Amber Archive May 2024: by date

Wednesday, 1 May 2024
- [AMBER-Developers] Release of Amber24 and AmberTools24 David A Case via AMBER-Developers
- Re: [AMBER] Interpretation of Native contacts analysis output in cpptraj Shah, Tejas V. via AMBER
Friday, 3 May 2024
- Re: [AMBER] Release of Amber24 and AmberTools24 Dr. Anselm Horn via AMBER
- [AMBER] Problems with amber24 installation Elvis Martis via AMBER
- Re: [AMBER] Cpptraj vs Leap residue number overflow David A Case via AMBER
- Re: [AMBER] Atom types more than 2 characters David A Case via AMBER
- Re: [AMBER] Thermodynamic Integration calculation: David A Case via AMBER
- [AMBER] Atom type not found for RNA Kavinda Kashi Juliyan Gunasinghe via AMBER
Saturday, 4 May 2024
- Re: [AMBER] Atom type not found for RNA Carlos Simmerling via AMBER
- [AMBER] Absolute simulation box size Istvan Kolossvary via AMBER
Sunday, 5 May 2024
- [AMBER] NetCDF variable compression requires compiling with HDF5 support Martin Juhás via AMBER
Monday, 6 May 2024
- [AMBER] Cpptraj distance for multiple copies of ligand vs protein Alexander Hung Lee via AMBER
- Re: [AMBER] Cpptraj distance for multiple copies of ligand vs protein Martin Juhás via AMBER
- Re: [AMBER] [EXTERNAL] Release of Amber24 and AmberTools24 Chakrabarti, Mayukh \(NIH/NCI\) \[C\] via AMBER
- Re: [AMBER] Cpptraj distance for multiple copies of ligand vs protein Daniel Roe via AMBER
- [AMBER] Does pdb4amber take care of protonation states? Abdelrahman, Noureen via AMBER
- Re: [AMBER] Does pdb4amber take care of protonation states? He, Amy via AMBER
- Re: [AMBER] Does pdb4amber take care of protonation states? David A Case via AMBER
Tuesday, 7 May 2024
- [AMBER] Alchemical membrane simulations with the AMBER TI code William Glass via AMBER
- [AMBER] Amber force fields for 5-Methylcytosine Nucleotide RNA Penumutchu, Srinivasa via AMBER
- [AMBER] Problems compiling with openHPC netcdf/-fortran Martin Juhás via AMBER
- Re: [AMBER] Amber force fields for 5-Methylcytosine Nucleotide RNA SATYAJIT KHATUA via AMBER
- Re: [AMBER] Alchemical membrane simulations with the AMBER TI code Dickson, Callum via AMBER
- Re: [AMBER] Problems compiling with openHPC netcdf/-fortran Martin Juhás via AMBER
- Re: [AMBER] Amber22/AmberTools23: Enabling of libtorch & cudnn libraries breaks pbsa binaries Chakrabarti, Mayukh \(NIH/NCI\) \[C\] via AMBER
- [AMBER] How to add new lipids into packmol-memgen for CHARMM Evan Collins via AMBER
- Re: [AMBER] How to add new lipids into packmol-memgen for CHARMM Stephan Schott via AMBER
- [AMBER] Call for papers - 18th German Conference on Cheminformatics (GCC 2024) Guessregen, Stefan /DE via AMBER
Wednesday, 8 May 2024
- Re: [AMBER] Amber22/AmberTools23: Enabling of libtorch & cudnn libraries breaks pbsa binaries Ray Luo via AMBER
- Re: [AMBER] [EXTERNAL] Re: Amber22/AmberTools23: Enabling of libtorch & cudnn libraries breaks pbsa binaries Chakrabarti, Mayukh \(NIH/NCI\) \[C\] via AMBER
Thursday, 9 May 2024
- [AMBER] Runtime errors when using nmropt restraints Pye, Aaron Wesley via AMBER
- Re: [AMBER] Runtime errors when using nmropt restraints David A Case via AMBER
- Re: [AMBER] Amber force fields for 5-Methylcytosine Nucleotide RNA SATYAJIT KHATUA via AMBER
