Amber Archive Feb 2024: by subject

[AMBER] [Sender Not Verified] RMSD values are low
- Steinbrecher, Thomas via AMBER (Wed Feb 28 2024 - 09:30:00 PST)
- Godbole, Shivani via AMBER (Wed Feb 28 2024 - 09:22:14 PST)
- Steinbrecher, Thomas via AMBER (Wed Feb 28 2024 - 09:16:49 PST)
[AMBER] AMBER 20 installation error on Rockey Linux 8
- David A Case via AMBER (Sun Feb 11 2024 - 08:10:53 PST)
- Michael Shokhen via AMBER (Tue Feb 06 2024 - 09:50:53 PST)
[AMBER] Amber installation
- David A Case via AMBER (Sun Feb 11 2024 - 08:26:17 PST)
- haiyangzhong via AMBER (Tue Feb 06 2024 - 21:59:08 PST)
- Karis Jimenes via AMBER (Tue Feb 06 2024 - 20:36:38 PST)
[AMBER] AMBER installation error on Rocky Linux 8
- Todd Minehardt via AMBER (Wed Feb 07 2024 - 09:41:02 PST)
- Michael Shokhen via AMBER (Wed Feb 07 2024 - 09:32:14 PST)
[AMBER] AMBER22 and AmberTools23 installation issue
- Todd Minehardt via AMBER (Mon Feb 05 2024 - 07:54:29 PST)
[AMBER] Best practises for running MD with RNA structures
- Darrin York via AMBER (Fri Feb 23 2024 - 13:12:27 PST)
- Christina Bergonzo via AMBER (Thu Feb 22 2024 - 05:50:24 PST)
- Debarati DasGupta via AMBER (Wed Feb 21 2024 - 13:44:02 PST)
[AMBER] Calculating RMSD between apoprotein and protein-ligand complex
- Alexander Hung Lee via AMBER (Fri Feb 02 2024 - 17:18:38 PST)
[AMBER] CHARMM Dual Membranes
- Stephan Schott via AMBER (Tue Feb 20 2024 - 13:07:42 PST)
- Thompson, Emma via AMBER (Tue Feb 20 2024 - 08:05:27 PST)
[AMBER] CM parameters missing in Amber
- Carlos Simmerling via AMBER (Tue Feb 06 2024 - 10:45:19 PST)
- Noureen Abdelrahman via AMBER (Tue Feb 06 2024 - 10:11:42 PST)
[AMBER] Compiling AmberTools on OSX-arm64
- Istvan Kolossvary via AMBER (Fri Feb 09 2024 - 10:20:50 PST)
[AMBER] Computational Chemistry summer intern position.
- Rodrigo Galindo-Murillo via AMBER (Thu Feb 08 2024 - 08:25:38 PST)
[AMBER] constant pH protonation states
- He, Amy via AMBER (Wed Feb 07 2024 - 16:21:50 PST)
- Yang, Li-Yen via AMBER (Wed Feb 07 2024 - 15:33:30 PST)
- He, Amy via AMBER (Tue Feb 06 2024 - 17:13:01 PST)
- Yang, Li-Yen via AMBER (Tue Feb 06 2024 - 16:49:16 PST)
- He, Amy via AMBER (Tue Feb 06 2024 - 16:10:49 PST)
- Yang, Li-Yen via AMBER (Tue Feb 06 2024 - 15:42:38 PST)
[AMBER] Constant pH remd
- Skanda Sastry via AMBER (Thu Feb 22 2024 - 17:05:36 PST)
- Dulal Mondal via AMBER (Wed Feb 21 2024 - 22:47:38 PST)
- Dulal Mondal via AMBER (Wed Feb 21 2024 - 21:54:38 PST)
- He, Amy via AMBER (Wed Feb 21 2024 - 12:42:54 PST)
- Skanda Sastry via AMBER (Wed Feb 21 2024 - 04:46:57 PST)
- Dulal Mondal via AMBER (Tue Feb 20 2024 - 22:45:06 PST)
- Adrian Roitberg via AMBER (Tue Feb 20 2024 - 07:39:51 PST)
- Dulal Mondal via AMBER (Tue Feb 20 2024 - 02:16:18 PST)
[AMBER] Constant pH replica exchange
- Dulal Mondal via AMBER (Wed Feb 28 2024 - 01:18:44 PST)
- Dulal Mondal via AMBER (Wed Feb 28 2024 - 00:20:35 PST)
[AMBER] Converting CGenFF CHARMM parameters in tleap
- Collin Nisler via AMBER (Wed Feb 21 2024 - 12:24:10 PST)
- He, Amy via AMBER (Tue Feb 20 2024 - 17:54:58 PST)
- Collin Nisler via AMBER (Tue Feb 20 2024 - 14:36:52 PST)
- David A Case via AMBER (Tue Feb 20 2024 - 12:51:46 PST)
- He, Amy via AMBER (Tue Feb 20 2024 - 12:43:26 PST)
- Collin Nisler via AMBER (Tue Feb 20 2024 - 10:47:45 PST)
[AMBER] Converting ff19SB data files for usage with GROMACS
- Carlos Simmerling via AMBER (Fri Feb 23 2024 - 07:01:58 PST)
- Vedran Miletic via AMBER (Fri Feb 23 2024 - 04:53:13 PST)
[AMBER] Cu2+ and Zn2+ modeling
- Omar Ben Mariem via AMBER (Wed Feb 28 2024 - 05:13:43 PST)
[AMBER] CUDA Toolkit Installation for WSL (Ubuntu 22.04)
- David A Case via AMBER (Tue Feb 20 2024 - 12:47:05 PST)
- Kaleem Arshad via AMBER (Mon Feb 19 2024 - 20:21:28 PST)
[AMBER] dev/shm memory errors in Amber 22
- Waqqas Zia via AMBER (Thu Feb 08 2024 - 02:56:35 PST)
[AMBER] Dihedral Parametrization in Amber19: Same QM level as for 94?
