Amber Archive Mar 2015 by subject
- [AMBER] "Error opening unit 30: File "inpcrd" is missing or unreadable" on Tutorial A15
- [AMBER] ** No torsion terms
- [AMBER] **No Torsion terms
- [AMBER] 10-12 Potentials, HBOND
- [AMBER] : Dimer Imaging Problem
- [AMBER] [Fwd: ]
- [AMBER] [q4md-fft] Fwd: D- amino acids in ff10
- [AMBER] [q4md-fft] Modify RNA's sugar and adding partial charges
- [AMBER] a question on molecular dynamics simulation
- [AMBER] About generalized restraints in AMBER14 with GPU support
- [AMBER] About TIP4-Ew water model usage
- [AMBER] acetyl lysine
- [AMBER] Amber 14 tests errors
- [AMBER] AMBER Digest, Vol 1160, Issue 1
- [AMBER] AMBER Digest, Vol 1169, Issue 1
- [AMBER] Amber on Red Hat?
- [AMBER] Amber standard residue name
- [AMBER] AMBER14 pmemd.cuda.MPI : *** in mdout files
- [AMBER] aMD boost parameters for CHARMM force field?
- [AMBER] ante-mmpbsa.py: problem with the mask syntax
- [AMBER] Antechamber - TURBOMOLE
- [AMBER] ATP and ADP-Pi simulations
- [AMBER] Backbone Rmsd
- [AMBER] Bond distance and Box shape
- [AMBER] calculating angle between to vectors
- [AMBER] calculating HB lifetime
- [AMBER] CHAMBER and CMAP difficulty
- [AMBER] Chamber problem
- [AMBER] Citation from the apostrophe police
- [AMBER] clustering in ptraj
- [AMBER] Cofactor parametrization
- [AMBER] COM restrain support in Amber14
- [AMBER] combinatorial library
- [AMBER] concave edge on torus has mismatched atoms
- [AMBER] CpHMD-pHREX AMBER14
- [AMBER] cpptraj H-bond: clarification sought
- [AMBER] CUDA problems
- [AMBER] D- amino acids in ff10
- [AMBER] Decomposition of the MMGBSA based on multi trajectory input
- [AMBER] Dielectric constant for dna-ligand in TIP3P system
- [AMBER] Differences in AMBER force fields
- [AMBER] diisopropylethylene parameter
- [AMBER] Drifting molecules despite strong restraints
- [AMBER] EGB and ESCF might not be converged if the net charge not equal to 0 in the QM/MM-GBSA
- [AMBER] Error during Adding Fragment(about MCPB )
- [AMBER] error in antechamber: Bond types are assigned for valence state 1 with penalty of 1
- [AMBER] error in MMPBSA.py
- [AMBER] Error message from FEW in Amber14 tutorial A24
- [AMBER] ERROR no map function for FE2 FE2 :data= 91 CYS SG 170 FE2 FE2 2.4
- [AMBER] error when doing lifetime calculation
- [AMBER] Error while creating force field
- [AMBER] error with mmpbsa.py
- [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius!
- [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program
- [AMBER] Errors in AmberTools14
- [AMBER] Evaluating hydrogen boding lifetime
- [AMBER] facing problem to create a prmtop file for oxonium cation
- [AMBER] finding angles
- [AMBER] Fitting velocity autocorrelation data
- [AMBER] flag for fast water
- [AMBER] Force field for Inositol triphosphate
- [AMBER] force field parameter for fructose 1 6 bisphosphate
- [AMBER] Format of solventhb.dat file in hydrogen bonding calculation
- [AMBER] Free energy calculation: Thermodynamic integration with use of restraints
- [AMBER] free energy plot
- [AMBER] Fwd: [Fwd: Purchase of Amber-14]
- [AMBER] Fwd: CPPTRAJ trajout results "weird" pdb
- [AMBER] Fwd: help in sdf
- [AMBER] Fwd: Regarding the MCPB tutorial
- [AMBER] General question about MM-PB(GB)SA
- [AMBER] Gromacs towards Amber conversion
- [AMBER] GTX TITAN X was introduced
- [AMBER] heat capacity
- [AMBER] help in getting 3D isodensity surface
- [AMBER] help in hbond analysis
- [AMBER] Help regarding appropriate analysis for correlated motion using cpptraj
- [AMBER] Histogram analysis of the dihedral distributions using cpptraj
- [AMBER] HMR
- [AMBER] How to calculate interaction energy between any two residues of one protein
- [AMBER] How to obtain potential energy using mdcrd trajectories in AMBER12
- [AMBER] how to use cpptraj for pdb files generated from external software
- [AMBER] ideal range values for distance restraint b/w 2 non-bonded atoms.
