Amber Archive Mar 2022: by subject

[AMBER] ** NFE-Error ** : Selection weight overflows, try smaller selection constant
- Feng Pan (Mon Mar 28 2022 - 11:34:54 PDT)
- Sruthi Sudhakar (Mon Mar 28 2022 - 11:08:19 PDT)
- Feng Pan (Mon Mar 28 2022 - 10:52:14 PDT)
- Sruthi Sudhakar (Mon Mar 28 2022 - 05:29:16 PDT)
- Sruthi Sudhakar (Wed Mar 23 2022 - 21:57:29 PDT)
[AMBER] 1D-RISM with 4-Point water models
- tluchko (Thu Mar 24 2022 - 15:03:31 PDT)
- Grunewald, Lukas (Thu Mar 24 2022 - 09:06:28 PDT)
- tluchko (Tue Mar 22 2022 - 10:30:03 PDT)
- Grunewald, Lukas (Tue Mar 22 2022 - 03:32:44 PDT)
[AMBER] [AMBER ] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered.
- Daniel Roe (Thu Mar 24 2022 - 09:48:25 PDT)
- Thomas Cheatham (Wed Mar 23 2022 - 22:15:00 PDT)
- Anita Meena (Wed Mar 23 2022 - 22:05:29 PDT)
[AMBER] [Amber]Not able to generate eq_density.cpptraj file while doing QM/MM calculations
- Daniel Roe (Thu Mar 10 2022 - 08:52:19 PST)
- Anita Meena (Wed Mar 09 2022 - 23:19:10 PST)
- Daniel Roe (Wed Mar 09 2022 - 09:40:03 PST)
- Anita Meena (Tue Mar 08 2022 - 22:03:49 PST)
- David A Case (Tue Mar 08 2022 - 05:06:13 PST)
- Anita Meena (Mon Mar 07 2022 - 21:18:33 PST)
[AMBER] A way to stop simulations when certain criteria are met?
- Carlos Simmerling (Thu Mar 17 2022 - 10:28:24 PDT)
- Dr. Anselm Horn (Thu Mar 17 2022 - 10:02:40 PDT)
- Hai Nguyen (Thu Mar 17 2022 - 09:10:16 PDT)
- Chris Lee (Wed Mar 16 2022 - 12:31:47 PDT)
[AMBER] AMBER Digest, Vol 3660, Issue 1
- liu kai (Thu Mar 17 2022 - 19:15:06 PDT)
[AMBER] Amber20 installation error
- David A Case (Fri Mar 25 2022 - 19:08:37 PDT)
- Chen, Guoquan (Fri Mar 25 2022 - 15:23:03 PDT)
[AMBER] Asking MMPBSA.PY
- David A Case (Sat Mar 05 2022 - 05:44:12 PST)
- Purnawan pontana putra (Fri Mar 04 2022 - 02:52:15 PST)
[AMBER] Atom coordinate disagreement error in running the TI calculation
- Bhakti Hirlekar (Thu Mar 24 2022 - 22:33:59 PDT)
[AMBER] calculate entropy using MMPBSA.py
- Ming Tang (Fri Mar 11 2022 - 16:05:57 PST)
- Thomas Cheatham (Thu Mar 10 2022 - 22:33:26 PST)
- Ming Tang (Thu Mar 10 2022 - 22:11:31 PST)
[AMBER] Calculate Lipid Surface Pressure/Tension from Lipid-Water Interface
- Mirza Ahmed Hammad (Wed Mar 09 2022 - 01:15:40 PST)
[AMBER] Cannot install AmberTools 21 due to errors in getline.c file
- Сергей Горелов (Mon Mar 21 2022 - 14:39:31 PDT)
- Scott Brozell (Mon Mar 21 2022 - 12:22:45 PDT)
- Сергей Горелов (Sun Mar 20 2022 - 11:45:09 PDT)
[AMBER] Clarification in 3DRISM
- Alexis Azucena (Mon Feb 28 2022 - 17:54:20 PST)
[AMBER] Constant pH MD Simulations for General Organic Compounds
- Vinicius Wilian Cruzeiro (Mon Mar 07 2022 - 20:43:33 PST)
- Nathan Black (Mon Mar 07 2022 - 20:36:53 PST)
[AMBER] Convergence issue in rism1d
- tluchko (Mon Mar 14 2022 - 10:50:01 PDT)
- David A Case (Fri Mar 11 2022 - 04:56:37 PST)
- angad sharma (Thu Mar 10 2022 - 23:07:17 PST)
[AMBER] Cpptraj - Density Action Command Units
- Gerardo Zerbetto De Palma (Thu Mar 03 2022 - 14:05:32 PST)
[AMBER] CPPTRAJ, Conflicting H-Bonding Results
- Matthew Guberman-Pfeffer (Fri Mar 18 2022 - 06:44:08 PDT)
- Daniel Roe (Fri Mar 18 2022 - 06:35:54 PDT)