- He, Amy via AMBER (Fri Feb 16 2024 - 10:49:12 PST)
- David A Case via AMBER (Fri Feb 16 2024 - 10:43:02 PST)
- Jones De Andrade via AMBER (Fri Feb 16 2024 - 09:24:06 PST)
- He, Amy via AMBER (Thu Feb 15 2024 - 11:06:14 PST)
- Jones de Andrade via AMBER (Thu Feb 15 2024 - 09:02:34 PST)
- Jones de Andrade via AMBER (Thu Feb 15 2024 - 04:57:09 PST)
- Carlos Simmerling via AMBER (Wed Feb 14 2024 - 04:00:52 PST)
- Jones De Andrade via AMBER (Tue Feb 13 2024 - 19:01:40 PST)
[AMBER] Energy decomposition of TI results using cpptraj.
- Fanyu Zhao via AMBER (Tue Feb 20 2024 - 19:55:27 PST)
[AMBER] Error building Amber22 with cuda
- Goetz, Andreas via AMBER (Thu Feb 29 2024 - 13:14:37 PST)
- Dhariwal, Rohit via AMBER (Wed Feb 28 2024 - 08:11:56 PST)
[AMBER] Error in incorporating a modified nucleoside into the 1BNA template
- Sruthi Sudhakar via AMBER (Wed Feb 07 2024 - 03:45:48 PST)
[AMBER] Error parametrizing ligand covalently bound to cysteine using GAFF
- David A Case via AMBER (Sun Feb 11 2024 - 11:29:42 PST)
- Noureen Abdelrahman via AMBER (Thu Feb 08 2024 - 10:02:06 PST)
[AMBER] failed to minimize after solvation from glycam web
- David A Case via AMBER (Fri Feb 16 2024 - 10:48:11 PST)
- BILASH MAITY via AMBER (Fri Feb 16 2024 - 02:46:27 PST)
[AMBER] Final MD Run in Parts
- Kaleem Arshad via AMBER (Thu Feb 22 2024 - 03:36:08 PST)
[AMBER] Force field for modified DNA (OL15 or PARMBSC1)
- Mac Kevin Braza via AMBER (Wed Feb 28 2024 - 16:51:12 PST)
[AMBER] Force field parameters for modified RNA
- Jenny 148 via AMBER (Mon Feb 19 2024 - 03:37:08 PST)
[AMBER] Fwd: dev/shm memory errors in Amber 22
- David A Case via AMBER (Tue Feb 13 2024 - 10:07:46 PST)
- Waqqas Zia via AMBER (Mon Feb 12 2024 - 02:14:10 PST)
[AMBER] Generating tleap input files for an organomtallic complex
- David A Case via AMBER (Fri Feb 02 2024 - 13:34:03 PST)
[AMBER] GPU perf: RTX3060TI < RTX2060 Super < RTX4090 ?