- [AMBER] Assistance with tleap Xylia Peters via AMBER
- Re: [AMBER] Assistance with tleap Carlos Simmerling via AMBER
- Re: [AMBER] Assistance with tleap Carlos Simmerling via AMBER
- [AMBER] printcharges using Amber24 GFN2-xtB method Niven Singh via AMBER
- Re: [AMBER] [EXTERNAL] Re: Amber22/AmberTools23: Enabling of libtorch & cudnn libraries breaks pbsa binaries Yongxian Wu via AMBER
- [AMBER] gnuplot of DCCM map Priyasha Majee via AMBER
Friday, 10 May 2024
- [AMBER] Restarting constant pH replica exchange MD Dulal Mondal via AMBER
- [AMBER] Errors using the ZAFF Modeling Tutorials with Center ID 4 saverio lemme via AMBER
- Re: [AMBER] Assistance with tleap Carlos Simmerling via AMBER
- Re: [AMBER] [EXTERNAL] Re: Amber22/AmberTools23: Enabling of libtorch & cudnn libraries breaks pbsa binaries Chakrabarti, Mayukh \(NIH/NCI\) \[C\] via AMBER
- [AMBER] Multiple types of water for SHAKE Tucker E. Burgin via AMBER
- Re: [AMBER] gnuplot of DCCM map Hector A. Baldoni via AMBER
- Re: [AMBER] Does pdb4amber take care of protonation states? Abdelrahman, Noureen via AMBER
- [AMBER] tleap can't distinguish two protein chains even though I used TER Abdelrahman, Noureen via AMBER
- Re: [AMBER] tleap can't distinguish two protein chains even though I used TER David A Case via AMBER
- Re: [AMBER] Restarting constant pH replica exchange MD He, Amy via AMBER
Saturday, 11 May 2024
- [AMBER] Regarding Advanced Thermodyanmic Integration Methods to mutate a ligand bound to a protein tutorial: Kankana Bhattacharjee via AMBER
- Re: [AMBER] Restarting constant pH replica exchange MD Dulal Mondal via AMBER
- Re: [AMBER] Restarting constant pH replica exchange MD Dulal Mondal via AMBER
- Re: [AMBER] Restarting constant pH replica exchange MD He, Amy via AMBER
- Re: [AMBER] [EXTERNAL] Re: Amber22/AmberTools23: Enabling of libtorch & cudnn libraries breaks pbsa binaries Yongxian Wu via AMBER
Monday, 13 May 2024
- [AMBER] Specifying a mask with scale in PARMED Ford, Baily Wayne via AMBER
- Re: [AMBER] Specifying a mask with scale in PARMED Carlos Simmerling via AMBER
- Re: [AMBER] [EXTERNAL] Re: Amber22/AmberTools23: Enabling of libtorch & cudnn libraries breaks pbsa binaries Chakrabarti, Mayukh \(NIH/NCI\) \[C\] via AMBER
- [AMBER] Register Now! Amber Free Energy Workshop 2024 at SDSC/UCSD, Aug. 12-16 Darrin York via AMBER
- Re: [AMBER] Register Now! Amber Free Energy Workshop 2024 at SDSC/UCSD, Aug. 12-16 King Wang via AMBER
Tuesday, 14 May 2024
- [AMBER] Gaussian accelerated (GAMD) Question Ramdhan,Peter A via AMBER
- Re: [AMBER] Regarding Advanced Thermodyanmic Integration Methods to mutate a ligand bound to a protein tutorial: David A Case via AMBER
- Re: [AMBER] [EXTERNAL] Re: Amber22/AmberTools23: Enabling of libtorch & cudnn libraries breaks pbsa binaries Chakrabarti, Mayukh \(NIH/NCI\) \[C\] via AMBER
Wednesday, 15 May 2024
- [AMBER] Parameters for HEM residues Enrico Martinez via AMBER
- Re: [AMBER] printcharges using Amber24 GFN2-xtB method Timothy Giese via AMBER
Thursday, 16 May 2024
- [AMBER] Changed atom name in NME cap residue library Jong Young Joung via AMBER
- [AMBER] Implicit solvent simulation of membrane system Enrico Martinez via AMBER
