Amber Archive Feb 2020 by subject
- [AMBER] "Bad inpcrd file!" when running pmemd.MPI but not pmemd
- [AMBER] (no subject)
- [AMBER] .crd error
- [AMBER] [LEaP] Atom does not have a type
- [AMBER] About utilities to convert Amber input files for MD into the Tinker, NAMD, Genesis, or Desmond input files
- [AMBER] Amber 16 or 20
- [AMBER] AMBER 18 installation issue
- [AMBER] Amber and Domains Conformational Dynamics
- [AMBER] Amber install error
- [AMBER] amber18 tests failure
- [AMBER] amber18 tests failures
- [AMBER] ante-MMPBSA.py
- [AMBER] AQUA-DUCT Summer School 22-25 June, Gliwice, Poland
- [AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available?
- [AMBER] BMRB Chemical shift values
- [AMBER] CalcError: /truba/sw/centos6.4/app/amber/amber14/bin/sander failed with prmtop gas.complex.prmtop!
- [AMBER] Clustering logistics
- [AMBER] combination of MD simulations with NMR
- [AMBER] Compatibility issue of Atom type naming in AMBER
- [AMBER] counter ions in TI calculations
- [AMBER] counterions present in topology files for the MMPSA calculation
- [AMBER] CPPTRAJ hydrogen bond analysis
- [AMBER] cpptraj_clucster
- [AMBER] Dihedral restraint problems in AMBER16/18
- [AMBER] DOCKED LIGAND CONFORMATION INTO AMBER MD
- [AMBER] Doubt in running mmpbsa
- [AMBER] facing problem in installation of Amber18 with CUDA
- [AMBER] facing problem in installation of Amber18 with CUDA support
- [AMBER] Force field for terminal phosphorylated residues
- [AMBER] frcmod.urea Parameters for urea (or urea-water mixtures).
- [AMBER] G quadruplex simulation
- [AMBER] Gas phase simulation for heat of vaporization calculation
- [AMBER] generate ligand frcmod and lib files
- [AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin.
- [AMBER] H++ processing non-standard amino acids: Atom does not have a type
- [AMBER] Help building a model of a 2F-2S protein with MDPB.py
- [AMBER] heme B parameter by mcpb
- [AMBER] hiii
- [AMBER] how to locate all parameters for specific AA in parm directory
- [AMBER] how to treat capped non-standard AA residue
- [AMBER] inquiry regarding minimum-image convention in cpptraj
- [AMBER] install amber
- [AMBER] installation of amber 18 failed - CUDA_HOME not set (although not true)
- [AMBER] installing
- [AMBER] kindly guide me
- [AMBER] kindly guide me.
- [AMBER] lack scripts for Continuous constant pH molecular dynamics
- [AMBER] make test MPI don't continue
- [AMBER] MCPB.py with mixed valence di-iron system?
- [AMBER] MMPBSA calculations
- [AMBER] mmpbsa.py
- [AMBER] MMPBSA.py error
- [AMBER] no bonds formed between AA and non-standard residue
- [AMBER] On QM/MM dummy atom and deprotonated TYR
- [AMBER] parameters for Si3N4
- [AMBER] pdb4amber strips atoms
- [AMBER] pmemd.cuda installation
- [AMBER] Production run in NVT ensemble
- [AMBER] QM/MM AMBER/ORCA: output
- [AMBER] query on a script called getdvdl.py in AMBER TI tutorial section
- [AMBER] Query regarding 3DRISM in Amber with CHARMM force field
- [AMBER] Question about LSC-IVR keep running without any output information after PIMD sampling
- [AMBER] question about pressure and sensible MD trajectories
- [AMBER] Reading Frames from Trajectory File
- [AMBER] Reg. Periodic Boundary Conditions
- [AMBER] Regarding compatibility of PLUMED with the MPI and CUDA versions of pmemd
- [AMBER] Regarding RMSD calculation and Clustering
- [AMBER] replica exchange with GPU
- [AMBER] Representative structures from `clusterdihedral`?
- [AMBER] Resolving overlapping atoms.
- [AMBER] Running Amber in a GPU cluster
- [AMBER] Several FAILED tests for AmberTools19 and Amber18
- [AMBER] Shaw DE RNA ff in Amber format
- [AMBER] Shearing useful tips for adding ions to biomolecular simulations
- [AMBER] Simulation of an asymmetric membrane model
- [AMBER] Single ion solvation free energy calculations.
- [AMBER] suggest an article for MD for covalent inhibitors
- [AMBER] sulfonamide parameters for correct geometry
- [AMBER] TI calculations in AMBER18
- [AMBER] TI on pmemd CUDA, AMBER18
- [AMBER] tLEaP error of the N-terminal OXT atom
- [AMBER] tleap/xleap performance enhancement
- [AMBER] Tutorial A08
- [AMBER] Unexpected reaction occurred in QM/MM umbrella sampling
- [AMBER] Using cutoffs smaller than 8 A
- [AMBER] Versions of AMBER
- [AMBER] vmd progress time
- [AMBER] Weird error with antechamber for metal ion / MCPB tutorial
- [AMBER] What Can I do for Mixture of Solutions simulation and what should I assign epsilon value for this?
- Reading Frames from Trajectory File
- Last message date: Sat Feb 29 2020 - 12:30:02 PST
- Archived on: Mon Dec 09 2024 - 05:55:52 PST