- David A Case via AMBER (Sun Feb 11 2024 - 08:21:13 PST)
- Thomas C. Bishop via AMBER (Tue Feb 06 2024 - 11:13:38 PST)
[AMBER] imaging membrane system
- Romero, Maria via AMBER (Fri Feb 23 2024 - 17:07:57 PST)
[AMBER] Improper torsion terms when building covalent bond in leap
- He, Amy via AMBER (Mon Feb 26 2024 - 18:05:03 PST)
- Nicole Vita via AMBER (Mon Feb 26 2024 - 16:17:56 PST)
[AMBER] Insufficient frames generated
- Godbole, Shivani via AMBER (Wed Feb 21 2024 - 07:07:41 PST)
- He, Amy via AMBER (Tue Feb 20 2024 - 13:05:49 PST)
- Godbole, Shivani via AMBER (Tue Feb 20 2024 - 08:02:43 PST)
[AMBER] Is it possible to model a protein with a linker covalently attached at a cysteine?
- Dr. Anselm Horn via AMBER (Mon Feb 26 2024 - 02:52:53 PST)
- Sasha Buzko via AMBER (Sun Feb 25 2024 - 20:27:16 PST)
[AMBER] Is it possible to model a protein with a linker covalently attached at a cysteine? Missing angle parameters
- David A Case via AMBER (Mon Feb 26 2024 - 14:58:37 PST)
- Sasha Buzko via AMBER (Mon Feb 26 2024 - 09:30:42 PST)
[AMBER] Is it possible to model a protein with a linker covalently attached at a cysteine? Mysterious "invisible" torsion parameters?
- Dr. Anselm Horn via AMBER (Wed Feb 28 2024 - 00:26:10 PST)
[AMBER] issue performing heating of protein in implicit solvent
- Carlos Simmerling via AMBER (Wed Feb 21 2024 - 07:09:02 PST)
- Carlos Simmerling via AMBER (Wed Feb 21 2024 - 03:03:42 PST)
- Ildar Garipov via AMBER (Tue Feb 20 2024 - 21:38:50 PST)
[AMBER] Issue with running NPT ensemble simulations on AMBER 22 using RTX 4500 ada
- Tru Huynh via AMBER (Wed Feb 14 2024 - 13:56:01 PST)
- Abhilash J via AMBER (Wed Feb 14 2024 - 12:16:04 PST)
- Abhilash J via AMBER (Wed Feb 14 2024 - 10:51:46 PST)
- Abhilash J via AMBER (Tue Feb 06 2024 - 11:37:03 PST)
- Abhilash J via AMBER (Tue Feb 06 2024 - 10:04:39 PST)
[AMBER] Long Bond length during simulation of nonstandard residue
- Cao, Dillon P. via AMBER (Tue Feb 27 2024 - 15:18:05 PST)
- Carlos Simmerling via AMBER (Tue Feb 27 2024 - 14:10:23 PST)
- Cao, Dillon P. via AMBER (Tue Feb 27 2024 - 10:49:13 PST)
[AMBER] make install error related to pmemd xray & MKL
- Pertschy, Florian via AMBER (Wed Feb 28 2024 - 07:46:55 PST)
[AMBER] Masking backbone interactions
- Prithviraj Nandigrami via AMBER (Thu Feb 08 2024 - 12:10:24 PST)
[AMBER] MMPBSA.py: entropy calculation options
- Dr. Anselm Horn via AMBER (Tue Feb 20 2024 - 02:54:44 PST)
- Bill Miller III via AMBER (Mon Feb 19 2024 - 16:03:17 PST)
- Dr. Anselm Horn via AMBER (Mon Feb 19 2024 - 01:41:53 PST)
[AMBER] NTWX Value Advice for Final MD Run
- Carlos Simmerling via AMBER (Sat Feb 24 2024 - 06:22:50 PST)
- Kaleem Arshad via AMBER (Fri Feb 23 2024 - 21:39:04 PST)
[AMBER] Please remove my email from mailing list. Thank you
- Adeleh Mokhles Gerami via AMBER (Tue Feb 27 2024 - 08:30:00 PST)
[AMBER] Prmtop Parmed and CPPTRAJ Check-Energy Minimization Failure
- David A Case via AMBER (Mon Feb 19 2024 - 07:56:22 PST)
- David A Case via AMBER (Fri Feb 16 2024 - 10:39:29 PST)
- Kaleem Arshad via AMBER (Wed Feb 14 2024 - 22:51:38 PST)
[AMBER] PSU residue parameters
- Rodrigo Galindo-Murillo via AMBER (Fri Feb 09 2024 - 12:09:23 PST)
- Debarati DasGupta via AMBER (Fri Feb 09 2024 - 11:09:31 PST)
[AMBER] Query regarding Temperature Replica Exchange Molecular Dynamics?
