Amber Archive Feb 2023: by subject

[AMBER] [Amber20] QM region of QM/MM computations cannot converge
- Adrian Roitberg via AMBER (Mon Feb 20 2023 - 06:34:04 PST)
- Maciej Spiegel via AMBER (Mon Feb 20 2023 - 05:09:46 PST)
- David A Case via AMBER (Mon Feb 20 2023 - 04:56:22 PST)
- Maciej Spiegel via AMBER (Sun Feb 19 2023 - 08:42:37 PST)
[AMBER] [Sender Not Verified] drug including B atom
- David A Case via AMBER (Thu Feb 16 2023 - 18:25:09 PST)
- laura zhang via AMBER (Thu Feb 16 2023 - 06:33:35 PST)
- Steinbrecher, Thomas via AMBER (Wed Feb 15 2023 - 23:56:29 PST)
[AMBER] [Sender Not Verified] How to do analysis on specific frames in cpptraj?
- Steinbrecher, Thomas via AMBER (Tue Feb 21 2023 - 05:02:13 PST)
[AMBER] [Sender Not Verified] Net charge of ligand
- Enrico Martinez via AMBER (Thu Feb 16 2023 - 06:28:33 PST)
[AMBER] [Sender Not Verified] tleap ion naming issues
- Steinbrecher, Thomas via AMBER (Mon Feb 13 2023 - 23:46:54 PST)
[AMBER] A query on using a non-standard solvent
- Steinbrecher, Thomas via AMBER (Wed Feb 01 2023 - 01:11:57 PST)
- devendra.prajapat.cys19--- via AMBER (Wed Feb 01 2023 - 00:49:02 PST)
[AMBER] amber install error
- Daniel Roe via AMBER (Tue Feb 28 2023 - 16:02:12 PST)
- Tang, Jun via AMBER (Tue Feb 28 2023 - 13:40:07 PST)
- David A Case via AMBER (Tue Feb 28 2023 - 13:26:41 PST)
- Tang, Jun via AMBER (Tue Feb 28 2023 - 06:17:13 PST)
[AMBER] AMBER simulation heating step
- David A Case via AMBER (Sun Feb 05 2023 - 09:04:45 PST)
[AMBER] amber20 installation failed on ubuntu
- David A Case via AMBER (Thu Feb 16 2023 - 18:29:12 PST)
- Renato Freitas via AMBER (Thu Feb 16 2023 - 14:30:54 PST)
- David A Case via AMBER (Thu Feb 16 2023 - 06:01:05 PST)
- Gert Kruger via AMBER (Thu Feb 16 2023 - 05:45:45 PST)
- Renato Freitas via AMBER (Thu Feb 16 2023 - 04:55:13 PST)
- Renato Freitas via AMBER (Wed Feb 15 2023 - 13:07:13 PST)
[AMBER] Amber2020 and Amber2022 comparability issue: alchemical free energy calc
- Michael T Kim via AMBER (Thu Feb 23 2023 - 10:51:26 PST)
- Michael T Kim via AMBER (Mon Feb 06 2023 - 13:59:00 PST)
- David A Case via AMBER (Sun Feb 05 2023 - 09:02:16 PST)
- Michael T Kim via AMBER (Fri Feb 03 2023 - 18:01:14 PST)
[AMBER] Ambertools on M2 pro
- mohamed marzouk via AMBER (Thu Feb 16 2023 - 06:28:41 PST)
[AMBER] Announcement: Release of DOCK 6.10
- Scott Brozell via AMBER (Wed Feb 01 2023 - 10:47:02 PST)
[AMBER] Antechamber Error
- Rana Rehan Khalid via AMBER (Thu Feb 16 2023 - 00:35:10 PST)
[AMBER] benchmarking Amber 22 with WSL2 on Windows 11
- Martin Juhás via AMBER (Wed Feb 15 2023 - 13:20:46 PST)
- Martin Juhás via AMBER (Wed Feb 15 2023 - 13:13:46 PST)
[AMBER] Calculating Electrostatic energy between 2 atoms
- angad sharma via AMBER (Mon Feb 13 2023 - 04:39:10 PST)
