AMBER Archive (2008) - May 2008 By Subject635 messages sorted by:
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Starting: Thu May 01 2008 - 00:57:35 CDT
Ending: Sat May 31 2008 - 19:02:17 CDT
- amber 9 compilation problem on IBM SP5
- Amber9 vs Amber10+MKL benchmark
- AMBER: $AMBERHOME/dat/slko
- AMBER: 3rd Annual CMM Workshop on QM/MM Simulations
- AMBER: about addles:“forrtl: severe (71): integer divide by z
- AMBER: about addles:“forrtl: severe (71): integer divide by zero”.
- AMBER: about glycam06
- AMBER: about hydrogen bond in amber force field
- AMBER: About Hydrophobic Interactions.
- AMBER: About reading in heme and CO molecule together with myoglobin
- AMBER: Adjust Force Field parameters
- AMBER: Amber 10 ambpdb bug?
- AMBER: AMBER entropy calculation
- AMBER: AMBER file preparation for protein-carbohydrate complex
- AMBER: AMBER Parallel test error
- AMBER: Amber Parameter Schema
- AMBER: AMBER PBSA
- AMBER: amber tools installation
- AMBER: amber10 installation
- AMBER: Amber10 installation error
- AMBER: Amber10 Installation error - incorrect file suffix
- AMBER: Amber10 testing problem
- AMBER: Amber10:Compiling with gcc 2.4.1
- AMBER: amber9 , ptraj vector commad issue
- AMBER: Amber9 vs Amber10+MKL benchmark
- AMBER: AmberTools on OS X fails tests
- AMBER: ambertools: static linking of user binaries is not supported on Mac OS X
- AMBER: An enquiry about dynamic simulations of oxygen binding to myoglobin (Ann N Y Acad Sci. 1986;482:222-
- AMBER: anal
- AMBER: analysis REMD
- AMBER: atom type in glycam06
- AMBER: Azobenzene: AMBER+Gromos Force Field parameters
- AMBER: B-factor calculation from data with different write frequencies
- AMBER: Bond-angle-dihedral-improper-vdw energy terms for part of a system
- AMBER: bugfix (imin=5) in amber9
- AMBER: build proline
- AMBER: building quadruplex with nab
- AMBER: bye
- AMBER: caculating nonpolar solvation energies
- AMBER: Calculate number of ions
- AMBER: Calculate the RESP charge Fe3+ of heme (p450)
- AMBER: calculating the energy from the restart file
- AMBER: can amber read .xyz files?
- AMBER: cannot read big .pdb files
- AMBER: CAVITY_SURFTEN & CAVITY_OFFSET default params
- AMBER: cfortran.h error with xlf90 compiler
- AMBER: COM RESTRAINT
- AMBER: Compilation of PMEMD
- AMBER: compilation problem with AMBER10
- AMBER: Compiling amber10 with xlf90 fortran compiler
- AMBER: Cysteine sulphonic acid parameters
- AMBER: DCCM correlation analysis
- AMBER: Deriving Force Field Parameters
- AMBER: DFTB parameters for O-P
- AMBER: Discontinuous Constant pH Restarts
- AMBER: distance
- AMBER: divcon
- AMBER: drawing repeated units
- AMBER: energy pairwise decomposition in GB/SA simulation
- AMBER: error in compilation elsize.cc
- AMBER: error when read inpcrd
- AMBER: Ewald error estimate
- AMBER: Ewald PARAMETER RANGE WRONG
- AMBER: Example .prepi file for nonstandard amino acids
- AMBER: ff94 vs. ff03
- AMBER: ff99 and ff03 forcefield parameters
- AMBER: Force field in water and in vacuum ??
- AMBER: Free Energy Calculations - parameters for MM
- AMBER: from Gromax to AMBER
- AMBER: GAFF Schema
- AMBER: gasteiger is not working with ambertools 1.0
- AMBER: GBSA SA calculation
- AMBER: Harmonic Force Constant
- AMBER: help MD running error
- AMBER: help to install AMBER9
- AMBER: Help with NMODE
- AMBER: how generate the final output file using mmpbsa
- AMBER: how to calculate delta G from IC50
- AMBER: how to extract energy
- AMBER: how to overcome theunusual bonds formation
- AMBER: How to set a ZN atom radius for PB calculations
- AMBER: How to transfer unformatted coordinates into formatted ones
- AMBER: Hybrid REMD amber10
- AMBER: Hydration free energies of charged ions using PME
- AMBER: Hydroxyprolines!!!
