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AMBER Archive (2007) - May 2007 By Subject
402 messages sorted by: [ author ] [ date ] [ thread ]About this archive
Starting: Tue May 01 2007 - 12:21:22 CDT
Ending: Thu May 31 2007 - 18:59:25 CDT
- AMBER:
- AMBER: (no subject)
- AMBER: 64-bit pgf90 revisited
- AMBER: [AMBER] QM/MM-DFTB
- AMBER: adding polar hydrogens
- AMBER: Amber 9 compile on OS X
- AMBER: Amber 9 install on Debian Linux amd64
- AMBER: AMBER8 compiler with intel 9.1 compiler
- AMBER: ambpdb gives empty cpin
- AMBER: Antechamber
- AMBER: antechamber question
- AMBER: assigning of head atom as null.
- AMBER: Atomic positional Fluctuations
- AMBER: Atoms closer to 2 angstroms to each other
- AMBER: Average PDB - Unusual Bonds
- AMBER: Average structure
- AMBER: B or E Dihedral Labels in RDPARM output
- AMBER: Backbone stability problems with parm94, glycam04 and AMBER 8
- AMBER: binding energy_decomposition per residue
- AMBER: bug in reprocessing with PB?
- AMBER: Calculating RMS for each residue?
- AMBER: Chemical shift: simulation vs. experiment
- AMBER: command line alternatives for teLeap
- AMBER: Compiling parallel Amber9 on Linux cluster
- AMBER: Complexes
- AMBER: constant pH with 25 titrable sites
- AMBER: correlation between PBTOT and GBTOT values in a MD trajectory
- AMBER: Covert NOEs form Xplor to Amber
- AMBER: cutoff & speed-up of GBSA
- AMBER: deeper problem with the energetics
- AMBER: dielectric constant in GB/SA
- AMBER: distance.restraint for two groups of atoms (center of mass)
- AMBER: DivCon calculation in Amber9
- AMBER: divcon missing in Antechamber 1.27
- AMBER: Docking with AMber
- AMBER: electric field calculation
- AMBER: Electrostatic Energy in MD Simulation (GB)
- AMBER: Energy Spread using GB & Langevin Dynamics (NAB)
- AMBER: error in running sander
- AMBER: Finding x-displacement
- AMBER: GB Energy Spreads for MD Structures
- AMBER: grid output: bulk water density
- AMBER: Group declaration question
- AMBER: hbond ptraj
- AMBER: hbond ptraj pls help.
- AMBER: Heat of Vaporization
- AMBER: high energy with mm_gbsa igb=5
- AMBER: how to solvate the protein with different solvents
- AMBER: hybrid remd
- AMBER: Hydration points
- AMBER: Ignore my reply to Amber protonate!
- AMBER: inconsistency between PBSA and GBSA
- AMBER: inconsistency between PBSA and GBSA - help
- AMBER: Ionic strength in pbsa
- AMBER: Is the simulation reasonable ? (SMD : dissocation antibody-antigen)
- AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj
- AMBER: junk in `Noshake mask` output section
- AMBER: Keq computations
- AMBER: Langevin dynamics in NAB
- AMBER: leap problem
- AMBER: LES
- AMBER: Les analyse
- AMBER: les/nudged elastic band
- AMBER: Less error
- AMBER: md output file
- AMBER: Minimization increases energy
- AMBER: Minimization with heme group
- AMBER: Missing BELE for MM in 1 (residue 47)
- AMBER: missing impropers for nitros?
- AMBER: MM-PBSA calculation with GB dynamic
- AMBER: mm-pbsa error with nm = 1
- AMBER: MM/GBSA error message
- AMBER: multiple excecution of sander
- AMBER: NAB Average Structure
- AMBER: NAB MD Output
- AMBER: NAB normal mode output
- AMBER: need help to calculate IR spectra from amber trajectory
- AMBER: NOC 3.0 is released
- AMBER: parameter file for Fe-S cluster
- AMBER: pi-pi interactions
- AMBER: PME memory requirement
- AMBER: PMEMD and restart files
- AMBER: pmemd source issues
- AMBER: PMF along 1D axis or every axis
- AMBER: PMF define dehedral angel and distance restrainst for center of mass of domains.
- AMBER: PMF for DG calculation.
- AMBER: PMF: WHAM result
- AMBER: polarizable water models.
- AMBER: polymer
- AMBER: Potential of mean force, how to calculate rate of dissociation?
- AMBER: problem about the coordinates out the box
- AMBER: Problem with calcpka.pl and constant pH
- AMBER: Problem with SCC-DFTB parameter files
- AMBER: protonate
- AMBER: QM/MM-DRFTB
- AMBER: query regarding parameter files for manganese
- AMBER: query regarding parameter files for manganese and mercuric ions
- AMBER: Question about determination of hydration points in binding sites
- AMBER: Rate of Dissociation
- AMBER: REF file problem
- AMBER: Reg restraint value obtained during umbrella sampling
- AMBER: REMD error
- AMBER: restraining atoms
- AMBER: restraint_wt and fixing chi
- AMBER: RESTRAINTMASK
- AMBER: rfree: Error input file
- AMBER: Rotations about center of mass of an isolated system
- AMBER: Sander (Amber 9) crash on cortex
- AMBER: Simulated Annealing - Best way to create randomness
- AMBER: Simulated Annealing - Start with Poor Structure
- AMBER: simulations stops in half way
- AMBER: single phospholipid molecule in vacuo
- AMBER: Small scale compute environments
- AMBER: software to extract data from the output file??
- AMBER: Solvent models
- AMBER: Some questions on mm_pbsa
- AMBER: Statictical significance of differences in energy mean values between different simulations
- AMBER: Steered MD & Jarzynski's equality
- AMBER: Steered MD & Jarzynski's equality]
- AMBER: Temperature Drift in MD (NAB)
- AMBER: thermodynamic integration
- AMBER: Thermodynamic Integration (TI) error: "numgroup must be 2 if icfe is set"
- AMBER: total energies during MM-PBSA
- AMBER: Tutorial 3: MM-PBSA.....implicit solvent for MD calculations?
- AMBER: Umbrella Sampling for the twist angle of a DNA base pairs
- AMBER: umbrella sampling: distance restraint
- AMBER: use of pucker function in ptraj
- AMBER: water count
- AMBER: work with constant pH on amber8
- divcon missing in Antechamber 1.27
- Fwd: AMBER: missing impropers for nitros?
- Fwd: AMBER: MM-PBSA: Can't finish the binding energy process
- Minimization with heme group
- missing impropers for nitros?
- Query regarding using tleap for preparing carbohydrate molecule
Last message date: Mon Dec 31 2007 - 15:27:41 CST
Archived on: Thu Jan 10 2008 - 17:13:09 CST
402 messages sorted by: [ author ] [ date ] [ thread ]
About this archive
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