- Re: [AMBER] Implicit solvent simulation of membrane system Enrico Martinez via AMBER
- Re: [AMBER] [EXTERNAL] Re: Amber22/AmberTools23: Enabling of libtorch & cudnn libraries breaks pbsa binaries Ray Luo via AMBER
Friday, 17 May 2024
- Re: [AMBER] Implicit solvent simulation of membrane system Enrico Martinez via AMBER
- Re: [AMBER] Implicit solvent simulation of membrane system Enrico Martinez via AMBER
- [AMBER] Fwd: bug report and gmail filtering amber digest Ross Walker via AMBER
- [AMBER] bug in cpptraj from amber tools 24 related to dcd trajectories ? Vlad Cojocaru via AMBER
- Re: [AMBER] bug in cpptraj from amber tools 24 related to dcd trajectories ? Daniel Roe via AMBER
- Re: [AMBER] Fwd: bug report and gmail filtering amber digest Ryan Snyder via AMBER
- [AMBER] TIP 3P IONS Ramírez, Gustavo via AMBER
- [AMBER] pmemd.cuda does not reflect the PLUMED-contributed potential energy for replica exchange probabilities Miroslav Krepl via AMBER
- Re: [AMBER] TIP 3P IONS David A Case via AMBER
- [AMBER] mcwat does not work in amber24 Juraj Dobias via AMBER
- Re: [AMBER] printcharges using Amber24 GFN2-xtB method Niven Singh via AMBER
Saturday, 18 May 2024
- Re: [AMBER] bug in cpptraj from amber tools 24 related to dcd trajectories ? Daniel Roe via AMBER
- Re: [AMBER] mcwat does not work in amber24 Carlos Simmerling via AMBER
- Re: [AMBER] bug in cpptraj from amber tools 24 related to dcd trajectories ? Daniel Roe via AMBER
- Re: [AMBER] mcwat does not work in amber24 Juraj Dobias via AMBER
- Re: [AMBER] bug in cpptraj from amber tools 24 related to dcd trajectories ? Daniel Roe via AMBER
Sunday, 19 May 2024
- Re: [AMBER] bug in cpptraj from amber tools 24 related to dcd trajectories ? Daniel Roe via AMBER
Monday, 20 May 2024
- [AMBER] Regarding using two basis sets in QUICK Kriti Shukla via AMBER
- [AMBER] Merge cpout files to analyze full simulation Abdelrahman, Noureen via AMBER
- Re: [AMBER] Merge cpout files to analyze full simulation He, Amy via AMBER
- Re: [AMBER] printcharges using Amber24 GFN2-xtB method Timothy Giese via AMBER
- Re: [AMBER] Regarding using two basis sets in QUICK Goetz, Andreas via AMBER
- Re: [AMBER] Merge cpout files to analyze full simulation Abdelrahman, Noureen via AMBER
- Re: [AMBER] Merge cpout files to analyze full simulation He, Amy via AMBER
- Re: [AMBER] Merge cpout files to analyze full simulation Abdelrahman, Noureen via AMBER
Tuesday, 21 May 2024
- [AMBER] Bond not formed in tleap for DNA phosphate Vaibhav Bhatt via AMBER
- Re: [AMBER] Merge cpout files to analyze full simulation He, Amy via AMBER
- Re: [AMBER] Bond not formed in tleap for DNA phosphate Carlos Simmerling via AMBER
Wednesday, 22 May 2024
- [AMBER] Error in production extension Priyasha Majee via AMBER
- [AMBER] Installing Amber24 in M3 Mac Marc Ciruela Jardí via AMBER
- Re: [AMBER] Error in production extension Carlos Simmerling via AMBER
- Re: [AMBER] Error in production extension Daniel Roe via AMBER
Thursday, 23 May 2024
- [AMBER] default lambda-sheduling in amber24 Juraj Dobias via AMBER
- [AMBER] Query on ASMD vs SMD Sruthi Sudhakar via AMBER
- [AMBER] easybuild for amber24 Mooers, Blaine H.M. \(HSC\) via AMBER