[AMBER] CIC Annual Meeting during WiFo 2023, Sep 4-6 in Leipzig – Call for Papers
- Guessregen, Stefan /DE via AMBER (Wed Feb 15 2023 - 11:51:54 PST)
[AMBER] Comparison of TIP3P vs AMOEBA water models
- Umesh Roy via AMBER (Fri Feb 17 2023 - 09:50:11 PST)
[AMBER] Conference Announcement: 35th MMWS in Erlangen, Germany
- Dr. Anselm Horn via AMBER (Sat Feb 04 2023 - 07:25:54 PST)
[AMBER] CPPTRAJ, PCA, Effect of Mutation
- Daniel Roe via AMBER (Mon Feb 06 2023 - 05:13:38 PST)
- Elvis Martis via AMBER (Tue Jan 31 2023 - 18:30:54 PST)
[AMBER] CPPTRAJ, Salt Bridge
- Daniel Roe via AMBER (Mon Feb 06 2023 - 05:27:49 PST)
- Matthew Guberman-Pfeffer via AMBER (Thu Feb 02 2023 - 07:55:27 PST)
[AMBER] cudaGetDeviceCount failed no CUDA-capable device is detected
- David A Case via AMBER (Tue Feb 28 2023 - 05:51:30 PST)
- ABDELATIF MESSAOUDI via AMBER (Fri Feb 24 2023 - 15:07:13 PST)
[AMBER] D-glucosamine GLYCAM parameters
- Michael Owen via AMBER (Wed Feb 01 2023 - 23:20:58 PST)
[AMBER] Density distribution
- angad sharma via AMBER (Mon Feb 06 2023 - 09:58:12 PST)
[AMBER] Distance calculation using cpptraj
- Daniel Roe via AMBER (Mon Feb 06 2023 - 05:12:18 PST)
- Dulal Mondal via AMBER (Tue Jan 31 2023 - 10:44:30 PST)
[AMBER] drug including B atom
- David A Case via AMBER (Thu Feb 16 2023 - 06:07:50 PST)
- laura zhang via AMBER (Wed Feb 15 2023 - 18:49:31 PST)
[AMBER] Electrostatic calculation
- angad sharma via AMBER (Tue Feb 14 2023 - 06:03:38 PST)
[AMBER] Error - Amber 22 Installation with Cuda
- David A Case via AMBER (Mon Feb 20 2023 - 17:41:50 PST)
- Osadchey Brown, Reilly via AMBER (Mon Feb 20 2023 - 11:56:40 PST)
- ABDELATIF MESSAOUDI via AMBER (Mon Feb 20 2023 - 11:37:18 PST)
[AMBER] Error in parmstrip
- Enrico Martinez via AMBER (Thu Feb 16 2023 - 06:26:22 PST)
[AMBER] Error in tests for pmemd.cuda.MPI
- Freddy Bernal via AMBER (Mon Feb 13 2023 - 01:16:22 PST)
- Freddy Bernal via AMBER (Wed Feb 08 2023 - 00:26:04 PST)
- Freddy Bernal via AMBER (Wed Feb 08 2023 - 00:22:12 PST)
- Hector A. Baldoni via AMBER (Mon Feb 06 2023 - 14:39:07 PST)
- Freddy Bernal via AMBER (Mon Feb 06 2023 - 01:36:26 PST)
[AMBER] Error similation with cuda
- David A Case via AMBER (Mon Feb 20 2023 - 17:44:42 PST)
- ABDELATIF MESSAOUDI via AMBER (Mon Feb 20 2023 - 16:14:40 PST)
[AMBER] explanation of extra TI control variables
- Michael T Kim via AMBER (Mon Feb 27 2023 - 16:21:57 PST)
[AMBER] Failures inamber test
- Scott Brozell via AMBER (Wed Feb 01 2023 - 11:27:57 PST)
- Freddy Bernal via AMBER (Wed Feb 01 2023 - 02:00:22 PST)
[AMBER] Fortran runtime error: Bad real number in item 1 of list input
- David A Case via AMBER (Mon Feb 06 2023 - 14:02:43 PST)
- Nishad Ankita Rudal via AMBER (Mon Feb 06 2023 - 11:19:36 PST)
