Amber Archive Feb 2022 by subject
- [AMBER] amber gaff parameters resource??
- [AMBER] Amber simulation of cyclic peptide
- [AMBER] Amber20 Installation run_cmake problem
- [AMBER] Ambrtool16 make install error
- [AMBER] any working singularity or docker recipe? (esp for CUDA and MPI)
- [AMBER] boron nitride
- [AMBER] Bug in mmpbsa.py internal energy when idecomp is 3 or 4
- [AMBER] bulk properties for SPAM in mixed solvents
- [AMBER] Cannot heat the lipid system
- [AMBER] Clarification in 3DRISM
- [AMBER] coordinate and topology not generated
- [AMBER] Could not import Amber Python modules! Centos 7
- [AMBER] CPPTRAJ, Comparing H-bonding in two trajectories
- [AMBER] Cpptrj : How to give two hbond calculation at the same time.
- [AMBER] Creating .lib files from prmtop/inpcrd files
- [AMBER] CUDART lib not found during install
- [AMBER] DNA breaking down during the simulation
- [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces
- [AMBER] Fast 3-point water residue error
- [AMBER] Finding percentage occupancy of pi-pi interactions
- [AMBER] Fortran runtime error: End of file
- [AMBER] Fwd: Ambrtool16 make install error
- [AMBER] How to run 3drism.snglpnt calculations in amber20 without rst or traj files
- [AMBER] In development of dihedral angle parameters; negative PK and negative PHASE values
- [AMBER] iron-sulphur clusters
- [AMBER] Issues with make test.parallel during installation of parallel version of Amber
- [AMBER] LEaP Not Reading a Parameter in .frcmod File
- [AMBER] Mass-weighted covariance matrix
- [AMBER] MCPB error for organometallic complex
- [AMBER] MD simulations for POPC membrane
- [AMBER] Meaning of "Multiple 'e' in NUMBER-like thing"
- [AMBER] MMPBSA internal energy when using idecomp 4
- [AMBER] MMPBSA.py for membrane proteins with per-residue decomposition
- [AMBER] MMPBSA.py.MPI error
- [AMBER] Modifying prmtop/inpcrd files
- [AMBER] Move a specific residue parallel using cpptraj
- [AMBER] mpi4py Problem
- [AMBER] pH replica exchange MD (pH-REMD) in explicit solvent, using CUDA MPI in AMBER 18
- [AMBER] Potential PDB and .lib file atom order mismatch
- [AMBER] problem finding packmol.f90
- [AMBER] problem in the protein-ligand system
- [AMBER] Problem with make test.parallel during installation of parallel version of Amber
- [AMBER] Problems of sander.quick.cuda
- [AMBER] Protocol to optimize bonded parameters for GAFF2
- [AMBER] Query regarding 3DRISM calculation
- [AMBER] Reg: Modified LYS residues - Can I use Gaff if so how to link with hybrid AMBERff14SB and GAFF
- [AMBER] Removing AmberTools binary files installed on .pyenv/shims
- [AMBER] Restart using Nosé-Hoover
- [AMBER] Running amber executable on multiple GPUs
- [AMBER] Running Umbrella Sampling simulations
- [AMBER] Same initial velocities with ig=NNN and NTT=1 (on GPU)?
- [AMBER] Segmentation Fault (Core Dumped) in xLEaP
- [AMBER] Simulation of proteins with D-amino acids
- [AMBER] Single-Molecule Mixing of Force Fields
- [AMBER] solvation failed with Amber 20
- [AMBER] Symmetric or mirrored boundary condition?
- [AMBER] test cuda parallel error message
- [AMBER] To know about the Forcefield of Pyrrolysine amino acid.
- [AMBER] trouble finding vdW parameters for methanol
- [AMBER] Unexpected TER chars with pdb4amber and phosphorylated amino acids
- [AMBER] Unused parameters in tip4pew?
- [AMBER] Void bubbles forming in minimization with single nucleoside/solvent?
- [AMBER] when amber22 is going to be released?
- [AMBER] Workstation Recommendations
- [AMBER] xleap problem
- Last message date: Mon Feb 28 2022 - 10:30:03 PST
- Archived on: Mon Nov 25 2024 - 05:56:03 PST