- Matthew Guberman-Pfeffer (Thu Mar 17 2022 - 09:23:00 PDT)
[AMBER] CPPTRAJ, Counting Per Residue Pair H-Bonding
- Matthew Guberman-Pfeffer (Thu Mar 31 2022 - 10:23:37 PDT)
- Matthew Guberman-Pfeffer (Wed Mar 30 2022 - 17:51:17 PDT)
- Daniel Roe (Wed Mar 30 2022 - 17:44:26 PDT)
- Matthew Guberman-Pfeffer (Wed Mar 30 2022 - 17:22:13 PDT)
- Daniel Roe (Wed Mar 30 2022 - 17:14:34 PDT)
- Matthew Guberman-Pfeffer (Wed Mar 30 2022 - 16:34:19 PDT)
- Daniel Roe (Wed Mar 30 2022 - 16:31:07 PDT)
- Matthew Guberman-Pfeffer (Wed Mar 30 2022 - 16:12:06 PDT)
- Daniel Roe (Wed Mar 30 2022 - 16:05:17 PDT)
- Matthew Guberman-Pfeffer (Wed Mar 30 2022 - 13:58:44 PDT)
- Matthew Guberman-Pfeffer (Wed Mar 30 2022 - 14:00:42 PDT)
- Daniel Roe (Wed Mar 30 2022 - 13:54:47 PDT)
- Daniel Roe (Wed Mar 30 2022 - 13:54:23 PDT)
- Matthew Guberman-Pfeffer (Wed Mar 30 2022 - 13:39:25 PDT)
- Daniel Roe (Wed Mar 30 2022 - 12:27:12 PDT)
- Kenneth Huang (Wed Mar 16 2022 - 13:48:10 PDT)
- Matthew Guberman-Pfeffer (Wed Mar 16 2022 - 09:57:43 PDT)
- Kenneth Huang (Wed Mar 16 2022 - 09:30:26 PDT)
- Matthew Guberman-Pfeffer (Wed Mar 16 2022 - 08:00:31 PDT)
- Kenneth Huang (Wed Mar 16 2022 - 07:37:57 PDT)
- Matthew Guberman-Pfeffer (Wed Mar 16 2022 - 06:45:28 PDT)
[AMBER] CPPTRAJ, Dipole autocorrelation?
- David A Case (Tue Mar 01 2022 - 16:43:01 PST)
[AMBER] CUDART lib not found during install
- Daniel Roe (Fri Mar 11 2022 - 12:06:27 PST)
- Charlotta Lebedenko (Thu Mar 10 2022 - 15:22:15 PST)
- Daniel Roe (Mon Mar 07 2022 - 15:38:34 PST)
- Daniel Roe (Mon Mar 07 2022 - 03:49:28 PST)
- Alexis Azucena (Sun Mar 06 2022 - 15:26:03 PST)
- Charlotta Lebedenko (Sun Mar 06 2022 - 10:43:59 PST)
- Charlotta Lebedenko (Thu Mar 03 2022 - 12:30:50 PST)
- Daniel Roe (Thu Mar 03 2022 - 06:31:31 PST)
- Charlotta Lebedenko (Wed Mar 02 2022 - 13:27:27 PST)
[AMBER] D-amino acids
- Daniel Konstantinovsky (Wed Mar 23 2022 - 09:45:28 PDT)
- Carlos Simmerling (Wed Mar 23 2022 - 09:27:15 PDT)
- Daniel Konstantinovsky (Wed Mar 23 2022 - 09:05:53 PDT)
[AMBER] Distance Restraints and/or Periodic Boundaries for Implicit Solvent
- Nathan Black (Tue Mar 29 2022 - 09:58:38 PDT)
[AMBER] Entropy calculations in GIST
- Franz Waibl (Thu Mar 24 2022 - 10:07:05 PDT)
- Daniella Hares (Tue Mar 08 2022 - 05:44:10 PST)
[AMBER] Entropy calculations upon covalent modification
- David A Case (Wed Mar 30 2022 - 05:54:35 PDT)
- Aravind R (Wed Mar 30 2022 - 04:09:12 PDT)
[AMBER] Error - corrupted size vs. prev_size
- Maria Nagan (Tue Mar 22 2022 - 08:48:27 PDT)
- saranya.cbmm.lodz.pl (Tue Mar 22 2022 - 08:02:58 PDT)
[AMBER] Error in parameter file preparation
- Carlos Simmerling (Tue Mar 29 2022 - 03:56:43 PDT)
- Debasish Mandal (Tue Mar 29 2022 - 00:04:07 PDT)
[AMBER] Error in using multiple distance restraints in a single RST file
- David A Case (Wed Mar 02 2022 - 05:07:08 PST)
- Prathit Chatterjee (Tue Mar 01 2022 - 18:37:04 PST)
[AMBER] error preparing ligand parameters
- Vaibhav Dixit (Fri Mar 04 2022 - 07:04:37 PST)
[AMBER] Error when using mmpbsa_py_nabnmode in parallel
- Ming Tang (Sun Mar 13 2022 - 03:36:01 PDT)
[AMBER] Error while running minimization run while doing thermodynamic integration.
