Amber Archive Jan 2024: by subject

[AMBER] [Sender Not Verified] Chain info in .prmtop file
- Steinbrecher, Thomas via AMBER (Tue Jan 23 2024 - 23:23:43 PST)
[AMBER] [Sender Not Verified] cpptraj: post-threatment of the PBC for membrane system
- Enrico Martinez via AMBER (Thu Jan 25 2024 - 08:42:53 PST)
[AMBER] [Sender Not Verified] Simulation of ZrO2 (zirconium dioxide)
- Victor Nazarychev via AMBER (Thu Jan 11 2024 - 07:20:58 PST)
- Matthew Guberman-Pfeffer via AMBER (Wed Jan 10 2024 - 12:51:25 PST)
- Victor Nazarychev via AMBER (Wed Jan 10 2024 - 11:24:06 PST)
[AMBER] AMBER constant pH
- Vinicius Cruzeiro \(Vinny\) via AMBER (Tue Jan 02 2024 - 08:38:52 PST)
- Hoang, Oanh Tu via AMBER (Tue Jan 02 2024 - 00:09:34 PST)
[AMBER] Amber to gromacs conversion
- 王世玉 via AMBER (Mon Jan 01 2024 - 18:51:35 PST)
- Todd Minehardt via AMBER (Mon Jan 01 2024 - 08:31:06 PST)
- Sourav Bhowmik via AMBER (Mon Jan 01 2024 - 03:30:34 PST)
[AMBER] AMBER22 and AmberTools23 installation issue
- Todd Minehardt via AMBER (Tue Jan 30 2024 - 07:14:32 PST)
- Ildar Garipov via AMBER (Tue Jan 30 2024 - 01:10:31 PST)
[AMBER] Amber22 Compilation Error
- Todd Minehardt via AMBER (Wed Jan 03 2024 - 05:29:17 PST)
- Matthew Guberman-Pfeffer via AMBER (Tue Jan 02 2024 - 22:55:03 PST)
[AMBER] analyze residue charges after constant pH MD simulation
- Yang, Li-Yen via AMBER (Fri Jan 05 2024 - 15:00:05 PST)
- He, Amy via AMBER (Thu Jan 04 2024 - 10:50:49 PST)
- Yang, Li-Yen via AMBER (Wed Jan 03 2024 - 10:04:08 PST)
[AMBER] Atom Index in the BONDS_INC_HYDROGEN Section of Topology
- He, Amy via AMBER (Sun Jan 21 2024 - 20:30:39 PST)
- Ge Song via AMBER (Sun Jan 21 2024 - 20:20:42 PST)
[AMBER] Best practises for running MD with RNA structures
- Darrin York via AMBER (Tue Jan 30 2024 - 06:32:11 PST)
- Debarati DasGupta via AMBER (Mon Jan 29 2024 - 14:53:00 PST)
[AMBER] Can cpptraj hbond command measure second order water bridge ?
- xiangyu via AMBER (Mon Jan 01 2024 - 03:21:07 PST)
[AMBER] Can leap create polymer structure using sequence command?
