Amber Archive Jun 2021 by subject
- [AMBER] .rst7 output coordinate file error
- [AMBER] 3080Ti Nvidia
- [AMBER] [MCPB.py]_KeyError: 'HZ2'
- [AMBER] [MCPB.py]_KeyError: 'HZ3'
- [AMBER] A40 vs A5000
- [AMBER] about pytraj/cpptraj
- [AMBER] Absolute Binding Free Energy of Protein+Ligand Complex in AMBER20 - Boresch restraints, Smoothstep
- [AMBER] Adding several Helium atoms to a Lipid bilayer structure in AMBER
- [AMBER] Amber for AMD GPUs?
- [AMBER] AMBER-Reflector e-mails being sent to SPAM
- [AMBER] Amber20 5 times slower than Amber18?
- [AMBER] Amber20 installation, Amber.pip file broken
- [AMBER] ambertools20 - request for older version
- [AMBER] an illegal memory access
- [AMBER] Antechamber error when attempting Tutorial B5
- [AMBER] Apply negative lateral pressure to membrane
- [AMBER] APR- Umbrella sampling of Receptor- ligand complex
- [AMBER] Breaking of complex molecule
- [AMBER] Calculation of ligand restraints in TI
- [AMBER] Can not locate tordef.lib file
- [AMBER] CMAP topology flag skipped
- [AMBER] compilation error
- [AMBER] Constant pH for large number of titratable residues
- [AMBER] cpptraj align using the same numbering
- [AMBER] Error charges ligand having Selenium
- [AMBER] Error in calculating pair distribution function
- [AMBER] Error in pca analysis
- [AMBER] Error in pdb4amber for AmberTools21
- [AMBER] Error in TI analysis
- [AMBER] error with solvate.sh at remove command tleap
- [AMBER] Error: Could not open file frcmod.ions1lm_126_hfe_opc: not found
- [AMBER] Estimating protein-protein interactions
- [AMBER] Execution Trouble
- [AMBER] Fluctuation in GPU usage
- [AMBER] gti_add_sc
- [AMBER] how does amber calculate the water bridge fraction
- [AMBER] How to create a model of a G-Quadruplex and imotif structure using the sequence information
- [AMBER] How to fix the numbering of amino acid that got shifted in topology file that created in amber Tleap
- [AMBER] How to set a check point in Amber
- [AMBER] How to use a relatively smaller cutoff in the GB simulation
- [AMBER] HREMD with similar replicas
- [AMBER] Identical results from thermodynamics integration runs
- [AMBER] Incomplete trajectory due to calculation halted error
- [AMBER] install Amber20 GPU Centos 7
- [AMBER] Installation error AMBERTOOLS21
- [AMBER] Installing compilers/libraries on Ubuntu 18.04 without root access
- [AMBER] issues in non-bonded and bonded force parameters
- [AMBER] issues with non-bonded and bonded force field parameterisation for Arsenic
- [AMBER] knlskintest error when using HMR with 4fs
- [AMBER] mmgbsa results
- [AMBER] Multi-Monomer Polymer
- [AMBER] NAB superimpose issue
- [AMBER] Nastruct reference file format
- [AMBER] Norleucine in ff99sb_ildn?
- [AMBER] pKa Calculation using PMEMD
- [AMBER] position coordinate precision
- [AMBER] Possible impact of cryptomining limitations on new NVidia GPUs on pmemd performances
- [AMBER] Preparation of i-Motif structures
- [AMBER] Pressure tensor components in the GPU code.
- [AMBER] Problem of running a simulation in A100 GPU server.
- [AMBER] Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
- [AMBER] query on principal component analysis trajectory
- [AMBER] Query on Rmsd between clusters and population
- [AMBER] Question about ff14SB parameters/atom types for TYR
- [AMBER] radiopt=1 in not working in MMPBSA.py
- [AMBER] Regarding MMPBSA calculation
- [AMBER] regarding parameters for protonated guanosine
- [AMBER] Regarding protein - nucleic acid contacts
- [AMBER] Restart the crashed MD run in Amber18
- [AMBER] RMSD plot in ns
- [AMBER] Running cpptraj in hpc
- [AMBER] Some Problems by using NAB of AmberTools21 to model Circle-DNA
- [AMBER] sqm seeks the Boron parameter file instead of Bromine
- [AMBER] strange tleap error with bond command
- [AMBER] The code for modeling circular DNA is in the attachment
- [AMBER] TI for inclusion complexes
- [AMBER] tleap error creating prmtop file
- [AMBER] To increase timesteps in MD simulations
- [AMBER] Troubleshooting long idle times in pmemd.MPI
- [AMBER] TypeError: %c requires int or char
- [AMBER] use QUICK for QM/MM simulation accelerated by gpu
- [AMBER] What does the UVV file output for a LJ only system and why cant I recreate it?
- [AMBER] Which gpu should I select between tesla k80 and RTX30 series
- [AMBER] xleap
- [josiah.bones.anu.edu.au: Calculation of ligand restraints in TI]
- Last message date: Wed Jun 30 2021 - 20:30:02 PDT
- Archived on: Fri Dec 20 2024 - 05:56:07 PST