- Divya Rai (Fri Mar 25 2022 - 00:48:31 PDT)
[AMBER] Error: an illegal memory access was encountered launching kernel kClearForces
- Állan Ferrari (Tue Mar 01 2022 - 05:08:08 PST)
[AMBER] EZAFF force field
- Elisa Frezza (Mon Mar 07 2022 - 23:51:06 PST)
[AMBER] Failed to generate rst file in partially deleted structure
- Yen Nguyen (Thu Mar 10 2022 - 10:46:08 PST)
- Daniel Roe (Mon Mar 07 2022 - 15:35:52 PST)
- Yen Nguyen (Mon Mar 07 2022 - 14:44:57 PST)
[AMBER] glibc causing amber install error
- David A Case (Tue Mar 08 2022 - 05:01:27 PST)
- Bruno Cramer (Mon Mar 07 2022 - 12:56:34 PST)
[AMBER] How to read netcdf files on VMD Windows version?
- Suchetana Gupta (Mon Mar 14 2022 - 12:55:24 PDT)
- Carlos Simmerling (Mon Mar 14 2022 - 11:44:38 PDT)
- Suchetana Gupta (Mon Mar 14 2022 - 11:23:12 PDT)
- Carlos Simmerling (Mon Mar 14 2022 - 04:43:13 PDT)
- Elvis Martis (Sun Mar 13 2022 - 22:30:28 PDT)
- Suchetana Gupta (Sun Mar 13 2022 - 22:09:15 PDT)
[AMBER] How to use artificial covariance matrix in PCA analysis of cpptraj?
- Daniel Roe (Fri Mar 04 2022 - 06:49:24 PST)
- wangjianing_mail (Fri Mar 04 2022 - 06:10:46 PST)
[AMBER] How to use GPU and GLYCAM force fields
- David A Case (Wed Mar 30 2022 - 05:39:14 PDT)
- Dr. Anselm Horn (Wed Mar 30 2022 - 00:37:47 PDT)
- s.ohno.tohoku-mpu.ac.jp (Tue Mar 29 2022 - 23:24:03 PDT)
[AMBER] How to visualize the results generated from the analysis of MD trajectory using Cpptraj in AMBER16 ?
- Daniel Roe (Thu Mar 24 2022 - 08:14:31 PDT)
- priya murugan (Thu Mar 24 2022 - 05:01:36 PDT)
[AMBER] Hubbard derivative not found and element Na not supported for a QM/MM system
- David A Case (Thu Mar 17 2022 - 05:00:28 PDT)
- Pau Mayorga Delgado (Thu Mar 17 2022 - 02:36:07 PDT)
[AMBER] I cannot find NAB in AmberTools 21
- David A Case (Tue Mar 15 2022 - 05:40:13 PDT)
- russ.brown.yahoo.com (Mon Mar 14 2022 - 22:29:36 PDT)
[AMBER] Installation errors of AmberTools 21 on Ubuntu 20.04 WSL2
- M. Reza Ganjalikhany (Sun Mar 20 2022 - 03:39:09 PDT)
[AMBER] Is it possible to use less replicas by freezing some atoms of protein in which I'm not interested?
- 云之彼端 (Fri Mar 25 2022 - 17:23:59 PDT)
[AMBER] Is there a way to restart MMPBSA.py calculation?
