AMBER Archive (2004) - Aug 2004 By Subject361 messages sorted by:
[ author ]
[ date ]
[ thread ]
About this archive
Starting: Mon Aug 02 2004 - 04:15:34 CDT
Ending: Tue Aug 31 2004 - 23:53:20 CDT
- about PME in Amber6
- AMBER:
- AMBER: A question about pheTI in AMBER8 test.
- AMBER: About the Amber constraint constant
- AMBER: About tree structure of TRP residue
- AMBER: Adding residues
- AMBER: Amber 03 Forcefield discrepancy
- AMBER: Amber 8 - Energy Minimization Parameters
- AMBER: Amber 8 Installation - C compiler?
- AMBER: AMBER7 plastocyanin tutorial problem.
- AMBER: Amber8 - Floating point
- AMBER: Amber8 - LAM MPI Compilation problems
- AMBER: Amber: Anal program format
- AMBER: Amber: xleap crash
- AMBER: ANAL memory problem.
- AMBER: angle bending
- AMBER: Angle parameters in phosphate groups
- AMBER: another cpinutil.pl error
- AMBER: Antechamber and dummy atoms
- AMBER: antechamber test
- AMBER: Atomic charges in Lactose
- AMBER: atomic positional fluctuation
- AMBER: atoms not in residue templates
- AMBER: bending
- AMBER: Biotin/streptavidin tutorial.
- AMBER: born radius and screening parameter for Br
- AMBER: Bug and Patch in ANAL
- AMBER: Bug: ptraj adds spurious box information
- AMBER: bugfix.all
- AMBER: can MM-PBSA be applied to Charmm format trajectory file?
- AMBER: charge not zero
- AMBER: charge perturbation - xleap question
- AMBER: cpinutil.pl error
- AMBER: density calculation in AMBER output
- AMBER: Differences in RESP charges for G in RG and DG residues
- AMBER: different cooling schedules for simulated annealing
- AMBER: Dr. Herman Von Grafenstein
- AMBER: error estimates in AMBER
- AMBER: error for performing MD
- AMBER: error of performing simulation
- AMBER: error while loading shared libraries: libcxa.so.5
- AMBER: freezing atoms in impliciti solvent
- AMBER: From Andrew Box: Invitation and new email address
- AMBER: Gaussian in RED
- AMBER: Glycam-04 Parameters in Amber 7
- AMBER: how to correct the charge of oligosaccharides
- AMBER: How to covalently bind a ligand to a residue?
- AMBER: how to deal with the initial structure?
- AMBER: how to read in CHARMM or AMBER binary trajectories
- AMBER: How to test the used parameters.
- AMBER: Improving PMEMD Performance on gigabit ethernet - CORRECTION
- AMBER: Improving PMEMD performance on gigabit ethernet Linux clusters
- AMBER: Increase lastrst in the &cntrl namelist
- AMBER: Increasing MAXATOM in antechamber
- AMBER: installing amber 8 on 64 bit amd opteron
- AMBER: installing amber8
- AMBER: intense and spectrum
- AMBER: intrinsic born radius of Br
- AMBER: leap: impose
- AMBER: Lennard-Jones particle simulation
- AMBER: lib file
- AMBER: MD & net charge
- AMBER: Membrane protein simulation
- AMBER: metal atoms in Xleap
- AMBER: Minimization error
- AMBER: minimization output file format
- AMBER: Minimum imaging
- AMBER: mm-gbsa
- AMBER: mm_pbsa Abmer8 example
- AMBER: mm_pbsa problem
- AMBER: mm_pbsa.pl in Amber8
- AMBER: mmpbsa question
- AMBER: Moil-view, prmtop, inpcrd question
- AMBER: mutation of Tyr to Leu with TI
- AMBER: Neutral C and N termini.
- AMBER: nonpalar energy contribution-DMSO
- AMBER: NTT=0 and TAUTP
- AMBER: One more question about the tree structure of looping residues
- AMBER: opteron 64 bit workstation
- AMBER: parameter
- AMBER: parm94
- AMBER: pb_bomb in setgrd()
- AMBER: PBC in sander
- AMBER: peoblemwith RED II
- AMBER: perturb a water to a dummy water with shake
- AMBER: pmemd config.h request for athlon
- AMBER: pmemd problems
- AMBER: pmemd.
- AMBER: pmemd. - OOPS!!!
- AMBER: problem loading molecule in leap
- AMBER: problem loading pdb in leap.
- AMBER: Problem: Installing Amber8 on PC with Windows XP
- AMBER: Problems with Carnal coordinate average
- AMBER: ptraj -- velocities set to zero?
- AMBER: ptraj and hbond
- AMBER: ptraj: load crd without hydrogen (i.e. missing parm file)
- AMBER: Pulling versus Distance Restraints
- AMBER: question about compilation of AMBER8 on MANDRAKE9.2
- AMBER: question about covariance matrix from ptraj
- AMBER: question on minimization
- AMBER: questions on mm_pbsa
- AMBER: rdparm problem
- AMBER: recompiling amber8
- AMBER: RED BUG!!!
- AMBER: RED BUG!!!!...perhaps I fixed it
- AMBER: RED fails to read g94 output
- AMBER: residue database
- AMBER: RESP calculation with different multiplicities
- AMBER: resp charge calculation for Fe+3 heme
- AMBER: RESP charge derivation
- AMBER: RESP charges in Fe+3 heme system
- AMBER: RESP partial charge calculation
- AMBER: restart a MD after replacing molecules
- AMBER: RMSD result from GB model
- AMBER: Sander
- AMBER: Sander : Vrand flag
- AMBER: sander error
- AMBER: sander.QMMM: CHARGE keyword in divcon.in file
- AMBER: simulated annealing
- AMBER: snapshots of MD trajectory
- AMBER: Temp control
- AMBER: temperature control in coupled potential runs
- AMBER: temperature scaling with ntt=3(Langevin thermostat)
- AMBER: thermal ellipsoid-DNA
- AMBER: tleap: automatically identify and connect disulfide bonds?
- AMBER: Trajectory file conversion between Amber & Charmm
- AMBER: trival question about format of pev file and covariance matrix
- AMBER: turning off HB interactions
- AMBER: units
- AMBER: unknown residue: ABA
- AMBER: Updating Amber 7
- AMBER: Using AMBER to simulate carbon nanotubes?
- AMBER: Using TIP4P water in free energy calculation
- AMBER: xleap problem fixed!
- Hello Sir,
- Imaging problem
- Phosphoserine residue in AMBER
- RED II and changepot
Last message date: Thu May 05 2005 - 14:26:38 CDT
Archived on: Thu May 05 2005 - 14:30:04 CDT
361 messages sorted by:
[ author ]
[ date ]
[ thread ]
About this archive
|