Amber Archive Dec 2007 by subject
- AMBER: (no subject)
- AMBER: ** No torsion terms for SNI-NI-SNI-CT
- AMBER: a question of ptraj
- AMBER: About protein-ligand binding
- AMBER: About RAMD
- AMBER: Amber 9 - bugfix.40 fails
- AMBER: amber 9 sander crashed with "forrtl: severe (174): SIGSEGV, segmentation fault occurred"
- AMBER: amber on AMD opteron-250
- AMBER: AMBER7 Si atom type
- AMBER: amber9/mmtsb
- AMBER: An enquiry about "Dynamics of ligand escape from the heme pocket of myoglobin (JACS, 1988, 110, 7690
- AMBER: angle between vectors
- AMBER: Backbone atoms
- AMBER: Bulk water simulation with centre of mass position restrain
- AMBER: calcium and zinc parameter
- AMBER: closest water molecules with 8 angstroms
- AMBER: compilation error in SGI Altix 4700 with Intel Fortran 10.1.008 and IMKL 10.0.1.014
- AMBER: compilation error in SGI Altix 4700 with Intel Fortran10.1.008 and IMKL 10.0.1.014
- AMBER: Continuing an amber 8 simulation with amber 9
- AMBER: correlation time
- AMBER: During the Sander process, does the pH of the solution change orr not
- AMBER: Electron density profile
- AMBER: equilibration
- AMBER: FATAL: Atom .R<CYF 17>.A<N 1> does not have a type.
- AMBER: Free Energy Calculations
- AMBER: Free energy for part of the system
- AMBER: Fwd: ptraj with protein-ligand
- AMBER: help in QM/MM simulation
- AMBER: How to apply psuedo-bonds for restraints
- AMBER: I need some help in PTRAJ
- AMBER: implicit solvent simulations
- AMBER: implicit solvent simulations with calcium ion
- AMBER: installation
- AMBER: installation of amber9 on suse linux 10.3
- AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine
- AMBER: leap restrainTorsion
- AMBER: Ligand-Residue interaction tracking
- AMBER: loading a crystal PDB file
- AMBER: make test.parallel not complete
- AMBER: Making movies in VMD
- AMBER: MD_model
- AMBER: Minimization amber9 segmentation fault
- AMBER: mm_pbsa continue run
- AMBER: MMPBSA
- AMBER: MMTSB Toolset
- AMBER: modifications to force field for Fe4S4 cubane
- AMBER: New 2 the board
- AMBER: nmode ntrun=2
- AMBER: No radius found for K+ (MM_PBSA)
- AMBER: phosphorylation
- AMBER: PME and counter ions
- AMBER: PMEMD compilation problems !!
- AMBER: PMEMD internals !!
- AMBER: pmemd: same rst, different result?
- AMBER: pmend vs sander.MPI
- AMBER: POPS Lipid Bilayer: Full Parameter/Topology File
- AMBER: Problem in running CARNAL
- AMBER: protein-ligand binding affinity
- AMBER: protein_model
- AMBER: ptraj with protein-ligand
- AMBER: R.E.D.-III bug fixes
- AMBER: replica exchange out files continually overwritten
- AMBER: RESP charge fitting using antechamber
- AMBER: RESP using antechamber
- AMBER: Restraintmask syntax
- AMBER: running equilibration
- AMBER: sander and pmemd
- AMBER: Scripts for md analysis
- AMBER: Solution Structure Determination Protocols - Simulated Annealing
- AMBER: some input problem
- AMBER: Steered MD
- AMBER: Surface
- AMBER: THF parameters
- AMBER: TI Approach - mass perturbation
- AMBER: Time step & non-bonded interactions updating
- AMBER: tleap crashing
- AMBER: Troubles installing amber
- AMBER: Troubling with installing Amber8
- AMBER: Use of Counter Ions in binding energy calculations
- AMBER: website problems
- AMBER: xleap loading files
- Amber_ifort_x86_64 test error
- divcon on AIX using xlf 10.1
- Last message date: Wed Jan 02 2008 - 06:07:19 PST
- Archived on: Mon Nov 03 2025 - 05:53:41 PST