- Mohd Farid Ismail via AMBER (Sat Jan 06 2024 - 15:34:38 PST)
[AMBER] Chain info in .prmtop file
- Shao, Qianzhen via AMBER (Wed Jan 24 2024 - 18:29:52 PST)
- David A Case via AMBER (Wed Jan 24 2024 - 13:10:08 PST)
- Shao, Qianzhen via AMBER (Tue Jan 23 2024 - 21:56:41 PST)
[AMBER] Conda installation of Ambertools23 does not [appear to] include 'OMP' programs
- Murray, Makay via AMBER (Mon Jan 08 2024 - 11:42:20 PST)
[AMBER] Conference announcement: MMWS2024 in Erlangen (Germany)
- Dr. Anselm Horn via AMBER (Tue Jan 09 2024 - 04:45:20 PST)
[AMBER] Convergence of the diffusion coefficient for single molecules
- Samuel Holmes via AMBER (Wed Jan 03 2024 - 11:08:05 PST)
[AMBER] CpHMD, Amber22, MAX_TITR_RES overflow
- Matthew Guberman-Pfeffer via AMBER (Tue Jan 02 2024 - 09:43:37 PST)
- Vinicius Cruzeiro \(Vinny\) via AMBER (Tue Jan 02 2024 - 08:44:31 PST)
- Matthew Guberman-Pfeffer via AMBER (Tue Jan 02 2024 - 05:36:26 PST)
[AMBER] cpptraj hbond measure second order water bridge
- 鱼翔 via AMBER (Sun Dec 31 2023 - 08:25:24 PST)
[AMBER] cpptraj.MPI mmap error
- Martin Juhás via AMBER (Thu Jan 04 2024 - 02:56:15 PST)
[AMBER] cpptraj: post-threatment of the PBC for membrane system
- Enrico Martinez via AMBER (Wed Jan 24 2024 - 08:52:44 PST)
[AMBER] DFTB3 and MMPBSA.py
- CA Mattelaer via AMBER (Mon Jan 29 2024 - 02:40:26 PST)
[AMBER] Disparities when comparing Coulomb energies between cpptraj and Gromacs
- David A Case via AMBER (Fri Jan 26 2024 - 08:15:50 PST)
- Carlos Simmerling via AMBER (Fri Jan 26 2024 - 07:54:29 PST)
- Adrian Roitberg via AMBER (Fri Jan 26 2024 - 07:41:38 PST)
- Albert Gauss via AMBER (Fri Jan 26 2024 - 07:07:08 PST)
- Albert Gauss via AMBER (Fri Jan 26 2024 - 06:42:08 PST)
- Albert Gauss via AMBER (Fri Jan 26 2024 - 02:51:50 PST)
[AMBER] Download Link to Amber20 for Project Compatibility
- Sharawy, Mahmoud via AMBER (Fri Jan 19 2024 - 21:00:42 PST)
[AMBER] Error during simulation: an illegal memory access was encountered launching kernel kClearForces
- Barbara Lech via AMBER (Tue Jan 09 2024 - 05:41:57 PST)
[AMBER] Error in tleap
- BILASH MAITY via AMBER (Thu Jan 04 2024 - 23:20:56 PST)
[AMBER] Failed to genarate parameters in Tleap
- Todd Minehardt via AMBER (Tue Jan 02 2024 - 07:29:57 PST)
[AMBER] fatal error: Windows.h: No such file or directory
- Jesse Aiton via AMBER (Tue Jan 23 2024 - 16:31:42 PST)
- Jesse Aiton via AMBER (Tue Jan 23 2024 - 08:38:36 PST)
- Jesse Aiton via AMBER (Tue Jan 23 2024 - 08:22:48 PST)
- K A SIVASANKER via AMBER (Mon Jan 22 2024 - 21:08:40 PST)
- Jesse Aiton via AMBER (Mon Jan 22 2024 - 17:52:46 PST)
[AMBER] GAMESS: How to resubmit SCF calculations?
- Ralph Roberts via AMBER (Tue Jan 09 2024 - 02:58:55 PST)
[AMBER] Generating tleap input files for an organomtallic complex
- MADHUSMITA DEVI via AMBER (Wed Jan 31 2024 - 11:00:32 PST)
[AMBER] GPU bug for replica MD with pmemd.cuda.MPI
- Zhenquan Hu via AMBER (Fri Jan 19 2024 - 17:05:48 PST)
- Stéphane Téletchéa via AMBER (Fri Jan 19 2024 - 06:09:01 PST)
- Zhenquan Hu via AMBER (Wed Jan 17 2024 - 09:59:26 PST)
- Adrian Roitberg via AMBER (Wed Jan 17 2024 - 06:33:20 PST)
- Zhenquan Hu via AMBER (Tue Jan 16 2024 - 19:18:17 PST)
- Zhenquan Hu via AMBER (Tue Jan 16 2024 - 17:26:57 PST)
[AMBER] Help with coda-enabled compilation
- Charo del Genio via AMBER (Thu Jan 04 2024 - 06:53:38 PST)
- Todd Minehardt via AMBER (Thu Jan 04 2024 - 06:42:49 PST)
- Matthew Guberman-Pfeffer via AMBER (Wed Jan 03 2024 - 22:15:55 PST)
[AMBER] How to set periodic boundary conditions for a membrane protein system?