Friday, 24 May 2024
- [AMBER] Proper way of using external OFF library files Danial Yousefi via AMBER
- [AMBER] Suspicion pKa shift in Constant pH Molecular Dynamics simulation Abuhasan, Osama via AMBER
- [AMBER] Regarding GIST analysis Jenny 148 via AMBER
- Re: [AMBER] Installing Amber24 in M3 Mac Stephan Schott via AMBER
- Re: [AMBER] Installing Amber24 in M3 Mac KazuoOhta via AMBER
- Re: [AMBER] Installing Amber24 in M3 Mac KazuoOhta via AMBER
Saturday, 25 May 2024
- [AMBER] amber19sb atom types doubts Jones De Andrade via AMBER
- Re: [AMBER] amber19sb atom types doubts Carlos Simmerling via AMBER
- [AMBER] License in Exxact workstation Ali Saad via AMBER
- Re: [AMBER] easybuild for amber24 David A Case via AMBER
- Re: [AMBER] License in Exxact workstation Carlos Simmerling via AMBER
- Re: [AMBER] Suspicion pKa shift in Constant pH Molecular Dynamics simulation David A Case via AMBER
- Re: [AMBER] License in Exxact workstation David A Case via AMBER
Monday, 27 May 2024
- [AMBER] Regarding FE_Workflow tool : Kankana Bhattacharjee via AMBER
- [AMBER] Regarding CG protein and Bilayer: Kankana Bhattacharjee via AMBER
- Re: [AMBER] Regarding FE_Workflow tool : Ryan Snyder via AMBER
- [AMBER] Question regarding SMD simulation of ligand-receptor system Frederico Henrique Ferreira via AMBER
- Re: [AMBER] Question regarding SMD simulation of ligand-receptor system Carlos Simmerling via AMBER
- Re: [AMBER] Regarding CG protein and Bilayer: David A Case via AMBER
- Re: [AMBER] Regarding FE_Workflow tool : Kankana Bhattacharjee via AMBER
- [AMBER] Query Regarding AMBER Advanced Thermodynamic Integration calculation: Kankana Bhattacharjee via AMBER
Tuesday, 28 May 2024
- Re: [AMBER] Regarding Packmol-Memgen: Stephan Schott via AMBER
- Re: [AMBER] Regarding Packmol-Memgen: Kankana Bhattacharjee via AMBER
- Re: [AMBER] Query Regarding AMBER Advanced Thermodynamic Integration calculation: Timothy Giese via AMBER
- Re: [AMBER] Regarding FE_Workflow tool : Timothy Giese via AMBER
- Re: [AMBER] Suspicion pKa shift in Constant pH Molecular Dynamics simulation David A Case via AMBER
- [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! AMANPREET KAUR via AMBER
Wednesday, 29 May 2024
- [AMBER] Problem with ZAFF Modeling Tutorial Center ID 4 saverio lemme via AMBER
- Re: [AMBER] Problem with ZAFF Modeling Tutorial Center ID 4 Erdem Yeler via AMBER
- Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Timothy Giese via AMBER
- [AMBER] NMR restraints slowing down simulations Skanda Sastry via AMBER
Thursday, 30 May 2024
- [AMBER] Installation of AMBER-18 Kriti Shukla via AMBER
- Re: [AMBER] Installation of AMBER-18 David A Case via AMBER
Friday, 31 May 2024
- [AMBER] Quantum mechanical calculation for charge Kriti Shukla via AMBER
- Re: [AMBER] Quantum mechanical calculation for charge Timothy Giese via AMBER
- [AMBER] Using TCPB with Terachem in Amber Abdelrahman, Noureen via AMBER
- Re: [AMBER] Using TCPB with Terachem in Amber Carlos Simmerling via AMBER
- Re: [AMBER] Using TCPB with Terachem in Amber Carlos Simmerling via AMBER

Last message date: Fri May 31 2024 - 14:00:02 PDT
Archived on: Mon Sep 16 2024 - 05:56:16 PDT

Amber Archive May 2024 by date