Amber Archive Feb 2008 by subject
- Amber Force field for CNT: leaprc.ff23
- AMBER: "Assuming uniform neutralizing plasma"
- AMBER: (no subject)
- AMBER: A new program for doing RESP
- AMBER: Amber 8 Equivalent of the Amber 5 - Edit program
- AMBER: AMBER 8 problems on RHEL4/Opteron/PGF 7.0-7
- AMBER: Amber 9 installation
- AMBER: Amber compilation with ifort
- AMBER: AMBER parameters for Chlorophyll
- AMBER: Amber: shared memory vs cluster
- AMBER: ambmask problem
- AMBER: Antechamber/mopac query
- AMBER: autodock pdb to obtain parm with tleap
- AMBER: Binary restart file !!
- AMBER: bond breaking in proteins
- AMBER: change in secondary structure during MD
- AMBER: charge derivation for modified amino acids
- AMBER: compiling PMEMD with MKL10.0
- AMBER: Deleting solute from box
- AMBER: DFTB/SCC-DFTB
- AMBER: dihedral energy in amber
- AMBER: Dimension of the solvated box?
- AMBER: Distance restraints between com of two groups of residues
- AMBER: disulfide bridge with ff03ua FF
- AMBER: Entropy calculations using NMODE
- AMBER: Error while compiling Amber
- AMBER: for NMR refinement
- AMBER: Force fields
- AMBER: gaff paramters
- AMBER: Generating RESP charges
- AMBER: hbonds in first solvation shells
- AMBER: infinite polymers in CHARMM
- AMBER: initial command?
- AMBER: Input file for Minimization
- AMBER: Is boiling point a good way to validate solvent paramters?
- AMBER: is that possible fix box size in constant pressure MD
- AMBER: leaprc help
- AMBER: Lennard-Jones parameters
- AMBER: Liquid/Gas Phase
- AMBER: matrix correl
- AMBER: mm_pbsa problem
- AMBER: mm_pbsa: vertex atom mismatch
- AMBER: mol2 save
- AMBER: Molecular dynamics simulation of large-scale domainmovement in a protein
- AMBER: More on tweaking a topology file
- AMBER: mpd error in submitting parallel job
- AMBER: NAB to calcuate entropy
- AMBER: NAB to calcuate entropy. .
- AMBER: Non aqueous implicit solvation
- AMBER: Non-polar Parameters For MM_PBSA Calculation
- AMBER: parameters for silicon atom
- AMBER: parameters of nonbonded potentials
- AMBER: PB Bomb in pb_atmlist(): maxnba too short
- AMBER: PKa calculation
- AMBER: Plea for REMD tutorial
- AMBER: principal component analysis
- AMBER: print distance between atoms during simulation within sander itsself
- AMBER: problem bull linux compiling
- AMBER: Problem with "trajout pdb"
- AMBER: problem with ambmask
- AMBER: problem with antechamber
- AMBER: Problem with energy decomposition in MMPBSA
- AMBER: Problem:neturalization
- AMBER: problems with 10-12 potential in amber8 sander
- AMBER: problems with Replica Exchange
- AMBER: QMMM with printcharges
- AMBER: Query related to implicit solvent EXTDIEL
- AMBER: Question: tweaking topology files to add SHAKE-constrained bonds
- AMBER: RDCs in AMBER 10
- AMBER: re MD simulations of NMR structures: minimized average structure vs. ensemble member
- AMBER: Regarding:PME and neturalization
- AMBER: sander error on Make test.serial
- AMBER: saveAmberPrep in internal coordinates
- AMBER: segmentation fault while generating the covariance matrix
- AMBER: setbox for solvateoct model
- AMBER: setting perioding box in AMBER
- AMBER: silica slab
- AMBER: silica slab / FF
- AMBER: simulated annealing
- AMBER: stops writing trajectory
- AMBER: TERs
- AMBER: time autocorrelation: ??
- AMBER: twin cut-off radii
- AMBER: united atom force field: antechamber
- AMBER: Using antechamber without AMBER program
- AMBER: using NAB to calculate entropy
- AMBER: using NAB to calculate entropy. .
- AMBER: using NAB to calculate normal modes
- AMBER: using NAB to calculate normal modes. .
- AMBER: Using restart files
- AMBER: varying restraint_wt with nmropt=1
- AMBER: Visualizing Periodc box
- AMBER: VLIMIT units; TGTFITMASK
- AMBER: WARNING in readAmberTrajectory(): fsetpos() failed on when looking for box coordinates!
- AMBER: Which install compiler and flags?
- AMBER: XLEaP
- AMBER: xmgr graphics display program
- bad atom type f(fluorine) in MM-PBSA
- Force field parameter file for CNT
- Fwd: AMBER: (no subject)
- Last message date: Sun Mar 02 2008 - 06:07:44 PST
- Archived on: Wed Dec 25 2024 - 05:53:41 PST
