Amber Archive Jul 2023: by date

Sunday, 2 July 2023
- Re: [AMBER] 回复: Keyerror about mmpbsa ZangRiran via AMBER
- [AMBER] Kerror about mmpbsa ZangRiran via AMBER
- Re: [AMBER] Kerror about MMPBSA Bill Miller III via AMBER
- [AMBER] QM+Link final coordinates Hector A. Baldoni via AMBER
- Re: [AMBER] QM+Link final coordinates Ross Walker via AMBER
- [AMBER] 回复: Kerror about MMPBSA Huang ZiJian via AMBER
Monday, 3 July 2023
- Re: [AMBER] 回复: Kerror about MMPBSA ZangRiran via AMBER
- Re: [AMBER] 回复: Kerror about MMPBSA SATYAJIT KHATUA via AMBER
- Re: [AMBER] QM+Link final coordinates Hector A. Baldoni via AMBER
- Re: [AMBER] unsuscribe Sara Mahmoud via AMBER
- Re: [AMBER] unsuscribe Ryan Novosielski via AMBER
- Re: [AMBER] unsuscribe Sara Mahmoud via AMBER
- [AMBER] output structure from tleap! Singh, Swapnil via AMBER
- Re: [AMBER] output structure from tleap! Carlos Simmerling via AMBER
Tuesday, 4 July 2023
- [AMBER] Original chain records in the prepared pdb Enrico Martinez via AMBER
- [AMBER] Amber22 Installation Waqqas Zia via AMBER
- Re: [AMBER] Amber22 Installation David Case via AMBER
- [AMBER] Short hydrogen bonds Siddhique via AMBER
- [AMBER] AmberTools23 changes antechamber behavior for GAFF2 John Chodera via AMBER
- [AMBER] [amber] ph constant simulation question Yang, Li-Yen via AMBER
- Re: [AMBER] [amber] ph constant simulation question SATYAJIT KHATUA via AMBER
- Re: [AMBER] AmberTools23 changes antechamber behavior for GAFF2 Junmei Wang via AMBER
- [AMBER] Error while running mmpbsa Riran via AMBER
- Re: [AMBER] Error while running mmpbsa SATYAJIT KHATUA via AMBER
Wednesday, 5 July 2023
- [AMBER] Capping the N and C residues of protein Enrico Martinez via AMBER
- Re: [AMBER] Original chain records in the prepared pdb Enrico Martinez via AMBER
- [AMBER] Multiple thermostats within one simulation Dmitry Suplatov via AMBER
- Re: [AMBER] [Sender Not Verified] Capping the N and C residues of protein Enrico Martinez via AMBER
- Re: [AMBER] AmberTools23 changes antechamber behavior for GAFF2 Junmei Wang via AMBER
- Re: [AMBER] [Sender Not Verified] Capping the N and C residues of protein Enrico Martinez via AMBER
Thursday, 6 July 2023
- [AMBER] Typo in amber manual German P. Barletta via AMBER
- Re: [AMBER] unsuscribe Giulia Sormani via AMBER
- [AMBER] How to deal with the metal center contain a phosphorylated amino acid by MCPB.py 吕思凡 via AMBER
- Re: [AMBER] cpptraj and nastruct Daniel Roe via AMBER
- [AMBER] Rmsf profile after removing periodicity Enrico Martinez via AMBER
- Re: [AMBER] AmberTools23 changes antechamber behavior for GAFF2 brian.radak--- via AMBER
Friday, 7 July 2023
- [AMBER] RESP fitting with constraints, qout output charges NaN Albert Gauss via AMBER
- Re: [AMBER] [Sender Not Verified] Rmsf profile after removing periodicity Enrico Martinez via AMBER
- Re: [AMBER] [Sender Not Verified] Rmsf profile after removing periodicity Enrico Martinez via AMBER
- [AMBER] Facing difficulty in performing Amber Crystal simulations KAJAL ABROL via AMBER
- Re: [AMBER] Facing difficulty in performing Amber Crystal simulations Maria Nagan via AMBER
- [AMBER] Atom mask corresponded to first or last residues Enrico Martinez via AMBER
