Amber Archive Jan 2024: by date

Sunday, 31 December 2023
- [AMBER] cpptraj hbond measure second order water bridge 鱼翔 via AMBER
- Re: [AMBER] Using tleap sequence command with non-protein Mohd Farid Ismail via AMBER
Monday, 1 January 2024
- [AMBER] Can cpptraj hbond command measure second order water bridge ? xiangyu via AMBER
- [AMBER] Amber to gromacs conversion Sourav Bhowmik via AMBER
- Re: [AMBER] Amber to gromacs conversion Todd Minehardt via AMBER
- Re: [AMBER] Amber to gromacs conversion 王世玉 via AMBER
- [AMBER] MMPBSA calculation Kriti Shukla via AMBER
Tuesday, 2 January 2024
- [AMBER] AMBER constant pH Hoang, Oanh Tu via AMBER
- [AMBER] CpHMD, Amber22, MAX_TITR_RES overflow Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] Failed to genarate parameters in Tleap Todd Minehardt via AMBER
- Re: [AMBER] AMBER constant pH Vinicius Cruzeiro \(Vinny\) via AMBER
- Re: [AMBER] CpHMD, Amber22, MAX_TITR_RES overflow Vinicius Cruzeiro \(Vinny\) via AMBER
- Re: [AMBER] CpHMD, Amber22, MAX_TITR_RES overflow Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] MMPBSA calculation Bill Miller III via AMBER
- [AMBER] Installation of amber22 with nccl Dulal Mondal via AMBER
- [AMBER] Amber22 Compilation Error Matthew Guberman-Pfeffer via AMBER
Wednesday, 3 January 2024
- Re: [AMBER] Amber22 Compilation Error Todd Minehardt via AMBER
- [AMBER] analyze residue charges after constant pH MD simulation Yang, Li-Yen via AMBER
- [AMBER] installation inquiry RUFAIDA AL ZOUBI via AMBER
- [AMBER] Convergence of the diffusion coefficient for single molecules Samuel Holmes via AMBER
- Re: [AMBER] installation inquiry Todd Minehardt via AMBER
- [AMBER] SCF optimization is on "repeat" Ralph Roberts via AMBER
- Re: [AMBER] SCF optimization is on "repeat" Matthew Guberman-Pfeffer via AMBER
- [AMBER] MMPBSA.py error: CalcError: cpptraj failed with prmtop pro_lig.parm7! Yang, Li-Yen via AMBER
- [AMBER] restraining specific lipid molecule during equilibration from CHARMM-GUI generated system Ryan Woltz via AMBER
- Re: [AMBER] MMPBSA.py error: CalcError: cpptraj failed with prmtop pro_lig.parm7! Todd Minehardt via AMBER
- [AMBER] Help with coda-enabled compilation Matthew Guberman-Pfeffer via AMBER
Thursday, 4 January 2024
- [AMBER] cpptraj.MPI mmap error Martin Juhás via AMBER
- [AMBER] Regarding constant pH md simulation with Amber Baibhabshri Roy via AMBER
- [AMBER] Regarding constant pH md simulation with Amber18 Baibhabshri Roy via AMBER
- Re: [AMBER] Help with coda-enabled compilation Todd Minehardt via AMBER
- Re: [AMBER] Help with coda-enabled compilation Charo del Genio via AMBER
- Re: [AMBER] MMPBSA.py error: CalcError: cpptraj failed with prmtop pro_lig.parm7! Todd Minehardt via AMBER
- [AMBER] Regarding constant pH md simulation with Amber18 cyz228615--- via AMBER
- Re: [AMBER] Regarding constant pH md simulation with Amber18 Hoang, Oanh Tu via AMBER
- Re: [AMBER] analyze residue charges after constant pH MD simulation He, Amy via AMBER
- Re: [AMBER] Regarding constant pH md simulation with Amber18 Vinicius Cruzeiro \(Vinny\) via AMBER
- [AMBER] Error in tleap BILASH MAITY via AMBER
Friday, 5 January 2024
- Re: [AMBER] Regarding constant pH md simulation with Amber18 cyz228615--- via AMBER
Thursday, 4 January 2024
- Re: [AMBER] Regarding constant pH md simulation with Amber18 Baibhabshri Roy via AMBER
Friday, 5 January 2024
- [AMBER] Run error on pmemd.cuda.MPI Dulal Mondal via AMBER
- [AMBER] pbsa error: PB Bomb in pb_aaradi(): No radius assigned for atom Yang, Li-Yen via AMBER
- Re: [AMBER] Run error on pmemd.cuda.MPI David A Case via AMBER
