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