- Nishad Ankita Rudal via AMBER (Mon Feb 06 2023 - 11:13:09 PST)
- David Case via AMBER (Mon Feb 06 2023 - 08:46:16 PST)
- Dr. Anselm Horn via AMBER (Mon Feb 06 2023 - 08:12:35 PST)
- Nishad Ankita Rudal via AMBER (Mon Feb 06 2023 - 07:10:24 PST)
[AMBER] GLH with HE1
- Carlos Simmerling via AMBER (Wed Feb 01 2023 - 16:17:28 PST)
- He, Amy via AMBER (Wed Feb 01 2023 - 15:39:21 PST)
- He, Amy via AMBER (Wed Feb 01 2023 - 15:23:58 PST)
[AMBER] GPU memory error during ABMD run
- Owen O'Reilly via AMBER (Mon Feb 06 2023 - 07:52:25 PST)
- David A Case via AMBER (Mon Feb 06 2023 - 05:33:21 PST)
- Owen O'Reilly via AMBER (Sun Feb 05 2023 - 15:33:39 PST)
[AMBER] H bonding
- Dulal Mondal via AMBER (Fri Feb 10 2023 - 03:51:29 PST)
[AMBER] How restart md simulation with amber22
- Carlos Simmerling via AMBER (Wed Feb 01 2023 - 03:14:48 PST)
- ABDELATIF MESSAOUDI via AMBER (Tue Jan 31 2023 - 23:42:01 PST)
[AMBER] How to do analysis on specific frames in cpptraj?
- Daniel Roe via AMBER (Tue Feb 21 2023 - 05:20:05 PST)
- XP Chen via AMBER (Tue Feb 21 2023 - 04:02:45 PST)
[AMBER] How to protonate ligand manually ?
- Enrico Martinez via AMBER (Mon Feb 13 2023 - 02:03:27 PST)
[AMBER] How to set water molecule without EPW dummy atom?
- Carlos Simmerling via AMBER (Mon Feb 27 2023 - 05:45:46 PST)
- Maciej Spiegel via AMBER (Sun Feb 26 2023 - 23:11:57 PST)
- Vinicius Wilian Cruzeiro via AMBER (Sun Feb 26 2023 - 23:00:21 PST)
- Maciej Spiegel via AMBER (Sun Feb 26 2023 - 22:14:30 PST)
[AMBER] Installation Error: miniconda issue
- Sumra Abbasi via AMBER (Mon Feb 06 2023 - 05:41:50 PST)
- Sumra Abbasi via AMBER (Sun Feb 05 2023 - 21:13:34 PST)
[AMBER] load amber trj using vmd automatically
- Daniel Roe via AMBER (Tue Feb 07 2023 - 17:30:58 PST)
- Matthew Guberman-Pfeffer via AMBER (Tue Feb 07 2023 - 12:45:12 PST)
- laura zhang via AMBER (Tue Feb 07 2023 - 12:17:02 PST)
[AMBER] Method (SHAKE/SETTLE, HMR) to conditionally constrain waters
- Brian Radak via AMBER (Fri Feb 17 2023 - 13:02:03 PST)
- Carlos Simmerling via AMBER (Fri Feb 17 2023 - 13:03:37 PST)
- Carlos Simmerling via AMBER (Fri Feb 17 2023 - 09:51:46 PST)
- He, Amy via AMBER (Fri Feb 17 2023 - 09:36:39 PST)
[AMBER] MMPBSA problem
- Bill Miller III via AMBER (Tue Feb 28 2023 - 09:41:53 PST)
- Jurica Novak via AMBER (Tue Feb 28 2023 - 07:52:10 PST)
- David A Case via AMBER (Tue Feb 28 2023 - 05:42:28 PST)
- Jurica Novak via AMBER (Fri Feb 24 2023 - 01:32:13 PST)
[AMBER] Net charge of ligand
- Enrico Martinez via AMBER (Wed Feb 15 2023 - 08:03:46 PST)
[AMBER] NMR refinement of G-Quadruplex DNA by AMBER22
- David A Case via AMBER (Mon Feb 13 2023 - 05:20:07 PST)
- Anirban Ghosh via AMBER (Sun Feb 12 2023 - 12:13:52 PST)
[AMBER] Nucleic acid simulation error
