AMBER Archive (2008) - Jan 2008 By Subject310 messages sorted by:
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Starting: Tue Jan 01 2008 - 19:44:34 CST
Ending: Thu Jan 31 2008 - 15:16:22 CST
- AMBER vs Gaussian : zero VDW parameters?
- AMBER:
- AMBER: (no subject)
- AMBER: A problem about antechamber
- AMBER: A problem to loadup the molecular in the xleap
- AMBER: a question of ptraj
- AMBER: about AM1-BCC in antechamber
- AMBER: About RAMD
- AMBER: Amber 9: Question regarding Test Failures and Compilers
- AMBER: Amber : neutralizing without adding ions
- AMBER: amber :antechamber problem
- AMBER: Amber DNA Model for X-ray Crystallography
- AMBER: AMBER installation problem
- AMBER: Amber parallel version on CPU power of 2 only
- AMBER: AMBER-8 parallel installation - test run failure
- AMBER: Amber9 fails test.parallel
- AMBER: ANTECHAMBER NAMING
- AMBER: antechamber problem
- AMBER: antechamber problems
- AMBER: antechamber run on charged system
- AMBER: Atomic restraints
- AMBER: Back on track
- AMBER: BCC charges
- AMBER: benchmark walltime to ps/day calculation
- AMBER: build RNA by nucgen
- AMBER: check COM velocity
- AMBER: chromophore parameters for Molecular Dynamics
- AMBER: Cluster analysis
- AMBER: collision with surface
- AMBER: Combine mdcrd
- AMBER: Combine mdcrd files
- AMBER: Combining multiple structures into single pdb
- AMBER: connectivity lose during the minimizations
- AMBER: connectivity problem
- AMBER: convergence of free energy calculations
- AMBER: diblock copolymer
- AMBER: Distorsion in protein and ligand during MD
- AMBER: distorted aromatic rings
- AMBER: Disturb you for help !?=
- AMBER: Disturb you for help!
- AMBER: disulfide bridge with ff03ua FF
- AMBER: ELAN_EXCEPTION @ --: 6 (Initialisation error) ELAN_EXCEPTION @ --: 6 (Initialisation error)
- AMBER: Entropy calculation
- AMBER: ff03-compatible parameters/charges for phosphothreonine and phosphotyrosine
- AMBER: flexible molecule parameterization
- AMBER: Fwd: Distorsion in protein and ligand during MD
- AMBER: GAFF atom types for flavin (again)
- AMBER: graphite
- AMBER: Has anyone seen a protein fall apart due to PBCs?
- AMBER: Help in radii
- AMBER: Help needed to analyze DNA Holliday Junction - Drug Binding MD simulations.
- AMBER: Help reg. input file
- AMBER: How to build a dimer using amber
- AMBER: How to determine the basic parameters of a Replica Exchange Molecular Dynamics(REMD?
- AMBER: input options for replica exchange simulations
- AMBER: Installing OpenMPI
- AMBER: LEAP: solute concentration
- AMBER: MD of protein-ligand comlex
- AMBER: MM-PBSA problem
- AMBER: mm/pbsa and saltcon effect
- AMBER: mmpbsa binding energy
- AMBER: NMR refinement
- AMBER: NMROPT=1 in minimisation
- AMBER: NPT to NVT
- AMBER: Nudged Elastic Band initial heating problem
- AMBER: Number of Hydrogen Bonds?
- AMBER: offset residue numbering
- AMBER: PEO-PLA/PCE
- AMBER: pmemd 9.0 compilation error
- AMBER: Problem about antechamber
- AMBER: problem in neturalization
- AMBER: problem to compile PMEMD?
- AMBER: problem with group input
- AMBER: Problem with: Increase lastrst in the &cntrl namelist
- AMBER: problem:capping
- AMBER: Problems in execution of Replica Exchange calculations Amber 9.0
- AMBER: problems of antechamber
- AMBER: problems with restart of MD
- AMBER: ptraj: new mask parser
- AMBER: QM/MM Heating
- AMBER: QM/MM: input conversion error
- AMBER: question about antechamber
- AMBER: radial distribution function in ptraj
- AMBER: Reference for rmsd
- AMBER: Reg cysteine protonaitons states in pH constant MD
- AMBER: Reg cysteine protonation states
- AMBER: regarding :scee
- AMBER: Regarding neutral Arginine unit
- AMBER: RESP
- AMBER: RMSD calculation using AMBER7
- AMBER: running AMBER in NAMD Trucated Octahedron
- AMBER: SANDER BOMB in subroutine nonbond_list
- AMBER: setting periodic box
- AMBER: solvateBox/solvateDontClip
- AMBER: Structure comparison-NMR and X-ray structure using AMBER9
- AMBER: Systematic drift
- AMBER: temperature spikes
- AMBER: The energy minimization of SIngle RNA chain
- AMBER: Thermodynamic integration with positional restraint?
- AMBER: Tinker 4.3
- AMBER: Torsional Forcing to generate PES?
- AMBER: Tough time with antechamber
- AMBER: Tough time with antechamber (UPDATE, still need help)
- AMBER: tutorial_8_section_6
- AMBER: Unable to create the top & crd files for a protein+ligand pdb structure
- AMBER: Units of atomicfluct
- AMBER: using hydrogen bond facility to monitor ion pair interaction
- AMBER: Using VMD to calculate end-to-end distance?
- AMBER: Visualizing Electrostatic Potential
- AMBER: vlimit exceeded error
- AMBER: Why LEap created a new H atom for CYM while generating TOPOLOGY file?
- Systematic drift
- timestep problem
Last message date: Wed Dec 31 2008 - 22:47:27 CST
Archived on: Thu Jan 08 2009 - 16:01:47 CST
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