- AMBER: igb and ibelly
- AMBER: Improper dihedral parameters
- AMBER: initial velocities of MD
- AMBER: Inquiry on B-factor of NMR
- AMBER: install amber tools
- AMBER: Installation error on IBM cluster
- AMBER: Installation problem of AMBER on cluster
- AMBER: Installing PMEMD with Amber10
- AMBER: Iron-Sulfur Cluster
- AMBER: is in vacuo simulation neccessary?
- AMBER: Jarzinsky relationship
- AMBER: Jarzynski
- AMBER: Ligand energy minimization
- AMBER: ligand unit charge is not zero
- AMBER: mass weighted rms fit
- AMBER: massively parallel computation
- AMBER: mbondi radii for gaff atom types
- AMBER: Minimization in Octahedric Box
- AMBER: misplacement of TER by leap
- AMBER: MKL libraries/Amber10
- AMBER: MM-PBSA for carbohydrates
- AMBER: MM_PBSA output file
- AMBER: MM_PBSA problem in binding_energy
- AMBER: mm_pbsa problem: bad atom type: IP
- AMBER: mm_pbsa.pl not reading parameters for nmode
- AMBER: MMPBSA error
- AMBER: Mn2+ parameters in AMBER
- AMBER: molsurf
- AMBER: nab
- AMBER: neutral C-terminus and N-terminus parameters for amber
- AMBER: nfft1-3 too large
- AMBER: nmode "Atom out of bounds" for min of multiple ligands
- AMBER: nmode: number of atoms limitation
- AMBER: NON-BONDED parameters
- AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error
- AMBER: NTC and NTF
- AMBER: Parallel Self-guided Langevin simulation
- AMBER: parallel test / libmpi_f90.so.0
- AMBER: parameters in ff03 and ff99
- AMBER: parmbsc0 parameters for RNA.DNA systems
- AMBER: PBC in 2D
- AMBER: peptide at the box center during NVT-MD
- AMBER: periodic bondary condition
- AMBER: periodic boundary condition
- AMBER: PGI amber9 problems
- AMBER: point charges
- AMBER: Points on a Sphere
- AMBER: potassium ion
- AMBER: Prepgen
- AMBER: Prepgen does not give correct result?
- AMBER: pressure regulation methods
- AMBER: printing dipoles in Amber10 (and earlier)
- AMBER: Problems installing Amber Tools for Amber 10
- AMBER: protonate in Amber10
- AMBER: ptraj analyze matrix
- AMBER: ptraj analyze modes from nmode
- AMBER: ptraj has trouble with x-plor psf file from VMD
- AMBER: ptraj mask not working with psf file
- AMBER: ptraj rmsd calculation
- AMBER: Ptraj | Multiple trajout commands?
- AMBER: QM/MM
- AMBER: reading PDB trajectory
- AMBER: Regarding binding free energy calculation using MM_PBSA method
- AMBER: regarding segfault during energy minimization
- AMBER: reset time and comments
- AMBER: RESP and Jaguar
- AMBER: RESP charges of an unusual substrate
- AMBER: Restart MD Simulation
- AMBER: restarting molecular dynamics
- AMBER: rms
- AMBER: rmsd per residue
- AMBER: rmsd vs frame
- AMBER: SANDER and PMEMD with openmpi
- AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd'
- AMBER: Sander instead of PMEMD
- AMBER: Segmentation faults trying to run sander mpi
- AMBER: self-diffusion coefficient and Berendsen
- AMBER: silhouette width/coefficient after clustering by PTRAJ9.9
- AMBER: simulate dipole moment
- AMBER: simulating the pull out of Carbon Nanotube from polymer with AMBER
- AMBER: single stranded DNA
- AMBER: solvatebox
- AMBER: solvatebox error
- AMBER: Solvent mixture box
- AMBER: STEERED MD
- AMBER: steered MD initial state
- AMBER: subscribe amber
- AMBER: test.parallel.QMMM problem
- AMBER: tleap error message
- AMBER: to unsubscribe email
- AMBER: Torsion angle restrains and Jarzinsky
- AMBER: trajectories into trajectory
- AMBER: Umbrella Sampling for proteins
- AMBER: unable to compile AmberTools 1.0
- AMBER: uninstall of AMBER
- AMBER: Units, units units
- AMBER: using amber ports in Gromacs
- AMBER: velocity autocorrelation function for SPC felxible water model
- AMBER: Versions of mopac
- AMBER: VMD Movie
- AMBER: VMD Movie 2
- AMBER: VMD Movie 3
- AMBER: VMD Movie 4
- AMBER: Water residue tracking
- AMBER: Water tracking
- AMBER: Weighting factors in RESP charge fitting
- AMBER: Which is best temperature controlling method
- AMBER: xleap (draw using edit)
- AMBER: xLeap compilation issues
- rmsd vs frame
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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