Amber Archive Oct 2021 by subject
- [AMBER] [SPAM] Help with carbohydrate nomenclature
- [AMBER] Accelerated dissociation events in MD simulation by temperature increase?
- [AMBER] Amber20 benchmarks for RTX A4000
- [AMBER] Amber20/AmberTools21 Installation Test Errors
- [AMBER] Amber21 installation using Docker will be Parallel or Serial?
- [AMBER] Ambertools18 tleap scripts not working when run on Ambertools21
- [AMBER] Atom type does not shown up in PARMCHK.DAT
- [AMBER] Atomistic Simulation Center - Invitation to virtual inauguration symposium
- [AMBER] Automated capping of missing loops?
- [AMBER] buffer overflow in tleap, AmberTools21, gcc 9.3
- [AMBER] bug in pmemd/src/cuda/gpu.cpp line 2852?
- [AMBER] calculate potential energies with imin=5
- [AMBER] Calculating viscosity, thermal conductivity and self-diffusion coefficient
- [AMBER] Can I used AMBER 16 CPPTRAJ to perform dynamic cross correlation map?
- [AMBER] Constant pH MD simulation
- [AMBER] CPPTRAJ
- [AMBER] Cpptraj hbond criteria
- [AMBER] cpptraj RMSD reference
- [AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered
- [AMBER] Distanced-based atom selection from the center of mass
- [AMBER] Does minimization require for average pdb structure extract from 2drms plot using CPPTRAJ AMBER 16
- [AMBER] Error installing amber macOS M1
- [AMBER] Error with PDB4AMBER
- [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces
- [AMBER] Explicit water molecules in MMPBSA.py: OPC vs TIP3P
- [AMBER] FixCondaShebang Error
- [AMBER] FixCondaShebang persists
- [AMBER] Freeze DNA during simulation.
- [AMBER] Fwd: Ambertools21 installation problems
- [AMBER] Fwd: Constant pH MD simulation
- [AMBER] Fwd: topology file and co-ordinate file making by amber tool (gaff.dat)
- [AMBER] Help with carbohydrate nomenclature
- [AMBER] How can I download amber 18?
- [AMBER] How I can Remove dna form .rst files
- [AMBER] How is correlation computed in cpptraj
- [AMBER] How many complex trajectories for mmpbsa computations ?
- [AMBER] How to characterize Binding Sites with cpptraj
- [AMBER] How to combine the coordinate and parm7 files of the glycolipid into a protein complex system
- [AMBER] How to Compare RDFs for different systems
- [AMBER] How to depict Atomic Fluctuations of a specific residue Versus Frames by CPPTRAJ
- [AMBER] How to generate different velocities for same structure during equilibration
- [AMBER] How to handle Ca2+ ion with 8 coordination Geometry in lectin domain for MD simulation.
- [AMBER] How to minimize a pdb format file in Amber 16
- [AMBER] How to minimize average structure (pdb) using Amber 16
- [AMBER] How to reshuffle traj frames
- [AMBER] How to set multiple positional restraints during minimization
- [AMBER] How to superpose the solvated box to the original pdb structure?
- [AMBER] How to turn H-bonding point charges
- [AMBER] Ligand is unstable in simulations
- [AMBER] LINMIN ERROR
- [AMBER] Maximizing GROMACS Throughput with Multiple Simulations per GPU Using MPS and MIG
- [AMBER] Meaning of 3D-RISM output files?
- [AMBER] mm_pbsa and MMPBSA.py
- [AMBER] MMGBSA error help
- [AMBER] MMPBSA (Unable to read script file because of error: invalid option argument "-O")
- [AMBER] Multiple Replicate Trajectories
- [AMBER] Mutation by pdb4amber
- [AMBER] On Ion Distribution and "Replicates"
- [AMBER] Organometallic RESP charge derivation for use with AmberTools
- [AMBER] parameters for ions
- [AMBER] parameters for ions in Amber
- [AMBER] Parameters for non-standard residues
- [AMBER] parmed for 12-6-4 LJ (Geng Dong)
- [AMBER] parmed for two atom type with the same LJ parameters
- [AMBER] Postdoctoral fellowship Computational Drug Discovery
- [AMBER] Problem measuring angle in CPPTRAJ
- [AMBER] Problems with mm_pbsa tests
- [AMBER] Protein-protein binding free energy MMPBSA
- [AMBER] Query regarding missing oxygen atom in RNA sequence
- [AMBER] Query regarding not integral charge in RNA
- [AMBER] Query regarding ZAFF Modeling Tutorial
- [AMBER] Question of Amber_ Sasaki
- [AMBER] reasonable GIST griddim values
- [AMBER] Reg: Cpptraj-Hierarchical Agglomerative Reference paper for methodology and result analysis
- [AMBER] Regarding Amber20 installation
- [AMBER] Regarding area calculation of protein cavity
- [AMBER] Regarding entropy calculations in MMPBSA.py when enthalpy is either from GBSA or PBSA?
- [AMBER] Regarding xleap error
- [AMBER] Restart/Reference file for targeted MD
- [AMBER] Restraining ligand for TI
- [AMBER] Restraining the distance between two groups of residues?
- [AMBER] Restraint COM between two proteins
- [AMBER] RMSD of residues within 3A of ligand
- [AMBER] Rotation Matrix
- [AMBER] Several postdoctoral positions available in EU
- [AMBER] Symmetrical voids during heating stage
- [AMBER] The silver ion parameter
- [AMBER] TI for DG when only cofactor charge changes
- [AMBER] Tohoku Medical and Pharmaceutical University Sasaki It's resolved
- [AMBER] trajectory of mutation generation (Geng Dong)
- [AMBER] unable to get response from mailing list
- [AMBER] Unwanted water protein interaction
- [AMBER] VDWAALS = ************* in minimization
- [AMBER] weired Ligand conformation during simulation
- [AMBER] What is the default value of tishake
- [AMBER] Wrong Angel Given by Cpptraj?
- [AMBER] ZAFF Simulation Error
- [AMBER] Zn sim
- [AMBER] {SPAM?} trajectory of mutation generation (Geng Dong)
- Last message date: Sun Oct 31 2021 - 13:30:02 PDT
- Archived on: Fri Nov 08 2024 - 05:56:16 PST