AMBER Archive (2008) - Dec 2008 By Subject341 messages sorted by:
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Starting: Mon Dec 01 2008 - 01:30:02 CST
Ending: Wed Dec 31 2008 - 22:44:33 CST
- AMBER:
- AMBER: (no subject)
- AMBER: a question about ff03ua
- AMBER: about mmpbsa out data
- AMBER: alascan error
- AMBER: alascan MUTANT_KEEP error
- AMBER: AMBER 10 PMEMD / SGI_MIPS
- AMBER: amber 9 compilation error with mvapich and intel compilers
- AMBER: amber 9 compilation error with mvapich and intelcompilers
- AMBER: AMBER minimization problems
- AMBER: AMBER10 AMBERTools antechamber
- AMBER: Building Amber 10 with Intel MKL and compiler mini howto
- AMBER: building new ions
- AMBER: Calculating the dielectrostatic constant from simulation?
- AMBER: comparison of MD trajectories recorded with pmemd and sander
- AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC
- AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90
- AMBER: Constant pH dynamics
- AMBER: definition of dihedral in amber
- AMBER: distance restraint between non-bonded molecules
- AMBER: distance restraint between non-bonded molecules]
- AMBER: distance restraint in minimization
- AMBER: Distorted ring...
- AMBER: DNA-Gold parameters
- AMBER: DNA: GB solvent with salt
- AMBER: Error: tutorial one for md simulation of DNA
- AMBER: FAD RESP charges and parameters
- AMBER: ff99 (PK/IDIVF)
- AMBER: forrtl severe(174) error with minimization and md
- AMBER: from dihe parameters to torsional energy
- AMBER: GB offset for proteins
- AMBER: How do you evaluate forces on a fixed atom?
- AMBER: how to add new solvent type in Amber
- AMBER: How to build a cubic box of a newly synthesized compound?
- AMBER: Hydroxide ion in POL3 water
- AMBER: idecomp=2 & RRES/LRES group specification
- AMBER: Initial velocities based on date and time are NOT changing ?
- AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64)
- AMBER: installation amber9 in fedora9
- AMBER: installation amber9 in fedora9 using bash shell
- AMBER: interaction energies
- AMBER: Is there an easy way to calculate the electric field at the center of a group of atoms
- AMBER: launching a job works with sander.MPI and fail with pmemd.MPI
- AMBER: ld: cannot find -lgcc_s
- AMBER: LINMIN error in geometrically constrained minimization @ MM-PB/SA conditions
- AMBER: makeDIST_RST computation of r3 value with IAT < 0
- AMBER: makeDIST_RST error -- no map function for HH TYR
- AMBER: Materials and methods
- AMBER: mdout file details
- AMBER: MM-PBSA : bad atom type: ZN
- AMBER: MM/GBSA Error during deccomposition
- AMBER: mpirun Permission denied.
- AMBER: mwcovar limit?
- AMBER: N(CN2)- ion
- AMBER: parallel installation
- AMBER: periodic boundary
- AMBER: Playstation 3 Benchmarks
- AMBER: prep files ATP-MG++ and for phosphorylated threonine
- AMBER: pressure component
- AMBER: Problem running NEB in AMBER10
- AMBER: Problem with MMPBSA
- AMBER: problem with toturial A3 (MM-PBSA)
- AMBER: ptraj: how to select all non-hydrogen atoms
- AMBER: Pulling using restraintmask
- AMBER: QM/MM and unpaired spin
- AMBER: Radial Distribution Function
- AMBER: reg unstability of structure in md
- AMBER: reg-adding ions
- AMBER: reg-antichamber run
- AMBER: reg.building ions
- AMBER: reg.concentration of ions
- AMBER: reg.dnasaveparm&tcrd
- AMBER: regad-tutorial-dna-polyAT
- AMBER: relative weight of RDC constraints
- AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III
- AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems
- AMBER: RESP GAUSSIAN AMBER
- AMBER: restraintmask - reference file is not working
- AMBER: RMS plot
- AMBER: Running Amber8 - Sander
- AMBER: Running md using glycam in AMBER
- AMBER: seeking help regrading Zinc protein GBSA minimization
- AMBER: sgi4700 the time of MD simulation is 30 minute for 1ps about 2500 atom using 1cpu
- AMBER: side chain expression
- AMBER: Simulating peptide linkers with AMBER
- AMBER: SMD-related questions
- AMBER: Solvatebox problem
- AMBER: solvent box again
- AMBER: subroutine Work : Jarynski work theorem
- AMBER: Switching function in NAMD
- AMBER: tutorial A1, file missing readit.f
- AMBER: unable to open pdb file
- AMBER: unsubscribe amber
- AMBER: using packmol file in Amber
- AMBER: Variable PBCAL values in MM-PBSA calculations
- AMBER: vertex atom mismatch
- AMBER: xleap (measureGeom)
- AMBER: xleap error
- bugfix 11 & 12
Last message date: Wed Dec 31 2008 - 22:47:27 CST
Archived on: Thu Jan 08 2009 - 16:01:50 CST
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