- David A Case via AMBER (Mon Jan 29 2024 - 08:07:27 PST)
- Kikuchi, Shinichi via AMBER (Mon Jan 29 2024 - 00:26:26 PST)
[AMBER] Increased Compactness of Protein-Protein Complex in NVT to NPT Ensemble
- zhangxiaochun via AMBER (Sun Jan 21 2024 - 23:46:47 PST)
[AMBER] Instalation errors of amber 22 on ubuntu22.04
- David A Case via AMBER (Wed Jan 24 2024 - 13:05:33 PST)
- Ming Tang via AMBER (Tue Jan 23 2024 - 15:36:13 PST)
[AMBER] installation inquiry
- Todd Minehardt via AMBER (Wed Jan 03 2024 - 11:46:42 PST)
- RUFAIDA AL ZOUBI via AMBER (Wed Jan 03 2024 - 10:50:55 PST)
[AMBER] Installation of amber22 with nccl
- Dulal Mondal via AMBER (Tue Jan 02 2024 - 21:59:01 PST)
[AMBER] Issue Linking C Shared Library libcifparse.so during AmberTools22 and Amber22 Installation (with INTEL ICX instead of ICC)
- David A Case via AMBER (Mon Jan 22 2024 - 11:20:31 PST)
- 디와쉬시 다스 via AMBER (Mon Jan 22 2024 - 11:03:37 PST)
[AMBER] MMGBSA problem
- Bill Miller III via AMBER (Mon Jan 15 2024 - 06:44:57 PST)
- VERONICA MARTIN HERNANDEZ via AMBER (Mon Jan 15 2024 - 05:00:54 PST)
[AMBER] MMPBSA calculation
- Bill Miller III via AMBER (Tue Jan 02 2024 - 19:24:28 PST)
- Kriti Shukla via AMBER (Mon Jan 01 2024 - 22:28:04 PST)
[AMBER] MMPBSA Stability Calculations
- Dr. Anselm Horn via AMBER (Tue Jan 30 2024 - 00:33:14 PST)
- Bill Miller III via AMBER (Wed Jan 24 2024 - 11:40:23 PST)
- Ramdhan,Peter A via AMBER (Wed Jan 24 2024 - 05:52:50 PST)
[AMBER] MMPBSA.py error: CalcError: cpptraj failed with prmtop pro_lig.parm7!
- Todd Minehardt via AMBER (Thu Jan 04 2024 - 07:34:50 PST)
- Todd Minehardt via AMBER (Wed Jan 03 2024 - 18:02:57 PST)
- Yang, Li-Yen via AMBER (Wed Jan 03 2024 - 14:11:52 PST)
[AMBER] MMPBSA.py reports ESCF for receptor when only ligand is chosen as QM region
- CA Mattelaer via AMBER (Wed Jan 31 2024 - 02:09:18 PST)
[AMBER] my RTX 3060 Ti is slower than my RTX 2060 SUPER by 2X
- Ross Walker via AMBER (Thu Jan 11 2024 - 11:13:53 PST)
- Thomas C. Bishop via AMBER (Thu Jan 11 2024 - 11:06:18 PST)
[AMBER] No restraint defined when using torsional restraints
- David A Case via AMBER (Wed Jan 17 2024 - 08:50:58 PST)
- Carlos Simmerling via AMBER (Mon Jan 15 2024 - 12:48:12 PST)
- Kari Gaalswyk via AMBER (Mon Jan 15 2024 - 11:35:19 PST)
[AMBER] Opening for Amber free energy/GPU developer
- Darrin York via AMBER (Fri Jan 12 2024 - 09:02:51 PST)
[AMBER] Parameters and charges for polymer functionalized with sugars (GLYCAM, GAFF ?)
