Amber Archive Aug 2005 by subject
- AMBER:
- AMBER: a problem encountered when trying to equalibrate alanine dipeptide in explicit water
- AMBER: a trivial question
- AMBER: about salt bridges
- AMBER: Add constraints over time
- AMBER: addles question
- AMBER: Amber 8: all_nucleic94.lib nucleotide geometry
- AMBER: AMBER on g5 10.4 w/g95 or gfortran
- AMBER: AMBER topology file format
- AMBER: AMBER8 crashes machine(nodes) under IBM compiler, Suse Linux, amd IBM loadleveler
- AMBER: AMBER8 limitation of memory in QM/MM calculation
- AMBER: amber8installation
- AMBER: Antechamber error "Cannot successfully assign bond type for this molecule"
- AMBER: antechamber problem using RESP
- AMBER: Atom type problem
- AMBER: bond breaking/ energetic ion
- AMBER: bond parameters
- AMBER: Boron and Amber
- AMBER: can I setup a simulation with restrain the COM of a group to a reference structure?
- AMBER: comparing md trajectories
- AMBER: compilation problem (Mac OS X.4)
- AMBER: Conformational energy (QM) for parameterization
- AMBER: Convert .prmtop (AMBER7/8) to old format (AMBER6)
- AMBER: coordinated water molecules deleted when addions
- AMBER: Creating protonated cytidine residue
- AMBER: difference of energy in sander and nmode in amber 7
- AMBER: disulfide bonds by "bond" or "edit -> draw" ?
- AMBER: Energy Comparisons
- AMBER: Error with antechamber
- AMBER: essential dynamics
- AMBER: ew_bspline.h error
- AMBER: floating point exception
- AMBER: Format of atom specifiication after FIND
- AMBER: glycan
- AMBER: group-based cutoff
- AMBER: How is the origin of the grid defined?(PBSA question)
- AMBER: How to calculate hydrogen bond involved with water molecules quickly?
- AMBER: How to construct a lipid bilayer
- AMBER: How to deal with the problem that a molecule go out the virtual box in vaccum
- AMBER: in vacuo?
- AMBER: Incorrect imaging when using Periodic Boundary Conditions in NAMD with AMBER parameters
- AMBER: installing amber7 on 64bit cluster
- AMBER: Interpreting Amber8 Benchmark Results
- AMBER: is calculated B-factors always smaller than experimental ones?
- AMBER: leap question
- AMBER: Leap set head/tail question
- AMBER: Lennard-Jones coeff...
- AMBER: memory_mm_pbsa
- AMBER: min problem
- AMBER: minimization
- AMBER: minimization stuck problem
- AMBER: MM-PBSA and 1-4 nonbonded interactions
- AMBER: mm_pbsa
- AMBER: mm_pbsa energy decomposition error
- AMBER: Modeling of a radical
- AMBER: molsurf: problem with calculate surface area
- AMBER: nmode
- AMBER: nmode minimization and normal mode calculation
- AMBER: NMR refinement
- AMBER: NRESPA
- AMBER: parallel amber8 with mpi through qsnet
- AMBER: params for cofactors
- AMBER: parm99.dat non-bonded parameters
- AMBER: PLease remove my post
- AMBER: power supply crash==>boot problems
- AMBER: ptraj command inputs
- AMBER: ptraj correlation facility
- AMBER: ptraj efficiency
- AMBER: ptraj help, how to enable disabled ptraj routine?
- AMBER: QM/MM
- AMBER: questions about MG ions
- AMBER: RED II and Gaussian
- AMBER: Replica exchange
- AMBER: residence time of electrons/holes in DNA
- AMBER: Restraints
- AMBER: shake
- AMBER: Solution for those who have mpich problem while building the parallel version of AMBER 8
- AMBER: solvent problem
- AMBER: Strange difference in speed between Altix (Itanium2) and Tezro (MIPS) SGI for small GB/SA run
- AMBER: strange minimalization output
- AMBER: structures extracted from mmpbsa
- AMBER: Temperature equilibration
- AMBER: Temperature regulation
- AMBER: The “crystallographic” waters should be retained or deleted?
- AMBER: Tutorial question and some more...
- AMBER: Why are some of the Lennard-Jones coeffs 0 ?
- AMBER: wtmol and resp
- AMBER: Zymeworks job posting
- Antechamber
- is calculated B-factors always smaller than experimental ones?
- Last message date: Wed Aug 31 2005 - 22:53:02 PDT
- Archived on: Mon Apr 22 2024 - 05:53:21 PDT
