Amber Archive Jul 2023 by subject
- [AMBER] [amber] ph constant simulation question
- [AMBER] [fglaser.technion.ac.il: Fwd: MaxNumberTIAtom on PPI-GaMD - BUG?]
- [AMBER] [Sender Not Verified] Aligning MD snapshots excluding loops
- [AMBER] [Sender Not Verified] Capping the N and C residues of protein
- [AMBER] [Sender Not Verified] Crystal Simulation, protein broken across unit cell
- [AMBER] [Sender Not Verified] Error about sander
- [AMBER] [Sender Not Verified] How to build a protein simulation in gaseous environment?
- [AMBER] [Sender Not Verified] Position restrains on the part of structure
- [AMBER] [Sender Not Verified] Rmsf profile after removing periodicity
- [AMBER] adQMMM multiple/shaped solvation regions
- [AMBER] Aligning MD snapshots excluding loops
- [AMBER] Amber 22 compilation
- [AMBER] AMBER aMD tutorial
- [AMBER] Amber22 Installation
- [AMBER] AmberTools23 changes antechamber behavior for GAFF2
- [AMBER] AMD hardware support
- [AMBER] Atom mask corresponded to first or last residues
- [AMBER] Capping the N and C residues of protein
- [AMBER] Compare trajectories
- [AMBER] Conversion of NAMD to Amber
- [AMBER] cpptraj and nastruct
- [AMBER] Crystal Simulation, protein broken across unit cell
- [AMBER] cutoff for pH constant simulation
- [AMBER] Default ensemble
- [AMBER] DNA topology file error
- [AMBER] Error about sander
- [AMBER] Error in generating prmtop and inpcrd file
- [AMBER] Error running MCPB.py script step3
- [AMBER] Error while running mmpbsa
- [AMBER] Facing difficulty in performing Amber Crystal simulations
- [AMBER] Facing problem with Ambertools topological files
- [AMBER] Force field parameters for Fructose-1,6-biphosphate
- [AMBER] GPU choice for CUDA simulations
- [AMBER] How to build a protein simulation in gaseous environment?
- [AMBER] How to deal with the metal center contain a phosphorylated amino acid by MCPB.py
- [AMBER] How to neutralize charge after replacing the charges calculated by antechamber
- [AMBER] how to remove/delete bonds w/ cpptraj or parmed in pytraj ??
- [AMBER] Kerror about MMPBSA
- [AMBER] Methylated DNA simulation
- [AMBER] MMPBSA error
- [AMBER] mpi4py build fails in AmberTools23 installation
- [AMBER] Multiple thermostats within one simulation
- [AMBER] NAMD TO AMBER
- [AMBER] Opening Job at UIUC VMD development team
- [AMBER] Original chain records in the prepared pdb
- [AMBER] output structure from tleap!
- [AMBER] pGM force field files?
- [AMBER] Position restrains on the part of structure
- [AMBER] pressure control in constant ph simulation
- [AMBER] pressure control question
- [AMBER] Problem with time records in cpout- files in REMD CpHMD simulation
- [AMBER] Problems running a membrane-bound protein with ATP-Mg complex using CHARMM-GUI parameters
- [AMBER] PyRESP tutorial available
- [AMBER] QM+Link final coordinates
- [AMBER] query
- [AMBER] Query regarding Hamiltonian Replica Exchange Molecular Dynamics (H-REMD)
- [AMBER] RESP fitting with constraints, qout output charges NaN
- [AMBER] RMS Fluctuation limit and difference in Temperature maximum Density (TMD)
- [AMBER] Rmsf profile after removing periodicity
- [AMBER] Short hydrogen bonds
- [AMBER] smaller cutoff resulting in NaNs
- [AMBER] Thermodynamic Integration problems
- [AMBER] TIP5P water model parameter files issue
- [AMBER] Typo in amber manual
- [AMBER] unsuscribe
- [AMBER] Zn protease
- [AMBER] 回复: Kerror about MMPBSA
- [AMBER] 回复: Keyerror about mmpbsa
- Capping the N and C residues of protein
- How to neutralize charge after replacing the charges calculated by antechamber
- Last message date: Mon Jul 31 2023 - 16:30:02 PDT
- Archived on: Fri Oct 04 2024 - 05:56:12 PDT