Amber Archive Dec 2019 by subject
- [AMBER] 34th Molecular Modelling Workshop (MMWS) February 17-19, 2020 in Erlangen, Germany
- [AMBER] AMBER 18 cuda installation
- [AMBER] amber 18 installation error
- [AMBER] amber update issue
- [AMBER] Amber18 download instructions
- [AMBER] Amber18 installation problem
- [AMBER] Amber18-bash: logFile: command not found...
- [AMBER] Announcement: 34th Molecular Modelling Workshop (MMWS) Feb 17-19, 2020 in Erlangen, Germany
- [AMBER] Any idea on this error and how to troubleshoot
- [AMBER] Any way of making protein rigid in MD simulation?
- [AMBER] Attaching Methoxy (OMe) Capping at C-terminal
- [AMBER] Charge distribution in molecule
- [AMBER] Chemical education for MD articles
- [AMBER] Conference Announcement: Molecular Modeling Workshop, Feb 17-19, 2020 in Erlangen, Germany
- [AMBER] cpptraj RMS calculations appear to be incorrect
- [AMBER] cpptraj.MPI versus cpptraj
- [AMBER] Definition of restraints to avoid ligand aggregation
- [AMBER] Equilibriation input file for TI
- [AMBER] error
- [AMBER] Error during installation
- [AMBER] Error when running MD
- [AMBER] FESetup
- [AMBER] ff19SB with end-caps pmemd.cuda problem
- [AMBER] Figured Amber 16 installation on Mac
- [AMBER] Fixed Minimization
- [AMBER] Flexible protein!
- [AMBER] Found an invalid periodicity in the prmtop file : MMPBSA
- [AMBER] Fwd: problem of compiling
- [AMBER] fxyz and outxyz
- [AMBER] GaMD problems with different computers.
- [AMBER] GPU installation error
- [AMBER] help needed for failed installation of CUDA for GPU-accelerated versions of pmemd for AMBER 18
- [AMBER] help on this error
- [AMBER] How can I get solute-solute energy information?
- [AMBER] How to deal with Dummy atoms of 4-coordinated Zinc in QM/MM
- [AMBER] How to use AMBER on Supercomputer
- [AMBER] If there is a method that can just use the soft-core potential for VDW interaction but not for electrostatic part
- [AMBER] imin=5 fails to produce output
- [AMBER] installing Amber 18 issues
- [AMBER] intel compiling failed
- [AMBER] Interaction entropy program (Geng Dong)
- [AMBER] Minimization equilibration of protein+ligand prior to TI setup
- [AMBER] MM-GBSA error
- [AMBER] mm-gbsa with more than one receptor
- [AMBER] MMGB/PBSA parameters
- [AMBER] MMGBSA script file
- [AMBER] MMPBSA mmpbsa_py_energy failed with prmtop
- [AMBER] Molecular dynamics of tripeptide like organic molecule
- [AMBER] nuc.nab:no such file found error
- [AMBER] NVT equilibriation followed by NPT in TI
- [AMBER] Obtaining excess molar volumes using Molecular Dynamics
- [AMBER] On deprotonated Tyr
- [AMBER] Parameters to be used for protein in implicit solvent
- [AMBER] PrmtopError: Complex natom != receptor natom + ligand natom
- [AMBER] problem of compiling
- [AMBER] Problems adding molecule on Metal-Water system
- [AMBER] Problems installing Amber 18
- [AMBER] Problems installing mpi for AMBER 18.
- [AMBER] Problems installing mpi for AMBER 18. I was trying to install mpi I was typing in
- [AMBER] question about Tleap
- [AMBER] reinstalling Amber 16 + Ambertools 16 on a Mac
- [AMBER] Segmentation Fault when running constant pH Replica Exchange on GPUs
- [AMBER] sequence command
- [AMBER] Sequential equilibration versus parallel runs in TI
- [AMBER] some queries
- [AMBER] Table 21.1 in Thermodynamic Integration section of amber18 manual
- [AMBER] TI calculation steps
- [AMBER] TI calculations linear scaling of atoms!
- [AMBER] TI on gpus
- [AMBER] Ti on pmemd.CUDA
- [AMBER] TI support for CHARMM FF
- [AMBER] Time shift.
- [AMBER] Timestep (dt) in TI calculations
- [AMBER] tip4p-d water forcefield parameters
- [AMBER] Tleap naming problem
- [AMBER] User-defined high precision AMBER trajectory file formats
- [AMBER] Virtual box with imin = 1 or imin = 5
- [AMBER] Warning: 2 or more molecules (3 and 4) share residue numbers (1003).
- [AMBER] Which language could tleap know?
- Last message date: Mon Dec 30 2019 - 06:30:04 PST
- Archived on: Mon Oct 14 2024 - 05:55:51 PDT