AMBER Archive (2007) - Sep 2007 By Subject288 messages sorted by:
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Starting: Sat Sep 01 2007 - 09:15:11 CDT
Ending: Sun Sep 30 2007 - 05:37:56 CDT
- AMBER9 Installation Help
- AMBER:
- AMBER: A question related with periodic boundary condition
- AMBER: about MD outputs
- AMBER: about restraining atoms
- AMBER: amber md movie using Chimera
- AMBER: amber md movie using Chimera. .
- AMBER: AMBER parametrization (??) for OAA and Mg++
- AMBER: AMBER sander
- AMBER: atomicfluct
- AMBER: calcium ion force-fields
- AMBER: calcium parameters
- AMBER: Can I set harmonic constraints in SMD simulations ?
- AMBER: chiral surfaces
- AMBER: Comparing explicit solvent/vacuum qmmm
- AMBER: Complexe Energy Analysis
- AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2-
- AMBER: Copper and Chlorine parameters
- AMBER: creating topology files for RNA DNA hybrid.molecule
- AMBER: cyclohexane and decalin on amber
- AMBER: decomposition energy
- AMBER: DelPhi
- AMBER: Dihedrals in Sander
- AMBER: DNA base planarity restraint
- AMBER: effective step period for constant pH simulations
- AMBER: electron density difference
- AMBER: energy calculation
- AMBER: Explicit water in implicit enviornment?
- AMBER: FF02: sander problem with irstdip=1
- AMBER: follow-up
- AMBER: for makeDIST_RST
- AMBER: for NMR restrains files
- AMBER: force field question
- AMBER: fragment parametrization tutorial?
- AMBER: Fwd: Comparing explicit solvent/vacuum qmmm
- AMBER: Fwd: System extending beyond of (non existent) virtual box
- AMBER: GBSA or PBSA: GPB or GGB are +ve or -ve?
- AMBER: GBSA: NMODE ERROR
- AMBER: Harmonic constraints
- AMBER: Help WARNING: The unperturbed charge of the unit
- AMBER: heme force-field (2)
- AMBER: heme forcefield atom types
- AMBER: How to fix the distance between two atoms.
- AMBER: implicit minimization
- AMBER: installing LMOD error
- AMBER: LINMIN Failure vs Parallelization
- AMBER: MacOSX installation help
- AMBER: MAXPR
- AMBER: Minimization and MD input files
- AMBER: Missplaced TERs
- AMBER: MM_PBSA with complex plus Ion
- AMBER: needing more detailed knowledge of tautp than the manual
- AMBER: NMR refinement
- AMBER: ntt parameter in vacuum
- AMBER: parallel implementation of Amber 9
- AMBER: PBradii
- AMBER: plotdat: Amber Data Plotting Program
- AMBER: PMF calculation - minimum conformer
- AMBER: Potential of mean force: how to extract the min structure?
- AMBER: Prepin error (?) in xleap
- AMBER: Pribelm with Minimization & MD
- AMBER: Problem compiling AMBER 9 on ppc64
- AMBER: problem compiling amber9 on IBM 64 bit machine with xlf90_suse compiler
- AMBER: Problem encountered during thermodynamic integration
- AMBER: Problem with Getting SHAKE to work
- AMBER: Problem with modelling ammonium ion?
- AMBER: problem with ptraj
- AMBER: Problem with Sander
- AMBER: problem with Thermodynamic Integration
- AMBER: Problems loading parameter file in tleap
- AMBER: Problems with Carbohydrate Non-standard Residue
- AMBER: refinement of NMR struture using AMBER
- AMBER: regarding energy calculation
- AMBER: replica exchange simulation
- AMBER: Reproducing constant pH results !!
- AMBER: restarting REMD simulations
- AMBER: rms and rms nofit
- AMBER: Running mpirun -np 1 on different processors
- AMBER: Simulation continuation problem. Cant read restart file!!!!!!
- AMBER: Solvation Issues
- AMBER: Solvation net forces
- AMBER: solvent box pyridine
- AMBER: Solvent in closest contact with solute
- AMBER: Statistical uncertainty estimation in Thermodynamic integration calculation..
- AMBER: step-by-ste weight changes of dwt -- patch?
- AMBER: System extending beyond of (non existent) virtual box
- AMBER: Targeted MD
- AMBER: Targetted MD and ptraj analysis
- AMBER: the box vectors for a Leap generated truncated octahedron
- AMBER: TIP5P questions
- AMBER: TMD and "Current RMSD from reference"
- AMBER: Too big EEL energy in energy minimization
- AMBER: Too big EEL energy in energy minimization. .
- AMBER: Torsion terms in xleap
- AMBER: total energy in sander and nmode
- AMBER: Tutorial protein-small-molecule-associates
- AMBER: Using ntr=1 in xleap
- AMBER: Water question
- AMBER: xleap question
- Asking for help
- Asking for help about heating
- Fwd: AMBER: Copper and Chlorine parameters
- Tutorial5 -- sustiva and xleap
- using RESP
Last message date: Mon Dec 31 2007 - 15:27:41 CST
Archived on: Thu Jan 10 2008 - 17:13:10 CST
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