- David DELLEMME via AMBER (Mon Jan 29 2024 - 08:36:33 PST)
[AMBER] pbsa error: PB Bomb in pb_aaradi(): No radius assigned for atom
- Ray Luo via AMBER (Mon Jan 08 2024 - 10:38:38 PST)
- David A Case via AMBER (Mon Jan 08 2024 - 10:01:37 PST)
- Yang, Li-Yen via AMBER (Mon Jan 08 2024 - 08:53:11 PST)
- Yang, Li-Yen via AMBER (Mon Jan 08 2024 - 07:57:45 PST)
- James Kress via AMBER (Fri Jan 05 2024 - 21:47:09 PST)
- Ray Luo via AMBER (Fri Jan 05 2024 - 20:51:38 PST)
- Yang, Li-Yen via AMBER (Fri Jan 05 2024 - 11:49:55 PST)
[AMBER] Please remove me from mail list
- Jelena Tosovic via AMBER (Fri Jan 26 2024 - 14:03:03 PST)
[AMBER] pmemd.cuda error running MD simulation
- David A Case via AMBER (Sat Jan 20 2024 - 15:13:46 PST)
- Arsene Marian Alain via AMBER (Sat Jan 20 2024 - 06:30:11 PST)
[AMBER] Problem in installing AMBER18
- Carlos Simmerling via AMBER (Mon Jan 22 2024 - 06:20:54 PST)
- Kriti Shukla via AMBER (Mon Jan 22 2024 - 05:40:04 PST)
[AMBER] Problem with autoimage. Overlapping with the Ligand and Protein
- Thomas Cheatham via AMBER (Tue Jan 09 2024 - 18:14:30 PST)
- Gabriel Rocha Dom?nguez via AMBER (Tue Jan 09 2024 - 08:13:36 PST)
[AMBER] Problems with installation
- David A Case via AMBER (Fri Jan 26 2024 - 14:22:14 PST)
- Todd Minehardt via AMBER (Fri Jan 26 2024 - 13:42:36 PST)
- Godbole, Shivani via AMBER (Fri Jan 26 2024 - 13:25:42 PST)
[AMBER] protein alignment and rmsd calculation of protein loop
- Abhilash J via AMBER (Fri Jan 19 2024 - 13:55:36 PST)
[AMBER] Query regading AMBER 22 installation
- David A Case via AMBER (Tue Jan 30 2024 - 08:36:02 PST)
- Saikat Pal via AMBER (Mon Jan 29 2024 - 10:46:32 PST)
[AMBER] Questions about paramfit
- Yang Wei via AMBER (Wed Jan 17 2024 - 07:43:16 PST)
[AMBER] QUICK QM/MM problem/bug
- Juraj Dobias via AMBER (Wed Jan 31 2024 - 01:33:37 PST)
[AMBER] RAMD in AMBER22
- Domenico Marson via AMBER (Thu Jan 11 2024 - 02:29:44 PST)
[AMBER] randomizeions with SIRAH
- Daniel Roe via AMBER (Tue Jan 23 2024 - 07:05:28 PST)
- Daniel Roe via AMBER (Tue Jan 23 2024 - 06:16:48 PST)
- Daniel Roe via AMBER (Tue Jan 23 2024 - 05:28:48 PST)
- Dr. Anselm Horn via AMBER (Tue Jan 23 2024 - 02:39:55 PST)
[AMBER] Regarding constant pH md simulation with Amber
- Baibhabshri Roy via AMBER (Thu Jan 04 2024 - 05:38:33 PST)
[AMBER] Regarding constant pH md simulation with Amber18
- Baibhabshri Roy via AMBER (Thu Jan 04 2024 - 23:55:20 PST)
- cyz228615--- via AMBER (Fri Jan 05 2024 - 00:04:50 PST)
- Vinicius Cruzeiro \(Vinny\) via AMBER (Thu Jan 04 2024 - 13:24:33 PST)
- Hoang, Oanh Tu via AMBER (Thu Jan 04 2024 - 09:51:03 PST)
- cyz228615--- via AMBER (Thu Jan 04 2024 - 09:36:56 PST)
- Baibhabshri Roy via AMBER (Thu Jan 04 2024 - 06:10:21 PST)
[AMBER] restraining specific lipid molecule during equilibration from CHARMM-GUI generated system
- Ryan Woltz via AMBER (Wed Jan 03 2024 - 17:41:07 PST)
[AMBER] Retaining Residue Numbering of GPCR Proteins When Utilising Ambertools for System Preparation
