Amber Archive Aug 2021 by subject
- [AMBER] "An All-Atom Force Field for Metallocenes"
- [AMBER] [Amber] Convert pqr to pdb
- [AMBER] [UCE] Combining MCPB.py results using tleap
- [AMBER] Adding distance restraint in amber
- [AMBER] AMBER 18 and A100?
- [AMBER] Amber parmeters for ACE-CYX bond
- [AMBER] Amber20 installation, pip not installed in Miniconda
- [AMBER] An question about Tutorial
- [AMBER] Boron containing molecules in GAFF
- [AMBER] Building pmemd.cuda.MPI with NCCL support
- [AMBER] Chloride ion atom type issue in tleap
- [AMBER] CMake Error
- [AMBER] Combining MCPB.py results using tleap
- [AMBER] constant ph md
- [AMBER] CPPTRAJ and data from PQR files
- [AMBER] CUDA installation for use with AMBER20
- [AMBER] descrepancy in net charge - TI output
- [AMBER] Developing Parameters for Bad Atom Types
- [AMBER] EEE_INVALID_FLAG IEEE_OVERFLOW_FLAG IEEE_UNDERFLOW_FLAG IEEE_DENORMAL.
- [AMBER] Error 11 Paramfit
- [AMBER] Error open-mai
- [AMBER] ERROR: I could not find enough velocities
- [AMBER] Freezing atoms in MCPB gaussian small_opt calculations
- [AMBER] Fwd:
- [AMBER] Fwd: leap error for modified amino acid
- [AMBER] Grumpy GROMBER over a ZeroDivisionError
- [AMBER] How to cap the residue/ nucleotide atoms
- [AMBER] How to get code modifications into AmberTools
- [AMBER] How to set a replusive force between two drug molecules or two atoms.
- [AMBER] how to set distance restraints in amber
- [AMBER] How to use parmed in Amber20 tools
- [AMBER] How to visualize the protein-implicit solvent boundary
- [AMBER] Installation Problem
- [AMBER] iron-sulfur clusters parameters
- [AMBER] Issue running sander
- [AMBER] Issue with MM/PBSA calculations on membrane system
- [AMBER] Lite Hash Rate and pmemd.cuda
- [AMBER] Loading RNA nucleotide (ADE) tleap error
- [AMBER] Lone Pair Issue
- [AMBER] Maximum coordination exceeded
- [AMBER] MCPB.py - ComplexWarning: Casting complex values to real discards the imaginary part
- [AMBER] Missing mtkpp directory after installation of AmberTools21
- [AMBER] Missing name.ncrst and name.nc files.
- [AMBER] MMGBSA_MPI for membrane-bound proteins
- [AMBER] N_OF_BONDS colvar and PBC
- [AMBER] Need help with MMPBSA-per residue decomp
- [AMBER] PCA and K-mean together scripting in CPPTRAJ
- [AMBER] Positive value of electrostatic and negative value of EPB
- [AMBER] query about MD analysis
- [AMBER] Question about thermodynamic integration.
- [AMBER] Question about using C-F with iRED
- [AMBER] Question on Paramfit QM File
- [AMBER] Questions about the TI methods in binding free energy calculations.
- [AMBER] Regarding filling missing residues in a DNA strand
- [AMBER] Regarding standard deviation and SEM in hbond analysis
- [AMBER] resp2.chg file is missing whilst processing 3rd stage of MCPB.py
- [AMBER] Restart interrupted sander.MPI calculation
- [AMBER] Restraint weight in minimization
- [AMBER] Rodrigues' rotation about a specified vector
- [AMBER] run_cmake with -DMPI=TRUE fails to produce MPI version of Amber20
- [AMBER] Solvate and manipulate order of atoms in Leap
- [AMBER] SolvateOct box volume and cubic box information
- [AMBER] Steered MD simulation
- [AMBER] Suggestions for Mn3O4
- [AMBER] system preparation error
- [AMBER] The paramters of TI
- [AMBER] tleap urea "[atom] does not have a type"
- [AMBER] Unit cell size has changed in trajcetory
- [AMBER] Why is self-correlation with atomiccorr in cpptraj zero?
- [AMBER] X-aligned.Box
- [AMBER] Yet again, MCPB.py for a ferrocene terminated monomer.
- [AMBER] {SPAM?} An question about Tutorial
- Last message date: Tue Aug 31 2021 - 15:30:02 PDT
- Archived on: Wed Dec 04 2024 - 05:56:04 PST