- Re: [AMBER] analyze residue charges after constant pH MD simulation Yang, Li-Yen via AMBER
- Re: [AMBER] pbsa error: PB Bomb in pb_aaradi(): No radius assigned for atom Ray Luo via AMBER
- Re: [AMBER] pbsa error: PB Bomb in pb_aaradi(): No radius assigned for atom James Kress via AMBER
Saturday, 6 January 2024
- [AMBER] Can leap create polymer structure using sequence command? Mohd Farid Ismail via AMBER
Monday, 8 January 2024
- Re: [AMBER] pbsa error: PB Bomb in pb_aaradi(): No radius assigned for atom Yang, Li-Yen via AMBER
- Re: [AMBER] pbsa error: PB Bomb in pb_aaradi(): No radius assigned for atom Yang, Li-Yen via AMBER
- Re: [AMBER] pbsa error: PB Bomb in pb_aaradi(): No radius assigned for atom David A Case via AMBER
- Re: [AMBER] pbsa error: PB Bomb in pb_aaradi(): No radius assigned for atom Ray Luo via AMBER
- [AMBER] Conda installation of Ambertools23 does not [appear to] include 'OMP' programs Murray, Makay via AMBER
Tuesday, 9 January 2024
- [AMBER] GAMESS: How to resubmit SCF calculations? Ralph Roberts via AMBER
- [AMBER] Conference announcement: MMWS2024 in Erlangen (Germany) Dr. Anselm Horn via AMBER
- [AMBER] Error during simulation: an illegal memory access was encountered launching kernel kClearForces Barbara Lech via AMBER
- [AMBER] Running Error Amber/ORCA Kriti Shukla via AMBER
- Re: [AMBER] Running Error Amber/ORCA David A Case via AMBER
- [AMBER] whitelisting Amber Martin Juhás via AMBER
- [AMBER] Problem with autoimage. Overlapping with the Ligand and Protein Gabriel Rocha Dom?nguez via AMBER
- Re: [AMBER] Problem with autoimage. Overlapping with the Ligand and Protein Thomas Cheatham via AMBER
Wednesday, 10 January 2024
- [AMBER] Simulation of ZrO2 (zirconium dioxide) Victor Nazarychev via AMBER
- Re: [AMBER] Running Error Amber/ORCA James Kress via AMBER
- Re: [AMBER] [Sender Not Verified] Simulation of ZrO2 (zirconium dioxide) Victor Nazarychev via AMBER
- [AMBER] FW: Conda installation of Ambertools23 does not [appear to] include 'OMP' programs Murray, Makay via AMBER
- Re: [AMBER] [Sender Not Verified] Simulation of ZrO2 (zirconium dioxide) Matthew Guberman-Pfeffer via AMBER
Thursday, 11 January 2024
- [AMBER] RAMD in AMBER22 Domenico Marson via AMBER
- [AMBER] Run error in cuda.MPI Dulal Mondal via AMBER
- Re: [AMBER] [Sender Not Verified] Simulation of ZrO2 (zirconium dioxide) Victor Nazarychev via AMBER
- [AMBER] my RTX 3060 Ti is slower than my RTX 2060 SUPER by 2X Thomas C. Bishop via AMBER
- Re: [AMBER] my RTX 3060 Ti is slower than my RTX 2060 SUPER by 2X Ross Walker via AMBER
- Re: [AMBER] whitelisting Amber David A Case via AMBER
- Re: [AMBER] FW: Conda installation of Ambertools23 does not [appear to] include 'OMP' programs David A Case via AMBER
- Re: [AMBER] Run error in cuda.MPI David A Case via AMBER
Friday, 12 January 2024
- [AMBER] Opening for Amber free energy/GPU developer Darrin York via AMBER
- Re: [AMBER] Running Error Amber/ORCA Goetz, Andreas via AMBER
Saturday, 13 January 2024
- [AMBER] Simulation of protein in solutions of guanidinium Cl Siavoush Dastmalchi via AMBER
- [AMBER] Simulation of protein in solutions of guanidinium Cl Siavoush Dastmalchi via AMBER
Monday, 15 January 2024
- [AMBER] MMGBSA problem VERONICA MARTIN HERNANDEZ via AMBER
- Re: [AMBER] MMGBSA problem Bill Miller III via AMBER
- [AMBER] No restraint defined when using torsional restraints Kari Gaalswyk via AMBER
- Re: [AMBER] No restraint defined when using torsional restraints Carlos Simmerling via AMBER
Tuesday, 16 January 2024
- [AMBER] GPU bug for replica MD with pmemd.cuda.MPI Zhenquan Hu via AMBER
- Re: [AMBER] GPU bug for replica MD with pmemd.cuda.MPI Zhenquan Hu via AMBER