- Carlos Simmerling via AMBER (Thu Feb 09 2023 - 08:11:12 PST)
- Carlos Simmerling via AMBER (Thu Feb 09 2023 - 07:35:33 PST)
- Carlos Simmerling via AMBER (Wed Feb 08 2023 - 08:09:52 PST)
- Carlos Simmerling via AMBER (Wed Feb 08 2023 - 04:20:13 PST)
- Prithviraj Nandigrami via AMBER (Mon Feb 06 2023 - 12:26:19 PST)
[AMBER] Opening for a PLUMED developer position
- Giovanni Bussi via AMBER (Thu Feb 02 2023 - 12:52:53 PST)
[AMBER] parallel pysander?
- liu junjun via AMBER (Thu Feb 16 2023 - 08:37:28 PST)
[AMBER] PCA porjection & representative structure
- Hocine EL KHAOUDI ENYOURY via AMBER (Mon Feb 06 2023 - 05:48:25 PST)
- Daniel Roe via AMBER (Mon Feb 06 2023 - 05:43:31 PST)
- Hocine EL KHAOUDI ENYOURY via AMBER (Fri Feb 03 2023 - 01:40:50 PST)
[AMBER] pmemd.cuda test possible failure
- David A Case via AMBER (Tue Feb 28 2023 - 05:38:52 PST)
- Freddy Bernal via AMBER (Thu Feb 23 2023 - 11:46:04 PST)
[AMBER] pmemd.cuda: error while loading shared libraries
- ABDELATIF MESSAOUDI via AMBER (Tue Feb 28 2023 - 13:50:32 PST)
- David A Case via AMBER (Tue Feb 28 2023 - 05:50:18 PST)
- Markowska (Fri Feb 24 2023 - 23:34:24 PST)
- ABDELATIF MESSAOUDI via AMBER (Fri Feb 24 2023 - 14:49:40 PST)
[AMBER] Problem with MMGBSA
- Suchetana Gupta via AMBER (Wed Feb 01 2023 - 15:57:19 PST)
- Suchetana Gupta via AMBER (Wed Feb 01 2023 - 15:49:14 PST)
- Suchetana Gupta via AMBER (Wed Feb 01 2023 - 15:44:01 PST)
- Suchetana Gupta via AMBER (Wed Feb 01 2023 - 14:50:00 PST)
[AMBER] problem with pmemd.cuda and RTX4090
- Martin Zacharias via AMBER (Thu Feb 23 2023 - 01:36:50 PST)
[AMBER] pysander for gas energy with belly?
- liu junjun via AMBER (Fri Feb 24 2023 - 01:58:10 PST)
- liu junjun via AMBER (Thu Feb 23 2023 - 08:15:34 PST)
[AMBER] Query regarding Acceptance ratio file
- Carlos Simmerling via AMBER (Thu Feb 23 2023 - 08:27:34 PST)
- Munazzah Fatima Ansari via AMBER (Thu Feb 23 2023 - 03:16:08 PST)
[AMBER] Regarding the visualization of the nmd file after pca in VMD
- Sruthi Sudhakar via AMBER (Sat Feb 25 2023 - 05:55:49 PST)
[AMBER] Removing rotational-transnational movements in dimmer protein
- Enrico Martinez via AMBER (Mon Feb 13 2023 - 06:07:42 PST)
[AMBER] RMSF calculation descrepancy of dimeric systems
- Prathit Chatterjee via AMBER (Sun Feb 05 2023 - 21:32:49 PST)
[AMBER] RTX 2080 vs RTX 3060 TI
- Renato Freitas via AMBER (Tue Feb 28 2023 - 13:06:00 PST)
[AMBER] RTX4070TI Benchmarks
- Ross Walker via AMBER (Fri Feb 03 2023 - 06:31:14 PST)
[AMBER] sander seeks for the .skf integral file for a single-empty atomtype
- David A Case via AMBER (Sat Feb 18 2023 - 05:39:01 PST)
- Maciej Spiegel via AMBER (Fri Feb 17 2023 - 00:41:05 PST)
[AMBER] scalpha and scbeta defaults are not right for TI calculations with smoothstep gti_lam_sch=1?