- Ming Tang (Tue Mar 29 2022 - 16:58:50 PDT)
[AMBER] mmpbsa divalent ion bug
- xiangyu (Fri Mar 25 2022 - 00:26:58 PDT)
[AMBER] mmpbsa.py divalent ion issue
- xiangyu (Tue Mar 29 2022 - 21:57:13 PDT)
[AMBER] MMPBSA.py.MPI and pytraj bugs
- David Poole (Tue Mar 22 2022 - 08:12:28 PDT)
[AMBER] Modeling cis-amide bonds in diketopiperazines
- Christian Schafmeister (Mon Mar 14 2022 - 08:03:20 PDT)
[AMBER] NFE-Error
- Tanmoy Paul (Mon Mar 14 2022 - 11:00:22 PDT)
[AMBER] Non-Integer Charge for Systems Comprised of Large Number of Residues
- David A Case (Sun Mar 13 2022 - 13:06:10 PDT)
- Nathan Black (Sun Mar 13 2022 - 11:32:05 PDT)
[AMBER] Penalty Scores for Amino Acid Dihedral Parameters
- David A Case (Wed Mar 09 2022 - 06:08:05 PST)
- Nathan Black (Tue Mar 08 2022 - 21:35:32 PST)
[AMBER] PMEMD does not support single H residues!
- Thomas Cheatham (Thu Mar 24 2022 - 20:23:10 PDT)
- Carlos Simmerling (Thu Mar 24 2022 - 20:08:36 PDT)
- Huimin Tian (Thu Mar 24 2022 - 19:44:27 PDT)
[AMBER] Problem with production run of cyclic peptide
- Carlos Simmerling (Tue Mar 22 2022 - 06:54:47 PDT)
- Suchetana Gupta (Mon Mar 21 2022 - 16:41:10 PDT)
[AMBER] problem with using amber
- David A Case (Thu Mar 31 2022 - 05:06:13 PDT)
- Feng Su (Wed Mar 30 2022 - 22:04:59 PDT)
[AMBER] problems installing Amber20 + AmberTools21 parallel version with open-mpi
- David A Case (Wed Mar 16 2022 - 05:18:31 PDT)
- Antonija Tomić (Tue Mar 15 2022 - 11:45:22 PDT)
- David A Case (Tue Mar 15 2022 - 05:42:36 PDT)
- Antonija Tomić (Mon Mar 14 2022 - 23:56:38 PDT)
- David A Case (Mon Mar 14 2022 - 10:26:49 PDT)
- Antonija Tomić (Mon Mar 14 2022 - 02:44:18 PDT)
- David A Case (Fri Mar 11 2022 - 08:28:00 PST)
- Antonija Tomić (Fri Mar 11 2022 - 05:44:54 PST)
- David A Case (Fri Mar 11 2022 - 05:02:14 PST)
- Antonija Tomić (Fri Mar 11 2022 - 04:28:07 PST)
[AMBER] Problems with DFTB3 and Na in Amber
- Pau Mayorga Delgado (Mon Mar 21 2022 - 05:46:51 PDT)
[AMBER] PySander availability in PyTraj
- David Poole (Sat Mar 19 2022 - 15:33:40 PDT)
- Hai Nguyen (Fri Mar 18 2022 - 06:45:44 PDT)
- David A Case (Fri Mar 18 2022 - 06:02:51 PDT)
- David Poole (Fri Mar 18 2022 - 05:08:08 PDT)
[AMBER] Query regarding AMBER meta dynamics
- Sruthi Sudhakar (Thu Mar 17 2022 - 02:00:19 PDT)
[AMBER] Query related to TIMD
- Carlos Simmerling (Tue Mar 22 2022 - 06:53:42 PDT)
- SATYAJIT KHATUA (Mon Mar 21 2022 - 23:09:09 PDT)
[AMBER] question about ATP-Mg2+ binding system
- Thomas Cheatham (Wed Mar 16 2022 - 20:25:11 PDT)
- liu kai (Wed Mar 16 2022 - 19:03:20 PDT)
- David A Case (Wed Mar 16 2022 - 10:35:10 PDT)
- Carlos Simmerling (Wed Mar 16 2022 - 08:52:11 PDT)
- liu kai (Wed Mar 16 2022 - 08:46:05 PDT)
[AMBER] Regarding treating ligand with QM level of theory
- Soumyajit Karmakar (Wed Mar 16 2022 - 12:32:17 PDT)
- David A Case (Wed Mar 16 2022 - 07:43:00 PDT)
- Soumyajit Karmakar (Wed Mar 16 2022 - 03:53:03 PDT)