- Re: [AMBER] cpptraj and nastruct Daniel Roe via AMBER
- Re: [AMBER] cpptraj and nastruct David A Case via AMBER
- Re: [AMBER] How to deal with the metal center contain a phosphorylated amino acid by MCPB.py David A Case via AMBER
- Re: [AMBER] Error while running mmpbsa David A Case via AMBER
- Re: [AMBER] cpptraj and nastruct Daniel Roe via AMBER
Sunday, 9 July 2023
- Re: [AMBER] Atom mask corresponded to first or last residues Enrico Martinez via AMBER
Monday, 10 July 2023
- [AMBER] Facing difficulty in performing Amber Crystal simulations KAJAL ABROL via AMBER
- Re: [AMBER] Facing difficulty in performing Amber Crystal simulations Carlos Simmerling via AMBER
- Re: [AMBER] cpptraj and nastruct Daniel Roe via AMBER
- Re: [AMBER] Facing difficulty in performing Amber Crystal simulations David A Case via AMBER
- Re: [AMBER] Facing difficulty in performing Amber Crystal simulations KAJAL ABROL via AMBER
- [AMBER] how to remove/delete bonds w/ cpptraj or parmed in pytraj ?? Thomas C. Bishop via AMBER
- [AMBER] AMBER aMD tutorial Prithviraj Nandigrami via AMBER
- [AMBER] NAMD TO AMBER Ramachandran, Balajee via AMBER
Tuesday, 11 July 2023
- Re: [AMBER] NAMD TO AMBER Vlad Cojocaru via AMBER
- Re: [AMBER] cpptraj and nastruct Daniel Roe via AMBER
- Re: [AMBER] Error while running mmpbsa Riran via AMBER
- [AMBER] Error about sander Riran via AMBER
- Re: [AMBER] [Sender Not Verified] Error about sander Steinbrecher, Thomas via AMBER
Wednesday, 12 July 2023
- [AMBER] Facing problem with Ambertools topological files fateme haghighi via AMBER
- Re: [AMBER] Short hydrogen bonds Siddhique via AMBER
- Re: [AMBER] Facing problem with Ambertools topological files Carlos Simmerling via AMBER
- Re: [AMBER] Error about sander Daniel Roe via AMBER
- Re: [AMBER] how to remove/delete bonds w/ cpptraj or parmed in pytraj ?? Daniel Roe via AMBER
- Re: [AMBER] how to remove/delete bonds w/ cpptraj or parmed in pytraj ?? Thomas C Bishop via AMBER
- Re: [AMBER] Error while running mmpbsa Bill Miller III via AMBER
Thursday, 13 July 2023
- [AMBER] Amber 22 compilation FyD via AMBER
- Re: [AMBER] Error about sander David A Case via AMBER
- [AMBER] Methylated DNA simulation Sneha Kandapal via AMBER
- [AMBER] pressure control in constant ph simulation Yang, Li-Yen via AMBER
- Re: [AMBER] Methylated DNA simulation Rodrigo Galindo-Murillo via AMBER
- [AMBER] Crystal Simulation, protein broken across unit cell Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] Methylated DNA simulation Rodrigo Galindo-Murillo via AMBER
Friday, 14 July 2023
- Re: [AMBER] [Sender Not Verified] Crystal Simulation, protein broken across unit cell Steinbrecher, Thomas via AMBER
- [AMBER] Conversion of NAMD to Amber Ramachandran, Balajee via AMBER
- Re: [AMBER] Amber 22 compilation FyD via AMBER
- Re: [AMBER] Amber 22 compilation David A Case via AMBER
- Re: [AMBER] Conversion of NAMD to Amber David A Case via AMBER
- [AMBER] pressure control question Yang, Li-Yen via AMBER
- Re: [AMBER] pressure control question Vinicius Wilian Cruzeiro via AMBER
- Re: [AMBER] Conversion of NAMD to Amber Ramachandran, Balajee via AMBER
- Re: [AMBER] Amber 22 compilation FyD via AMBER