- Skanda Sastry via AMBER (Sun Feb 12 2023 - 23:47:36 PST)
[AMBER] SHAKE failed for hydrogens that interact with soft-core and/or no-SHAKE atoms
- He, Amy via AMBER (Wed Feb 15 2023 - 14:17:14 PST)
[AMBER] Suspicious pKas from CpHMD
- Adrian Roitberg via AMBER (Thu Feb 09 2023 - 08:07:35 PST)
- Vinicius Wilian Cruzeiro via AMBER (Wed Feb 08 2023 - 23:00:43 PST)
- Matthew Guberman-Pfeffer via AMBER (Wed Feb 08 2023 - 22:36:21 PST)
- Vinicius Wilian Cruzeiro via AMBER (Wed Feb 08 2023 - 21:57:50 PST)
- Matthew Guberman-Pfeffer via AMBER (Wed Feb 08 2023 - 21:08:35 PST)
[AMBER] Terminal phosphates with RNA
- Piia Bartos via AMBER (Fri Feb 24 2023 - 03:05:38 PST)
- Piia Bartos via AMBER (Wed Feb 22 2023 - 10:46:38 PST)
- David A Case via AMBER (Wed Feb 22 2023 - 07:14:59 PST)
- Piia Bartos via AMBER (Wed Feb 22 2023 - 01:39:48 PST)
[AMBER] tleap error
- Prithviraj Nandigrami via AMBER (Tue Feb 21 2023 - 13:45:09 PST)
[AMBER] tleap ion naming issues
- Gonzalo R. Vazquez-Jimenez via AMBER (Mon Feb 13 2023 - 11:41:08 PST)
[AMBER] Using amber19sb forcefield to simulate cyclic peptide
- Carlos Simmerling via AMBER (Fri Feb 17 2023 - 16:30:12 PST)
- Ho, Minh via AMBER (Fri Feb 17 2023 - 14:56:18 PST)
[AMBER] Warning in MMPBSA calculation with glycoprotein
- 王霂生 via AMBER (Fri Feb 10 2023 - 02:03:16 PST)
[AMBER] Warning tells me to report
- David A Case via AMBER (Wed Feb 15 2023 - 06:39:56 PST)
- Bryan Cox via AMBER (Tue Feb 14 2023 - 12:19:16 PST)
[AMBER] Where to install Amber on an Ubuntu Server
- David A Case via AMBER (Thu Feb 16 2023 - 10:06:57 PST)
Bad atom type: i
- Zachariah Schuurs via AMBER (Tue Feb 07 2023 - 00:02:19 PST)
Suspicious pKas from CpHMD
- Adrian Roitberg via AMBER (Fri Feb 10 2023 - 12:58:34 PST)
- brian.radak--- via AMBER (Fri Feb 10 2023 - 05:46:11 PST)
- Matthew Guberman-Pfeffer via AMBER (Thu Feb 09 2023 - 12:19:17 PST)
- Matthew Guberman-Pfeffer via AMBER (Thu Feb 09 2023 - 08:17:17 PST)
Using amber19sb forcefield to simulate cyclic peptide
- Carlos Simmerling via AMBER (Mon Feb 20 2023 - 08:06:21 PST)

Amber Archive Feb 2023 by subject