Wednesday, 17 January 2024
- Re: [AMBER] GPU bug for replica MD with pmemd.cuda.MPI Adrian Roitberg via AMBER
- [AMBER] Questions about paramfit Yang Wei via AMBER
- Re: [AMBER] No restraint defined when using torsional restraints David A Case via AMBER
- Re: [AMBER] Simulation of protein in solutions of guanidinium Cl David A Case via AMBER
- Re: [AMBER] GPU bug for replica MD with pmemd.cuda.MPI Zhenquan Hu via AMBER
- [AMBER] Reply: Re: Simulation of protein in solutions of guanidinium Cl Siavoush Dastmalchi via AMBER
Friday, 19 January 2024
- Re: [AMBER] GPU bug for replica MD with pmemd.cuda.MPI Stéphane Téletchéa via AMBER
- [AMBER] protein alignment and rmsd calculation of protein loop Abhilash J via AMBER
- Re: [AMBER] GPU bug for replica MD with pmemd.cuda.MPI Zhenquan Hu via AMBER
- [AMBER] Download Link to Amber20 for Project Compatibility Sharawy, Mahmoud via AMBER
Saturday, 20 January 2024
- [AMBER] What energy does the keyword 'dielc' change? Fanyu Zhao via AMBER
- [AMBER] pmemd.cuda error running MD simulation Arsene Marian Alain via AMBER
- Re: [AMBER] Simulation of protein in solutions of guanidinium Cl David A Case via AMBER
- Re: [AMBER] What energy does the keyword 'dielc' change? David A Case via AMBER
- Re: [AMBER] pmemd.cuda error running MD simulation David A Case via AMBER
Sunday, 21 January 2024
- [AMBER] Atom Index in the BONDS_INC_HYDROGEN Section of Topology Ge Song via AMBER
- Re: [AMBER] Atom Index in the BONDS_INC_HYDROGEN Section of Topology He, Amy via AMBER
- [AMBER] Increased Compactness of Protein-Protein Complex in NVT to NPT Ensemble zhangxiaochun via AMBER
Monday, 22 January 2024
- [AMBER] Problem in installing AMBER18 Kriti Shukla via AMBER
- Re: [AMBER] Problem in installing AMBER18 Carlos Simmerling via AMBER
- [AMBER] Why the Order of ATOM_TYPE_INDEX Section Matters 1-4 VdWaals Ge Song via AMBER
- Re: [AMBER] Why the Order of ATOM_TYPE_INDEX Section Matters 1-4 VdWaals Carlos Simmerling via AMBER
- [AMBER] Issue Linking C Shared Library libcifparse.so during AmberTools22 and Amber22 Installation (with INTEL ICX instead of ICC) 디와쉬시 다스 via AMBER
- Re: [AMBER] Issue Linking C Shared Library libcifparse.so during AmberTools22 and Amber22 Installation (with INTEL ICX instead of ICC) David A Case via AMBER
- [AMBER] fatal error: Windows.h: No such file or directory Jesse Aiton via AMBER
- Re: [AMBER] fatal error: Windows.h: No such file or directory K A SIVASANKER via AMBER
Tuesday, 23 January 2024
- [AMBER] randomizeions with SIRAH Dr. Anselm Horn via AMBER
- Re: [AMBER] randomizeions with SIRAH Daniel Roe via AMBER
- Re: [AMBER] randomizeions with SIRAH Daniel Roe via AMBER
- Re: [AMBER] randomizeions with SIRAH Daniel Roe via AMBER
- Re: [AMBER] fatal error: Windows.h: No such file or directory Jesse Aiton via AMBER
- Re: [AMBER] fatal error: Windows.h: No such file or directory Jesse Aiton via AMBER
- [AMBER] Instalation errors of amber 22 on ubuntu22.04 Ming Tang via AMBER
- Re: [AMBER] fatal error: Windows.h: No such file or directory Jesse Aiton via AMBER
- [AMBER] Chain info in .prmtop file Shao, Qianzhen via AMBER
- Re: [AMBER] [Sender Not Verified] Chain info in .prmtop file Steinbrecher, Thomas via AMBER
Wednesday, 24 January 2024
- [AMBER] MMPBSA Stability Calculations Ramdhan,Peter A via AMBER
- [AMBER] 回复: [Sender Not Verified] Chain info in .prmtop file Shao, Qianzhen via AMBER
- Re: [AMBER] 回复: [Sender Not Verified] Chain info in .prmtop file Dr. Anselm Horn via AMBER
- [AMBER] cpptraj: post-threatment of the PBC for membrane system Enrico Martinez via AMBER