- Carlos Simmerling via AMBER (Mon Feb 12 2024 - 05:27:03 PST)
- Munazzah Fatima Ansari via AMBER (Mon Feb 12 2024 - 04:47:03 PST)
[AMBER] Question about amber mask for restrains
- Enrico Martinez via AMBER (Fri Feb 02 2024 - 05:38:42 PST)
[AMBER] Question about λ adjustable acceleration parameter in aMD
- 李美玲 via AMBER (Sat Feb 03 2024 - 02:11:50 PST)
[AMBER] QUICK QM/MM problem/bug
- David A Case via AMBER (Mon Feb 05 2024 - 08:35:52 PST)
- Juraj Dobias via AMBER (Mon Feb 05 2024 - 00:34:19 PST)
- David A Case via AMBER (Fri Feb 02 2024 - 13:24:57 PST)
- Juraj Dobias via AMBER (Fri Feb 02 2024 - 02:55:12 PST)
[AMBER] Ranges in generated PRMTOP for Atomic Numbers
- Dr. Anselm Horn via AMBER (Wed Feb 28 2024 - 03:10:23 PST)
- Trevor Kramer via AMBER (Tue Feb 27 2024 - 08:09:36 PST)
[AMBER] Regarding Problems with Amber22 Installation on M1 & M2
- David A Case via AMBER (Fri Feb 23 2024 - 11:01:26 PST)
- Hoonsung Lee via AMBER (Thu Feb 22 2024 - 03:20:42 PST)
[AMBER] Renumber residues (Error: No change type specified) - AMBER MD 18
- Rodrigo Galindo-Murillo via AMBER (Wed Feb 28 2024 - 09:26:22 PST)
- Daniel Hall via AMBER (Wed Feb 28 2024 - 09:19:15 PST)
[AMBER] Residues Naming Advice
- He, Amy via AMBER (Tue Feb 13 2024 - 20:06:43 PST)
- Kaleem Arshad via AMBER (Tue Feb 13 2024 - 19:50:59 PST)
[AMBER] RMSD values are low
- Godbole, Shivani via AMBER (Wed Feb 28 2024 - 09:05:47 PST)
[AMBER] Sander.mpi haults at 999 steps
- Montalvillo, Fernando via AMBER (Mon Feb 26 2024 - 16:21:19 PST)
[AMBER] Simulation of a membrane containing system in implicit solvent
- Sergey Samsonov via AMBER (Mon Feb 26 2024 - 06:13:15 PST)
[AMBER] Solvation models with RNA
- Debarati DasGupta via AMBER (Wed Feb 14 2024 - 12:11:23 PST)
[AMBER] Thermodynamic Integration of Loosening Restraints
- Skanda Sastry via AMBER (Fri Feb 23 2024 - 14:08:08 PST)
- Darrin York via AMBER (Fri Feb 23 2024 - 13:04:11 PST)
- David A Case via AMBER (Fri Feb 23 2024 - 11:15:48 PST)
- Helmut Carter via AMBER (Thu Feb 22 2024 - 13:49:11 PST)
[AMBER] Too many TI atoms ERROR
- Mehrnoosh Khodam Hazrati via AMBER (Mon Feb 26 2024 - 03:12:22 PST)
[AMBER] Two questions about CPPTRAJ processing
- Enrico Martinez via AMBER (Fri Feb 02 2024 - 06:27:33 PST)
- Enrico Martinez via AMBER (Fri Feb 02 2024 - 05:44:35 PST)
[AMBER] uncertainty in atomic positional fluctuations
- Adrian Roitberg via AMBER (Thu Feb 29 2024 - 11:42:57 PST)
- Duggan, Brendan via AMBER (Thu Feb 29 2024 - 11:29:42 PST)
[AMBER] using 12_6_4 ion parameters with OPC water model
- Carlos Simmerling via AMBER (Tue Feb 27 2024 - 08:34:05 PST)
- haiyangzhong via AMBER (Tue Feb 27 2024 - 08:26:18 PST)
- Giulio RASTELLI via AMBER (Tue Feb 27 2024 - 08:19:20 PST)
- Carlos Simmerling via AMBER (Fri Feb 23 2024 - 11:03:25 PST)
- Giulio RASTELLI via AMBER (Thu Feb 22 2024 - 06:55:10 PST)
[AMBER] Using AM1-BCC charges for Organometalls
- Miriam Sprick via AMBER (Wed Feb 14 2024 - 03:47:06 PST)
Constant pH remd
- Adrian Roitberg via AMBER (Fri Feb 23 2024 - 09:58:09 PST)
non superuser installation
- David A Case via AMBER (Mon Feb 05 2024 - 08:32:15 PST)
- Joel Gallardo via AMBER (Sat Feb 03 2024 - 05:13:07 PST)

Amber Archive Feb 2024 by subject