- [AMBER] Immediate Postdoctoral Position Opening In Dr. Khaled Barakat’s Lab, Faculty Of Pharmacy, University Of Alberta
- [AMBER] Implicit solvent simulation with Andersen thermostat
- [AMBER] Improper torsions in NMA
- [AMBER] Inability to use antechamber on Anion
- [AMBER] Intel Compiler and MKL
- [AMBER] Invitation to Computational Chemical Biology Conference (Aug 6th to 9th 2015), Cairns, Australia (http://tinyurl.com/nyblv7o)
- [AMBER] issue with LRT calculation in sander
- [AMBER] iterative calculation in CPPTRAJ using "for... do... done"
- [AMBER] leap and centering
- [AMBER] Leap warning
- [AMBER] Lipid14 POPE lipids
- [AMBER] loading molecule in xleap and saving it in mol2 format
- [AMBER] loading molecule in xleap and saving it in mol2 formatDear
- [AMBER] Manual still ambiguous about igb=8 and pmemd
- [AMBER] matrix newtransform command
- [AMBER] mm-pbsa & extra-point
- [AMBER] MMGBSA error
- [AMBER] MMGBSA pairwise decomposition - differences in Non-Polar Solv. & TOTAL for same residue pairs
- [AMBER] mmpbsa conflict with Ca2+ ?
- [AMBER] MMPBSA error
- [AMBER] MMPBSA tutorial: MMPBSA.py
- [AMBER] Multiple MEPs option in R.E.D tools
- [AMBER] NetCDF AMBER file corrupted
- [AMBER] Non-Standard Residue / Non-Integer Charge
- [AMBER] Nuclicacid forcefield in AMBER
- [AMBER] On the clustering of the ligand position within the cavity
- [AMBER] on the force field
- [AMBER] organic molecule
- [AMBER] Param PROC does not exist (MM-PBSA)
- [AMBER] Param PROC does not exist --- MM-PBSA problem
- [AMBER] PCA_representation_in_Cpptraj
- [AMBER] Per-residue decomposition energy MMGBSA.py
- [AMBER] pmemd.MPI error
- [AMBER] PMF for dimer dissociation
- [AMBER] post processing temperature replica exchange trajectories
- [AMBER] Predefined number of water molecules in waterbox
- [AMBER] Pressure units in 1D-RISM
- [AMBER] Problem in calculation per residue free energy decomposition
- [AMBER] Problem in capping ACE and NME.
- [AMBER] Problem in protonating.
- [AMBER] Problem Regarding Different PMF Graph
- [AMBER] Problem Regarding Different PMF Graphs
- [AMBER] Problem with Creating Unit for Non-standard N-Cap Residue
- [AMBER] Problem with heating lipid bilayer in amber 12
- [AMBER] Problems with Amber installation
- [AMBER] Projection on distance covariance modes
- [AMBER] Projection on modes calculated by distcovar matrix
- [AMBER] Putting oxygen molecules around protein structure
- [AMBER] Reading two units from same .mol2 file
- [AMBER] Reduce not working properly
- [AMBER] Reg: Query on distance restrain and its effect on conformation
- [AMBER] REGARDING ATOM TYPE ERROR
- [AMBER] REMD jobs crashing repeatedly on GPUs
- [AMBER] Replacing water with oxygen molecules
- [AMBER] Replica Exchange on a single Titan-X GPU
- [AMBER] Restrained MD
- [AMBER] RMSF & changes of the secondary structure of protein
- [AMBER] RNA Simulation
- [AMBER] RNA's sugar modification
- [AMBER] sander.MPI error
- [AMBER] script to convert the Gromacs topology to Amber topology?
- [AMBER] set command and VMD
- [AMBER] SMD average work
- [AMBER] Solvent Box Issue When Running AMBER Dynamics
- [AMBER] Stability MMPBSA
- [AMBER] Starting antechamber for preparing ligand molecule
- [AMBER] Sudden RMSD blow-up in trajectory analysis
- [AMBER] Syntax Confusion on Radial Command
- [AMBER] Targeted MD shows blank output file!
- [AMBER] temp ramping in tutorial A5
- [AMBER] The unperturbed charge of the unit: -2.980000 is not integral
- [AMBER] tleap box neutralization
- [AMBER] topology file, segment id and the pathways plugin
- [AMBER] trajectory of minimization using generalized Born
- [AMBER] trouble running pmemd.cuda
- [AMBER] Truncated octahedron
- [AMBER] Tutorial B0
- [AMBER] Unable to load OLS OLT NLN in tleap (AmberTools14)
- [AMBER] unfolding protein and solvent density
- [AMBER] using internal geometry
- [AMBER] Using WHAM to get 3D free energy surface in AMBER12
- [AMBER] vdw energy and electrostatic energy calculation for osmolyte
- [AMBER] Water sigma parameters
- [AMBER] | ERROR: PMEMD does not support intermolecular PRFs!
- GTX980 PERFORMANCE
- how to use cpptraj for pdb files generated from external software
- Last message date: Wed Apr 01 2015 - 00:00:03 PDT
- Archived on: Sun Nov 10 2024 - 05:55:05 PST