mar 23 2024 - 09:56:09 PDT)
[AMBER] Quick QM/MM fails with GPUs but not with CPUs
- Montalvillo, Fernando via AMBER (Thu Mar 28 2024 - 08:38:34 PDT)
- Montalvillo, Fernando via AMBER (Fri Mar 08 2024 - 08:56:22 PST)
- Montalvillo, Fernando via AMBER (Thu Mar 07 2024 - 14:10:20 PST)
- Hector A. Baldoni via AMBER (Thu Mar 07 2024 - 13:52:46 PST)
- Montalvillo, Fernando via AMBER (Thu Mar 07 2024 - 10:31:42 PST)
- Goetz, Andreas via AMBER (Thu Mar 07 2024 - 02:31:26 PST)
- Montalvillo, Fernando via AMBER (Wed Mar 06 2024 - 15:40:02 PST)
- Montalvillo, Fernando via AMBER (Wed Mar 06 2024 - 10:45:24 PST)
- Goetz, Andreas via AMBER (Tue Mar 05 2024 - 13:44:15 PST)
- Montalvillo, Fernando via AMBER (Tue Mar 05 2024 - 11:58:05 PST)
[AMBER] Regarding MMPBSA calculation:
- Ray Luo via AMBER (Thu Mar 28 2024 - 22:36:35 PDT)
- Kankana Bhattacharjee via AMBER (Thu Mar 28 2024 - 21:50:25 PDT)
[AMBER] Renumber residues (Error: No change type specified) - AMBER MD 18
- David A Case via AMBER (Fri Mar 01 2024 - 17:39:17 PST)
[AMBER] RMSD Calculation Advice
- Kaleem Arshad via AMBER (Thu Mar 14 2024 - 11:02:04 PDT)
[AMBER] RMSD of protein with domain insertion
- Carlos Simmerling via AMBER (Fri Mar 29 2024 - 10:15:47 PDT)
- Carlos Simmerling via AMBER (Fri Mar 29 2024 - 09:47:38 PDT)
- Colin Pierce via AMBER (Fri Mar 29 2024 - 09:38:16 PDT)
[AMBER] Running TI calculations
- VERONICA MARTIN HERNANDEZ via AMBER (Mon Mar 11 2024 - 00:57:40 PDT)
[AMBER] Sander.mpi haults at 999 steps
- Montalvillo, Fernando via AMBER (Mon Mar 04 2024 - 10:37:19 PST)
- Carlos Simmerling via AMBER (Mon Mar 04 2024 - 09:29:19 PST)
- Montalvillo, Fernando via AMBER (Mon Mar 04 2024 - 09:00:06 PST)
- Carlos Simmerling via AMBER (Sat Mar 02 2024 - 03:56:49 PST)
- David A Case via AMBER (Fri Mar 01 2024 - 17:29:59 PST)
[AMBER] Simulation not running on more than one MPI process with 12-6-4 parameters
- Markowska (Mon Mar 11 2024 - 00:10:17 PDT)
[AMBER] Suitable water model for solvent-exposed structures?
- Carlos Simmerling via AMBER (Mon Mar 04 2024 - 17:39:08 PST)
- Sasha Buzko via AMBER (Mon Mar 04 2024 - 17:30:39 PST)
[AMBER] Unable to compile with CUDA
- David A Case via AMBER (Fri Mar 01 2024 - 17:42:45 PST)
- Weatherby,Gerard via AMBER (Fri Mar 01 2024 - 10:53:40 PST)
[AMBER] Unable to reproduce the results from Amber RISM tutorial with Amber22
- Markowska (Mon Mar 25 2024 - 01:25:43 PDT)
- Markowska (Tue Mar 19 2024 - 10:13:02 PDT)
[AMBER] uncertainty in atomic positional fluctuations
- Duggan, Brendan via AMBER (Fri Mar 01 2024 - 11:36:16 PST)
[AMBER] using 12_6_4 ion parameters with OPC water model
- Carlos Simmerling via AMBER (Mon Mar 04 2024 - 09:54:33 PST)
[AMBER] Using PLUMED to Calculate Collective Variables and GaMD Reweighting in Amber
- Munazzah Fatima Ansari via AMBER (Fri Mar 01 2024 - 05:35:14 PST)
[AMBER] 回复: Maximum coordination exceeded on metal ions
- 郭家藩 via AMBER (Sun Mar 17 2024 - 06:15:55 PDT)
[AMBER] 回复: NaN error during heating in building 12-6-4 LJ multisite Mg2+ model of DNA gyrase.
- 郭家藩 via AMBER (Sat Mar 16 2024 - 21:57:41 PDT)
AMBER error vlimit exceed for step
- He, Amy via AMBER (Thu Mar 21 2024 - 15:59:30 PDT)
- He, Amy via AMBER (Wed Mar 20 2024 - 12:21:02 PDT)
- David A Case via AMBER (Wed Mar 20 2024 - 07:29:53 PDT)
- VERONICA MARTIN HERNANDEZ via AMBER (Wed Mar 20 2024 - 04:24:06 PDT)
- VERONICA MARTIN HERNANDEZ via AMBER (Mon Mar 18 2024 - 07:37:16 PDT)
Cpptraj Question
- Daniel Roe via AMBER (Thu Mar 14 2024 - 09:00:41 PDT)
- Mariam Ibrahim via AMBER (Thu Mar 14 2024 - 08:32:06 PDT)
Why uinsg a cutoff or 8.0 for proteins and 10.0 for proteins embeded in a membrane?
- Téletchéa Stéphane via AMBER (Mon Mar 11 2024 - 11:24:59 PDT)

Amber Archive Mar 2024 by subject