Sunday, 16 July 2023
- [AMBER] Error running MCPB.py script step3 Ritwika Chatterjee via AMBER
Monday, 17 July 2023
- [AMBER] Error in generating prmtop and inpcrd file Priyasha Majee via AMBER
- [AMBER] [fglaser.technion.ac.il: Fwd: MaxNumberTIAtom on PPI-GaMD - BUG?] David A Case via AMBER
- Re: [AMBER] Error in generating prmtop and inpcrd file David A Case via AMBER
- Re: [AMBER] pressure control question Yang, Li-Yen via AMBER
- [AMBER] RMS Fluctuation limit and difference in Temperature maximum Density (TMD) Zafar,Muhammad Saqlain via AMBER
- [AMBER] Compare trajectories yunshi11 via AMBER
Tuesday, 18 July 2023
- [AMBER] How to build a protein simulation in gaseous environment? Sayan Poddar via AMBER
- Re: [AMBER] Compare trajectories Dr. Anselm Horn via AMBER
- Re: [AMBER] pressure control question Adrian Roitberg via AMBER
- [AMBER] DNA topology file error Sneha Kandapal via AMBER
- Re: [AMBER] pressure control question David A Case via AMBER
- Re: [AMBER] RMS Fluctuation limit and difference in Temperature maximum Density (TMD) David A Case via AMBER
- Re: [AMBER] DNA topology file error David A Case via AMBER
- [AMBER] Zn protease Hector A. Baldoni via AMBER
- Re: [AMBER] [Sender Not Verified] How to build a protein simulation in gaseous environment? Steinbrecher, Thomas via AMBER
Wednesday, 19 July 2023
- Re: [AMBER] [Sender Not Verified] Re: Capping the N and C residues of protein Enrico Martinez via AMBER
- Re: [AMBER] [Sender Not Verified] Re: Capping the N and C residues of protein Enrico Martinez via AMBER
- Re: [AMBER] pressure control question Vinicius Wilian Cruzeiro via AMBER
- [AMBER] Problem with time records in cpout- files in REMD CpHMD simulation Elvira Tarasova via AMBER
- Re: [AMBER] RMS Fluctuation limit and difference in Temperature maximum Density (TMD) David A Case via AMBER
- [AMBER] MMPBSA error Ramachandran, Balajee via AMBER
- Re: [AMBER] MMPBSA error Bill Miller III via AMBER
Thursday, 20 July 2023
- [AMBER] Problems running a membrane-bound protein with ATP-Mg complex using CHARMM-GUI parameters Markowska
- [AMBER] cutoff for pH constant simulation Yang, Li-Yen via AMBER
- Re: [AMBER] cutoff for pH constant simulation Carlos Simmerling via AMBER
Friday, 21 July 2023
- [AMBER] Position restrains on the part of structure Enrico Martinez via AMBER
- Re: [AMBER] [Sender Not Verified] Position restrains on the part of structure Enrico Martinez via AMBER
- Re: [AMBER] [Sender Not Verified] Position restrains on the part of structure Enrico Martinez via AMBER
- [AMBER] pGM force field files? Jones De Andrade via AMBER
- Re: [AMBER] [Sender Not Verified] Position restrains on the part of structure Enrico Martinez via AMBER
- Re: [AMBER] pGM force field files? Ray Luo via AMBER
Sunday, 23 July 2023
- [AMBER] TIP5P water model parameter files issue Zafar,Muhammad Saqlain via AMBER
Monday, 24 July 2023
- [AMBER] AMD hardware support Gerardo Zerbetto De Palma via AMBER
- Re: [AMBER] [Sender Not Verified] Position restrains on the part of structure Enrico Martinez via AMBER
- Re: [AMBER] pGM force field files? Shiji Zhao via AMBER
- Re: [AMBER] TIP5P water model parameter files issue David A Case via AMBER
