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AMBER Archive (2008) - Aug 2008 By Subject
342 messages sorted by: [ author ] [ date ] [ thread ]About this archive
Starting: Fri Aug 01 2008 - 01:59:00 CDT
Ending: Sun Aug 31 2008 - 16:30:08 CDT
- AMBER: addles
- AMBER: aggregation or cluster detection
- AMBER: all & united atoms force field
- AMBER: amber 9 on Intel Harpertown
- AMBER: Amber compile
- AMBER: AMBER under cygwin on 64 bit Vista
- AMBER: amber9 hangas after job submission
- AMBER: bacteriochlorophyll ff
- AMBER: Bennett acceptance ratio with Amber10
- AMBER: Biased MD with Amber 10
- AMBER: Bonds getting shorter in sander
- AMBER: Compailation problum in Amber 10
- AMBER: compilation problem
- AMBER: Compile AMBER 9 on TACC Ranger super computer
- AMBER: Compile Error
- AMBER: constant ph (cpinutil file)
- AMBER: constph
- AMBER: conversion from crd to netcdf returns almost identical file!
- AMBER: coordinate change of pdb structure using xleap
- AMBER: Critical patch for pmemd 10 extra points code
- AMBER: Dell 2 Quad Core System Performance
- AMBER: DFTB QMMM parameters ambiguity in AMBER10 docs
- AMBER: divcon.rst ??
- AMBER: empty frcmod file but missing parameters
- AMBER: entropy of released water
- AMBER: error in parallel amber 9 test
- AMBER: Error runing Addles
- AMBER: Error when compiling and testing AmberTools
- AMBER: Force field equation
- AMBER: frcmod:attn needs revision
- AMBER: Fwd: Welcome to amber
- AMBER: general question
- AMBER: generate topology file for alanine scanning (mmpbsa)
- AMBER: Glycoprotein once again..........
- AMBER: glycoprotein setup
- AMBER: Gohlke in-house iRED Simulated Order Parameter Script
- AMBER: GPCR membrane simulation, setting surface tension
- AMBER: GPCR membrane simulation, setting surface tension - Message is from an unknown sender
- AMBER: Help compiling Nab programs for AMBER tools
- AMBER: help me for filling a nanotube with water??
- AMBER: how to choose the appropriate ensemble for a given problem
- AMBER: How to convert a CHARMM trajectory to AMBER format?
- AMBER: IGB=10 in Amber10
- AMBER: impropers over bonds between sidechains
- AMBER: Initial structure from NMR structures
- AMBER: installation amber on suse11.0
- AMBER: interaction energies
- AMBER: Is G_disp calculated in MM_PBSA now?
- AMBER: Is there a way to cluster frames of a trajectory?
- AMBER: join two units in amber9 or amber10
- AMBER: latest update on residuegen
- AMBER: LES
- AMBER: LES trajectories
- AMBER: linear interaction energy
- AMBER: MD with NMR restraints
- AMBER: Membrane simulations
- AMBER: Minimization methods
- AMBER: minimization stops or does not write anything
- AMBER: mm-pbsa / sander.MPI ?
- AMBER: MM-PBSA Issue in Amber 10
- AMBER: MM-PBSA multiple trajectory problem
- AMBER: MM_PBSA snapshot statistic calc problem
- AMBER: mmpbsa
- AMBER: modified parmtop file from ptraj?
- AMBER: MOIL-View is for SGI. How do we analyze LES trajectories?
- AMBER: MOIL-View: is there a command line version?
- AMBER: mol2, xleap, Segmentation fault
- AMBER: molecular structure
- AMBER: NAB conjgrad returns error?
- AMBER: NAB: getseq_from_pdb()
- AMBER: Need help with force field parameters for Lipopolysaccharide (LPS)
- AMBER: Negative dihedral coefficients in amber99 - Possible?
- AMBER: net charge
- AMBER: new residues in AMOEBA
- AMBER: NMR average structure
- AMBER: NMR structure as initial structure
- AMBER: Not integral charge increasing with number of lipids
- AMBER: output file format in SANDER.MPI & PMEMD
- AMBER: parameters
- AMBER: Parameters for chloride ion in contact with a protein
- AMBER: PBCAL in MM_PBSA
- AMBER: pdb file ??
- AMBER: PDB files in Amber10
- AMBER: pmemd iwrap trouble
- AMBER: Prepgen
- AMBER: Problem in calculation of resp charges using RED III
- AMBER: Problem loading the leaprc.amoeba force field file in Amber 10.
- AMBER: problem with minimization
- AMBER: problem with prep file generation
- AMBER: Problem with setting the NMR restraints
- AMBER: Problem with the prmtop file generated by sleap and leaprc.amoeba in Amber 10.
- AMBER: Problems with sleap and amoeba
- AMBER: Problems with the charge (membrane simulation)
- AMBER: Proton Parameters
- AMBER: Querry
- AMBER: Querry about simulating a glycopeptide
- AMBER: Questions about Locally enhanced sampling (LES) and Replica exchange
- AMBER: questions about previous posts
- AMBER: RDF output file format
- AMBER: RESP charges fitting for polarizable force fields
- AMBER: respgen -a charge groups function ineffective unless
- AMBER: SANDER Parallel
- AMBER: Set 251 is corrupted, ptraj error...
- AMBER: silhouette width/coefficient after clustering by PTRAJ9.9
- AMBER: Silicon parameters
- AMBER: Simulating protein conformational changes?
- AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro
- AMBER: Solvent Accesible Surface Area (SASA) - Confused
- AMBER: solvent interaction in active site
- AMBER: Source FIles of SANDER
- AMBER: tan luo radii
- AMBER: to understand how frcmod.ff99SB works
- AMBER: Trans proline
- AMBER: Trouble installing Amber 9
- AMBER: trying ff99SP
- AMBER: united atom force field
- AMBER: unsubscribe
- AMBER: Using Na+ ions as input to leap?
- AMBER: Using Na+ ions as input to leap? - solved
- AMBER: Using RDCs for structure refinement
- AMBER: value of Pi in Amber
- AMBER: vdw 6-9 potential
- AMBER: vlimit exceeded
- AMBER: Vlimit Exceeded and inhomogeneous system !!!!!!
- AMBER: wrapping w/ ptraj
- AMBER: xleap fails to savemol2
- Dell 2 Quad Core System Performance
- entropy of released water
- Fwd: AMBER: prepare an initial structure in Amber
- Personal favor
Last message date: Wed Dec 31 2008 - 22:47:27 CST
Archived on: Thu Jan 08 2009 - 16:01:48 CST
342 messages sorted by: [ author ] [ date ] [ thread ]
About this archive
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