- Re: [AMBER] MMPBSA Stability Calculations Bill Miller III via AMBER
- Re: [AMBER] Instalation errors of amber 22 on ubuntu22.04 David A Case via AMBER
- Re: [AMBER] Chain info in .prmtop file David A Case via AMBER
- [AMBER] Two New AI GPT-Based Assistants for AMBER - CPPTRAJ and AUTODOCK / ASSIGN_V2.PY Barış KURT via AMBER
- Re: [AMBER] Chain info in .prmtop file Shao, Qianzhen via AMBER
Thursday, 25 January 2024
- Re: [AMBER] [Sender Not Verified] cpptraj: post-threatment of the PBC for membrane system Enrico Martinez via AMBER
Friday, 26 January 2024
- Re: [AMBER] 回复: [Sender Not Verified] cpptraj: post-threatment of the PBC for membrane system Dr. Anselm Horn via AMBER
- [AMBER] Disparities when comparing Coulomb energies between cpptraj and Gromacs Albert Gauss via AMBER
- Re: [AMBER] Disparities when comparing Coulomb energies between cpptraj and Gromacs Albert Gauss via AMBER
- Re: [AMBER] Disparities when comparing Coulomb energies between cpptraj and Gromacs Albert Gauss via AMBER
- Re: [AMBER] Disparities when comparing Coulomb energies between cpptraj and Gromacs Adrian Roitberg via AMBER
- Re: [AMBER] Disparities when comparing Coulomb energies between cpptraj and Gromacs Carlos Simmerling via AMBER
- Re: [AMBER] Disparities when comparing Coulomb energies between cpptraj and Gromacs David A Case via AMBER
- [AMBER] Problems with installation Godbole, Shivani via AMBER
- [AMBER] Retaining Residue Numbering of GPCR Proteins When Utilising Ambertools for System Preparation Yu Chen via AMBER
- Re: [AMBER] Problems with installation Todd Minehardt via AMBER
- Re: [AMBER] Retaining Residue Numbering of GPCR Proteins When Utilising Ambertools for System Preparation Todd Minehardt via AMBER
- [AMBER] Please remove me from mail list Jelena Tosovic via AMBER
- Re: [AMBER] untested CUDA 12.3 for Amber 2022 and pmemd.cuda not found Errors David A Case via AMBER
- Re: [AMBER] Problems with installation David A Case via AMBER
- Re: [AMBER] Retaining Residue Numbering of GPCR Proteins When Utilising Ambertools for System Preparation David A Case via AMBER
- Re: [AMBER] Retaining Residue Numbering of GPCR Proteins When Utilising Ambertools for System Preparation Todd Minehardt via AMBER
Monday, 29 January 2024
- [AMBER] How to set periodic boundary conditions for a membrane protein system? Kikuchi, Shinichi via AMBER
- [AMBER] DFTB3 and MMPBSA.py CA Mattelaer via AMBER
- Re: [AMBER] How to set periodic boundary conditions for a membrane protein system? David A Case via AMBER
- [AMBER] Parameters and charges for polymer functionalized with sugars (GLYCAM, GAFF ?) David DELLEMME via AMBER
- [AMBER] Query regading AMBER 22 installation Saikat Pal via AMBER
- [AMBER] Best practises for running MD with RNA structures Debarati DasGupta via AMBER
Tuesday, 30 January 2024
- Re: [AMBER] MMPBSA Stability Calculations Dr. Anselm Horn via AMBER
- [AMBER] AMBER22 and AmberTools23 installation issue Ildar Garipov via AMBER
- Re: [AMBER] Best practises for running MD with RNA structures Darrin York via AMBER
- Re: [AMBER] AMBER22 and AmberTools23 installation issue Todd Minehardt via AMBER
- Re: [AMBER] Query regading AMBER 22 installation David A Case via AMBER
Wednesday, 31 January 2024
- [AMBER] QUICK QM/MM problem/bug Juraj Dobias via AMBER
- [AMBER] MMPBSA.py reports ESCF for receptor when only ligand is chosen as QM region CA Mattelaer via AMBER
- [AMBER] Generating tleap input files for an organomtallic complex MADHUSMITA DEVI via AMBER

Last message date: Wed Jan 31 2024 - 11:30:02 PST
Archived on: Wed May 08 2024 - 05:56:05 PDT

Amber Archive Jan 2024 by date