[AMBER] Request help modifying a force field
- Carlos Simmerling (Sun Mar 13 2022 - 08:53:57 PDT)
- Dr. Anselm Horn (Sun Mar 13 2022 - 03:41:36 PDT)
- russ.brown.yahoo.com (Fri Mar 11 2022 - 09:19:43 PST)
[AMBER] Small Cutoffs Not Supported for Implicit Solvent GPU Simulation Runs
- David A Case (Tue Mar 22 2022 - 13:13:02 PDT)
- Nathan Black (Tue Mar 22 2022 - 12:55:21 PDT)
- Nathan Black (Tue Mar 22 2022 - 07:32:29 PDT)
- Carlos Simmerling (Mon Mar 21 2022 - 10:34:14 PDT)
- David A Case (Mon Mar 21 2022 - 10:13:42 PDT)
- Nathan Black (Mon Mar 21 2022 - 07:28:16 PDT)
[AMBER] Stripping waters from trajectory except those forming bridged H-bond between Protein and Ligand
- Rakesh Srivastava (Thu Mar 17 2022 - 01:42:35 PDT)
- Daniel Roe (Wed Mar 16 2022 - 13:06:37 PDT)
- Rakesh Srivastava (Mon Mar 14 2022 - 19:20:29 PDT)
- Daniel Roe (Mon Mar 14 2022 - 08:19:42 PDT)
- Rakesh Srivastava (Fri Mar 11 2022 - 21:12:50 PST)
[AMBER] T-REMD
- Carlos Simmerling (Fri Mar 18 2022 - 04:32:21 PDT)
- Juliette Newell (Fri Mar 18 2022 - 04:27:41 PDT)
- Carlos Simmerling (Fri Mar 18 2022 - 04:18:19 PDT)
- Juliette Newell (Fri Mar 18 2022 - 02:57:03 PDT)
[AMBER] The tutorial 6.8 Westpa Tutorials
- Maria Nagan (Tue Mar 22 2022 - 18:33:49 PDT)
[AMBER] TLEAP error when adding Ag+
- David A Case (Mon Mar 07 2022 - 12:53:02 PST)
- Alysia Mandato (Mon Mar 07 2022 - 12:23:56 PST)
[AMBER] tleap error: "expected 'default'"
- Scott Brozell (Mon Mar 14 2022 - 18:05:29 PDT)
[AMBER] tleap: keep crystallographic waters?
- David A Case (Fri Mar 11 2022 - 08:30:02 PST)
- Daniel Konstantinovsky (Fri Mar 11 2022 - 07:13:34 PST)
- David A Case (Thu Mar 10 2022 - 17:36:32 PST)
- Carlos Simmerling (Thu Mar 10 2022 - 16:12:13 PST)
- Daniel Konstantinovsky (Thu Mar 10 2022 - 16:05:54 PST)
[AMBER] Toluene solvent box equilibration
- David A Case (Thu Mar 31 2022 - 05:02:06 PDT)
- Pedro Miguel Reis Figueiredo (Wed Mar 30 2022 - 13:17:02 PDT)
[AMBER] Tyrosine anion simulation
- Kellon Belfon (Tue Mar 29 2022 - 09:53:05 PDT)
- Kellon Belfon (Tue Mar 29 2022 - 09:40:21 PDT)
- Dr. Anselm Horn (Tue Mar 29 2022 - 05:00:01 PDT)
- Пушкарев Сергей (Mon Mar 28 2022 - 22:54:39 PDT)
[AMBER] Unit 9 Error on OPEN: inpcrd When Running GPU Simulation on PMEMD.CUDA
- Nathan Black (Thu Mar 31 2022 - 06:47:45 PDT)
[AMBER] Unit cell size changed and coords overlap problems
- Daniel Roe (Fri Mar 11 2022 - 08:44:10 PST)
- chanyann06.stu.scu.edu.cn (Thu Mar 10 2022 - 18:00:49 PST)
- Daniel Roe (Thu Mar 10 2022 - 09:57:13 PST)
- Dr. Anselm Horn (Thu Mar 10 2022 - 00:45:42 PST)
- chanyann06.stu.scu.edu.cn (Wed Mar 09 2022 - 23:45:38 PST)
[AMBER] Watershell like command for lipids
- Daniel Roe (Mon Mar 07 2022 - 08:04:00 PST)
- Vic De Roo (Mon Mar 07 2022 - 03:56:47 PST)
Tyrosine anion simulation
- Matthew Guberman-Pfeffer (Tue Mar 29 2022 - 05:53:51 PDT)

Amber Archive Mar 2022 by subject