- Re: [AMBER] Thermodynamic Integration problems Carlos Simmerling via AMBER
- [AMBER] Thermodynamic Integration problems Prokopios Andrikopoulos via AMBER
- Re: [AMBER] Thermodynamic Integration problems Carlos Simmerling via AMBER
- Re: [AMBER] Thermodynamic Integration problems Maria Nagan via AMBER
- Re: [AMBER] Thermodynamic Integration problems Maria Nagan via AMBER
- Re: [AMBER] Thermodynamic Integration problems accuratefreeenergy--- via AMBER
- Re: [AMBER] Thermodynamic Integration problems Shi Zhang via AMBER
- [AMBER] PyRESP tutorial available Shiji Zhao via AMBER
- Re: [AMBER] TIP5P water model parameter files issue Zafar,Muhammad Saqlain via AMBER
- Re: [AMBER] Compare trajectories yunshi11 via AMBER
Tuesday, 25 July 2023
- [AMBER] Force field parameters for Fructose-1,6-biphosphate ANANDITA MITRA via AMBER
- Re: [AMBER] Thermodynamic Integration problems Prokopios Andrikopoulos via AMBER
- [AMBER] smaller cutoff resulting in NaNs Yang, Li-Yen via AMBER
- Re: [AMBER] smaller cutoff resulting in NaNs Carlos Simmerling via AMBER
Wednesday, 26 July 2023
- [AMBER] Query regarding Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Munazzah Fatima Ansari via AMBER
- [AMBER] Aligning MD snapshots excluding loops Bhattacharjee, Sinjini via AMBER
- Re: [AMBER] [Sender Not Verified] Aligning MD snapshots excluding loops Steinbrecher, Thomas via AMBER
- Re: [AMBER] TIP5P water model parameter files issue David A Case via AMBER
- Re: [AMBER] TIP5P water model parameter files issue Zafar,Muhammad Saqlain via AMBER
- Re: [AMBER] Thermodynamic Integration problems accuratefreeenergy--- via AMBER
- Re: [AMBER] TIP5P water model parameter files issue SATYAJIT KHATUA via AMBER
- [AMBER] How to neutralize charge after replacing the charges calculated by antechamber Amin Sagar via AMBER
- [AMBER] Opening Job at UIUC VMD development team Md Fulbabu Sk via AMBER
Thursday, 27 July 2023
- Re: [AMBER] How to neutralize charge after replacing the charges calculated by antechamber Dr. Anselm Horn via AMBER
- [AMBER] query SOMA ROY via AMBER
- [AMBER] mpi4py build fails in AmberTools23 installation Kotaro TANAKA via AMBER
- Re: [AMBER] TIP5P water model parameter files issue Brent Krueger via AMBER
- Re: [AMBER] SPAM: Re: How to neutralize charge after replacing the charges calculated by antechamber Amin Sagar via AMBER
Friday, 28 July 2023
- Re: [AMBER] query Dr. Anselm Horn via AMBER
- Re: [AMBER] query SOMA ROY via AMBER
- [AMBER] Default ensemble Shuo-Lin Weng via AMBER
- Re: [AMBER] Default ensemble Carlos Simmerling via AMBER
Saturday, 29 July 2023
- [AMBER] GPU choice for CUDA simulations Joanna Michelle Chua via AMBER
Sunday, 30 July 2023
- Re: [AMBER] mpi4py build fails in AmberTools23 installation Kotaro TANAKA via AMBER
- Re: [AMBER] mpi4py build fails in AmberTools23 installation accuratefreeenergy--- via AMBER
Monday, 31 July 2023
- Re: [AMBER] Problems running a membrane-bound protein with ATP-Mg complex using CHARMM-GUI parameters Markowska
- [AMBER] adQMMM multiple/shaped solvation regions Holden Paz via AMBER

Last message date: Mon Jul 31 2023 - 16:30:02 PDT
Archived on: Wed May 08 2024 - 05:56:04 PDT

Amber Archive Jul 2023 by date