Amber Archive Mar 2021 by subject
- [AMBER] 3D-RISM solvent placement with MoFT
- [AMBER] About the extract snapshop as input files from a trajectory files
- [AMBER] Addition of hydrogens - isoelectric point of protein
- [AMBER] AMBER 18 Installation error
- [AMBER] AMBER Digest, Vol 3300, Issue 1
- [AMBER] Amber-forcefield for QM/MM calculation
- [AMBER] AmberTools20 fails to compile with gcc10 (with workaround)
- [AMBER] Ambertools20 with amber18
- [AMBER] Antechamber and mol2 file with .<TRIPOS>UNITY_ATOM_ATTR
- [AMBER] Apply Lennar-Jones potential between small molecules
- [AMBER] atom number difference in topology and simulated trajectory
- [AMBER] Benchmarks for new RTX3060
- [AMBER] Calculating displacement from PMF
- [AMBER] Calculating SASA using Surf and Molsurf
- [AMBER] Calculation halted on pmemd.cuda
- [AMBER] CHARMM Output - Empty Restraint File
- [AMBER] Clustering based on predefined centroids
- [AMBER] constant ph md
- [AMBER] Conversion of CHARMM optimized pdb to AMBER compatible pdb
- [AMBER] Convert SIRAH coarse-grained model back to all-atomic pdb file format?
- [AMBER] CpHMD with structurally different protonation states?
- [AMBER] cpptraj killed
- [AMBER] Discrepancy in pb binding energy (MMPBSA.py tutorial)
- [AMBER] Distance tolerance for identifying common atoms in thermodynamics integration
- [AMBER] Effect of different gamma_ln values
- [AMBER] Electric Field Gradient
- [AMBER] Energy minimization problem
- [AMBER] erro: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered
- [AMBER] Error in tleap
- [AMBER] Error when compiling AMBER20
- [AMBER] Force field parameters for TYS ?
- [AMBER] Free Energy Calculations using LIE and FEW
- [AMBER] GB-HCP Example File and Setup
- [AMBER] gcc9
- [AMBER] Generating library from cif file.
- [AMBER] GPU installation error amber18
- [AMBER] hbond cpptraj
- [AMBER] How to assess mutant-induced instability with MM-GBSA
- [AMBER] How to define COM for groups in ASMD
- [AMBER] How to plot the Phi-Psi picture in Section 7 of “Tutorial 6.6 Nudged Elastic Band (NEB) simulations”?
- [AMBER] Installation Ambertools20 Mac M1 (arm64)
- [AMBER] Interaction energy by MM-PBSA for a superantigen with important Zn(II) center
- [AMBER] Is it possible to create a deb for ubuntu or a pypi one ?
- [AMBER] Is it possible to obtain vacuum charges (and only vacuum charges) with mdgx?
- [AMBER] Ligand moving out of active site after 250ns
- [AMBER] LJ parameters
- [AMBER] Loading Topology & Trajectory Files
- [AMBER] makeDIST_RST
- [AMBER] MCPB.py ZINC Mediated interactions parameterization
- [AMBER] Missing atom types for ligand with chlorine atoms
- [AMBER] MMPBSA errors
- [AMBER] MMPBSA per residue decomposition - Calculation speed
- [AMBER] MMPBSA/ Parmed error
- [AMBER] New in CPPTRAJ
- [AMBER] Pair interaction energy
- [AMBER] Parametrization of Virtual sites in Halogens
- [AMBER] Pending deprecation of paramfit: Amber21 or Amber22?
- [AMBER] Pmemd to run TI on protein mutations
- [AMBER] pmemd.cuda unstable with ff19SB+OPC and HMassRepartition
- [AMBER] positional and NMR distance restraints together
- [AMBER] Practical questions on NMR-refinment
- [AMBER] Problem Running E-REMD on GPUs
- [AMBER] Problem with AMBER20 compilation using Intel/20.4 compiler
- [AMBER] Problem with CG minimization in implicit solvent
- [AMBER] Problem with packmol-memgen when I try to installing Amber20 in GPU
- [AMBER] Request for the sha256sum od amber20
- [AMBER] Running MMPBSA on protein membrane system built using CHARMMGUI
- [AMBER] sander/orca/xtb :Low parallel efficiency
- [AMBER] saving pdb and rst at specific frames in trajectory
- [AMBER] Secstruct error
- [AMBER] Seeking suggestions for breaking a covalent link between atoms
- [AMBER] segmentation fault error
- [AMBER] Selection of forcefield for protein-ligand simulations
- [AMBER] Simulation of optimized ligand without docking
- [AMBER] Single Point QM/MM energy using Amber-Q-Chem interface
- [AMBER] SIRAH CG Protein with Implicit Solvent
- [AMBER] Solvating my box with specified number of water molecules
- [AMBER] Superimpose
- [AMBER] The issue regarding to list index out of range
- [AMBER] The issue regarding to list index out of range (???)
- [AMBER] Tleap Fatal error
- [AMBER] Turning initial velocity off for continuous MD runs
- [AMBER] Unit of Electric field frequency
- [AMBER] Unknown PB option use_sav=0
- [AMBER] use orca in amber
- [AMBER] Using average frame for nmode entropy calculation?
- [AMBER] Using DFT-D3(BJ) during QM/MM calculations
- [AMBER] Visualizing NetCDF in VMD - ERROR
- [AMBER] Why a target ion failed to move along the pathway in the simulated annealing version of Nudged Elastic Band (NEB) calculations?
- [AMBER] x=sequence
- [AMBER] 答复: How to plot the Phi-Psi picture in Section 7 of “Tutorial 6.6 Nudged Elastic Band (NEB) simulations”?
- [AMBER] 答复: Why a target ion failed to move along the pathway in the simulated annealing version of Nudged Elastic Band (NEB) calculations?
- Last message date: Wed Mar 31 2021 - 20:30:02 PDT
- Archived on: Wed Nov 13 2024 - 05:56:02 PST