- Todd Minehardt via AMBER (Fri Jan 26 2024 - 14:51:19 PST)
- David A Case via AMBER (Fri Jan 26 2024 - 14:31:33 PST)
- Todd Minehardt via AMBER (Fri Jan 26 2024 - 13:58:09 PST)
- Yu Chen via AMBER (Fri Jan 26 2024 - 13:36:12 PST)
[AMBER] Run error in cuda.MPI
- David A Case via AMBER (Thu Jan 11 2024 - 11:28:28 PST)
- Dulal Mondal via AMBER (Thu Jan 11 2024 - 04:39:32 PST)
[AMBER] Run error on pmemd.cuda.MPI
- David A Case via AMBER (Fri Jan 05 2024 - 12:46:57 PST)
- Dulal Mondal via AMBER (Fri Jan 05 2024 - 03:10:17 PST)
[AMBER] Running Error Amber/ORCA
- Goetz, Andreas via AMBER (Fri Jan 12 2024 - 15:29:11 PST)
- James Kress via AMBER (Wed Jan 10 2024 - 08:53:22 PST)
- David A Case via AMBER (Tue Jan 09 2024 - 07:32:09 PST)
- Kriti Shukla via AMBER (Tue Jan 09 2024 - 07:00:02 PST)
[AMBER] SCF optimization is on "repeat"
- Matthew Guberman-Pfeffer via AMBER (Wed Jan 03 2024 - 13:38:45 PST)
- Ralph Roberts via AMBER (Wed Jan 03 2024 - 13:28:00 PST)
[AMBER] Simulation of protein in solutions of guanidinium Cl
- David A Case via AMBER (Sat Jan 20 2024 - 15:07:47 PST)
- David A Case via AMBER (Wed Jan 17 2024 - 08:44:39 PST)
- Siavoush Dastmalchi via AMBER (Sat Jan 13 2024 - 08:40:41 PST)
- Siavoush Dastmalchi via AMBER (Sat Jan 13 2024 - 04:08:51 PST)
[AMBER] Simulation of ZrO2 (zirconium dioxide)
- Victor Nazarychev via AMBER (Wed Jan 10 2024 - 07:05:42 PST)
[AMBER] Two New AI GPT-Based Assistants for AMBER - CPPTRAJ and AUTODOCK / ASSIGN_V2.PY
- Barış KURT via AMBER (Wed Jan 24 2024 - 18:20:06 PST)
[AMBER] untested CUDA 12.3 for Amber 2022 and pmemd.cuda not found Errors
- David A Case via AMBER (Fri Jan 26 2024 - 14:17:13 PST)
[AMBER] Using tleap sequence command with non-protein
- Mohd Farid Ismail via AMBER (Sun Dec 31 2023 - 17:32:54 PST)
[AMBER] What energy does the keyword 'dielc' change?
- David A Case via AMBER (Sat Jan 20 2024 - 15:12:25 PST)
- Fanyu Zhao via AMBER (Sat Jan 20 2024 - 04:24:37 PST)
[AMBER] whitelisting Amber
- David A Case via AMBER (Thu Jan 11 2024 - 11:16:45 PST)
- Martin Juhás via AMBER (Tue Jan 09 2024 - 07:45:24 PST)
[AMBER] Why the Order of ATOM_TYPE_INDEX Section Matters 1-4 VdWaals
- Carlos Simmerling via AMBER (Mon Jan 22 2024 - 10:22:08 PST)
- Ge Song via AMBER (Mon Jan 22 2024 - 10:17:26 PST)
[AMBER] 回复: [Sender Not Verified] Chain info in .prmtop file
- Dr. Anselm Horn via AMBER (Wed Jan 24 2024 - 08:44:45 PST)
- Shao, Qianzhen via AMBER (Wed Jan 24 2024 - 08:23:59 PST)
[AMBER] 回复: [Sender Not Verified] cpptraj: post-threatment of the PBC for membrane system
- Dr. Anselm Horn via AMBER (Fri Jan 26 2024 - 00:15:49 PST)
Conda installation of Ambertools23 does not [appear to] include 'OMP' programs
- David A Case via AMBER (Thu Jan 11 2024 - 11:23:49 PST)
- Murray, Makay via AMBER (Wed Jan 10 2024 - 12:15:23 PST)
Simulation of protein in solutions of guanidinium Cl
- Siavoush Dastmalchi via AMBER (Wed Jan 17 2024 - 12:00:37 PST)

Amber Archive Jan 2024 by subject