Amber Archive Feb 2021 by subject
- [AMBER] [lsimon.usal.es: MDGX charge fitting with some charges fixed or restrained]
- [AMBER] About changes in frcmod.parmbsc0
- [AMBER] Acpype error: Timed out process killed
- [AMBER] Altering ligand positions in Xleap
- [AMBER] AMBER HREMD replica trajectory
- [AMBER] Amber18 + Ambertools20
- [AMBER] Amber20 GPU plus PLUMED
- [AMBER] AmberTools20 parallel test errors
- [AMBER] Apply Lennar-Jones potential between small molecules
- [AMBER] atom number difference in topology and simulated trajectory
- [AMBER] Bug in the Mol2 format: space converted into a new oxygen atom
- [AMBER] Calculating forces
- [AMBER] Calculating pairwise RMSD of two proteins
- [AMBER] case studies of MD based drug discovery
- [AMBER] configure_mpich error
- [AMBER] CPPTRAJ - KMeans Value for K
- [AMBER] CPPTRAJ cannot open RXSGLD trajectories out of the box
- [AMBER] cpptraj CMAP flag issue with charmm-gui parm7 files
- [AMBER] CPPTRAJ mindist comand
- [AMBER] CUDE upgrade question and AMBER
- [AMBER] curiosity about sander reading a traj being written by GPU code
- [AMBER] decompose running error
- [AMBER] dimer shifts under NPT ensemble
- [AMBER] Disparities between dG solv from GB and PB Models
- [AMBER] erro free energy calculation
- [AMBER] error while building Amber20 with Intel + CUDA
- [AMBER] Error while setting up constant pH MD simulations
- [AMBER] error with AMBER installation
- [AMBER] External electric fields cannot be used when npt > 0
- [AMBER] Fix the dihedral angle during the simulation
- [AMBER] Found bug in sander in restarting SGLD replica exchange runs
- [AMBER] Fwd: GaMD output (gamd.log) file analysis
- [AMBER] Fwd: MMPBSA Error
- [AMBER] Fwd: Prepare pbd file modified cyclodextrin
- [AMBER] Fwd: unreadable *.mdcrd
- [AMBER] GaMD output (gamd.log) file analysis
- [AMBER] GPU power usage drop for igb = 8 compared to igb = 2
- [AMBER] GPU TI PROBLEM
- [AMBER] help with cpptraj error (segmentation fault)
- [AMBER] Help with installation
- [AMBER] High value for force constant is acceptable?
- [AMBER] how does tleap choose missing side chain conformations
- [AMBER] How to recompile AmberTools
- [AMBER] Hydrogen bond analysis tutorial
- [AMBER] IEEE_OVERFLOW_FLAG
- [AMBER] Interaction energy by MM-PBSA for a superantigen with important Zn(II) center
- [AMBER] leap hangs on dihedral in frcmod?
- [AMBER] Making sense of tip3p.frcmod
- [AMBER] max pairlist cutoff must be less than unit cell max sphere radius!
- [AMBER] maximum no of atoms for simulation
- [AMBER] MAXPR error in sander sp job
- [AMBER] MDGX charge fitting with some charges fixed or restrained
- [AMBER] mdgx ipolQ charges of a charged residue
- [AMBER] Membrane protein-ligand simulation - application of multiple FF - compatibility and reliability
- [AMBER] MMPBSA, signal SIGSEGV failure
- [AMBER] MMPBSA.py Error: Could not import Amber Python modules
- [AMBER] ModuleNotFoundError: No module named 'MMPBSA_mods'
- [AMBER] Molecule volume in cpptraj?
- [AMBER] multi source calls in tleap
- [AMBER] Multiple Harmonic Restraints
- [AMBER] Non zero ligand warning
- [AMBER] Nudged Elastic Band solvent choice and initial heating problem
- [AMBER] Odd number of electrons
- [AMBER] OPC monovalent ion parameters
- [AMBER] Parameters for Iron Oxide
- [AMBER] polarizable FF in amber18 or 20
- [AMBER] Preparation of i-Motif structures
- [AMBER] Prepare pbd file modified cyclodextrin
- [AMBER] Prmtop missing resid and resname info
- [AMBER] problem deriving implicit polarised charges charges with mdgx
- [AMBER] Problem with pmemd.MPI
- [AMBER] Probmlems compiling under macOS
- [AMBER] QM/MM in Amber
- [AMBER] query regarding heme forcefield parameters
- [AMBER] Questions about loading FF02 and MMGBSA
- [AMBER] RAMD question (Xiaodong Wu)
- [AMBER] RAMD simulation (Xiaodong)
- [AMBER] Random seed for restart files that have velocities?
- [AMBER] Regarding restarting of Gaussian Accelerated MD.
- [AMBER] single strand RNA parameters
- [AMBER] Solution to the replica exchange SGLD restart bug
- [AMBER] Stacking energy calculation
- [AMBER] Steered MD
- [AMBER] Sufficiently equilibrated or not
- [AMBER] suggestion of a patch for building MPI version of MMPBSA.py
- [AMBER] Testing pmemd.cuda.MPI - how many failed file comparisons are innocuous?
- [AMBER] theoretical doubt about TI
- [AMBER] Thermodynamic integration for protein-protein interactions
- [AMBER] TI with igb. = 6
- [AMBER] tip3p water model in amber14
- [AMBER] tLeap, Fatal: Atom does not have a type
- [AMBER] Using divalent ions in LEaP
- [AMBER] Why do trajectories get corrupted?
- [AMBER] ZAFF force field
- Last message date: Sun Feb 28 2021 - 03:30:02 PST
- Archived on: Fri Sep 06 2024 - 05:56:03 PDT