AMBER Archive (2006) - Nov 2006 By Subject495 messages sorted by:
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Starting: Wed Nov 01 2006 - 02:38:55 CST
Ending: Thu Nov 30 2006 - 19:28:10 CST
- AMBER:
- AMBER: <kein Betreff>
- AMBER: ab initio terminology query
- AMBER: Acetone box
- AMBER: ACS Chicago potential symposia and OASYS abstracts
- AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft
- AMBER: Amber H-bond print?
- AMBER: Amber9 installation error
- AMBER: amber9 parralel compiling
- AMBER: Amber9 patch bugfix.all issue on SunOS 5.1
- AMBER: amber9 serial compile with pathscale on SuSe10.1/AMD64
- AMBER: Amber: disufide bond
- AMBER: ambpdb -pqr
- AMBER: ammonia parameters
- AMBER: Antechamber and gaussian questions
- AMBER: antechamber:tutorial
- AMBER: antechamber:tutorial. .
- AMBER: Atom Exclusion
- AMBER: big bond energy change from minimization and md (heating)
- AMBER: Biomolecular Simulation 2007
- AMBER: bond command between Zn and a CYM residue in one chain of a protein complex
- AMBER: bond information
- AMBER: bondtype problem
- AMBER: building a box
- AMBER: Building Library
- AMBER: Can we use the distance restraint in Replica-exchange simulation with AMBER8
- AMBER: Charge fitting in Amber
- AMBER: Closest(closest water)
- AMBER: Combine amber-force field and gaff94 for one molecule?
- AMBER: Combining Residues in LEaP for Lipid Bilayers
- AMBER: compile amber8 on IBM-sp4
- AMBER: Confusion about PBC
- AMBER: Did Antechamber support tertiary amines? How can I get the prepin file for it?
- AMBER: dihedral angle equation
- AMBER: DNA helix end stable?
- AMBER: energy minimizations in amber8 vs. amber9
- AMBER: erroneous placement of TER card
- AMBER: error about the number of snapshots
- AMBER: Error in compliling LEAP on Fedora 5
- AMBER: error in tleap test
- AMBER: Ethanol
- AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines
- AMBER: ff03 GLY HAs atom type
- AMBER: Flag for removal of translational and rotational center-of-mass (COM) motion
- AMBER: Format of the prmtop file (NUMBER_EXCLUDED_ATOMS) & (EXCLUDED_ATOMS_LIST)
- AMBER: GBSA implicit chloroform
- AMBER: gfortran and amber9 success on FreeBSD
- AMBER: gfortran/gcc versus ifort/icc
- AMBER: GLYCAM and ff98 atom-types
- AMBER: GLYCAM and ff98 atom-types]
- AMBER: grid output
- AMBER: H-bond analysis (Ptraj)
- AMBER: H-Bond Terms in amber force field
- AMBER: helices in GB simulations
- AMBER: how can i treat with long "mask" in ptraj analysis.
- AMBER: How the ensemble average calculated in Gibbs, AMBER7?
- AMBER: How to apply a force to some atom in a residues?
- AMBER: how to choose the parameter for the production/sampling run after the equilibration run
- AMBER: how to get complete prepin file
- AMBER: How to recompile sander for single-processor use in AMBER 8?
- AMBER: how to remove the rotation of system in periodic condition?
- AMBER: How to run MD simulation of a silicon containing complex with AMBER9?
- AMBER: How to run QM/MM simulation of DNA duplex bound with platinum moietes
- AMBER: How to specify a box with few walls rigid and others with periodic boundary conditions and then apply a pressure gradient across it?
- AMBER: How to specify user defined force fields or its parameters in amber??
- AMBER: How to start a Simulation of a peptide in bilayer
- AMBER: I got the error meassage in testcase of QMMM
- AMBER: Interaction Energy Calculation
- AMBER: klambda for TI method.
- AMBER: Langevin temperature control vs berendson heat bath
- AMBER: leap - compilation error
- AMBER: leap usage
- AMBER: Mass weights
- AMBER: matrix correl
- AMBER: minimization of Hydrogens with xLeaP
- AMBER: MM-PBSA problem
- AMBER: MM_PBSA
- AMBER: mm_pbsa does not terminate
- AMBER: Modifying a Force Field
- AMBER: Mutual exclusion of atoms
- AMBER: NAD ??
- AMBER: NEWPDB.PDB from antechamber
- AMBER: nmode output with ptraj
- AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5?
- AMBER: NONB values adjusted?
- AMBER: NTR for implicit solvent? How to defin restrain for two disconnected sequences?
- AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences?
- AMBER: ntt=1 in simulated annealing
- AMBER: opls_aa in amber
- AMBER: optimatized structure is so much different from the original pdb structure
- AMBER: parameters for beta peptides
- AMBER: parameters for silicon atom
- AMBER: PCA and projections
- AMBER: PCA results with explicit Vs Implicit solvation
- AMBER: Performing Interactive Essential Dynamics in Ptraj
- AMBER: Periodic simulations with net charge
- AMBER: phantom sander8 in dmesg
- AMBER: pmemd installation problem
- AMBER: Potential Energy Calculation
- AMBER: pqr file
- AMBER: prepin file nan
- AMBER: Probelm with running Amber 9 parallelly
- AMBER: Problem about dummy atoms when running antechamber
- AMBER: problem in calculating EGB using sander for ligand containing F atom
- AMBER: Problem Installing Amber in SGI Irix 6.5
- AMBER: problem installing amber9 with g95 gcc on a fc5 m/c
- AMBER: Problem of QM/MM calculation with amber 9 parallel version
- AMBER: problem of the REMD with nmr constraints
- AMBER: Problem with mask when using distance in ptraj
- AMBER: problem with NAD+ parameters
- AMBER: Problems amber mask in distance?
- AMBER: Problems with equilibrating the starting density
- AMBER: problems with saving self-built molecules parameters
- AMBER: protonated phosphate
- AMBER: ptraj and mdvel question
- AMBER: ptraj grid
- AMBER: PTRAJ RMS: dumping RMSd vs time data
- AMBER: Ptraj syntax change Amber8->Amber9 ?
- AMBER: ptraj----radial output files
- AMBER: Ptraj: correlation time
- AMBER: Ptraj: diffusion rate
- AMBER: Ptraj: radial distribution and correlation coefficient
- AMBER: PTRAJ: radius of gyration
- AMBER: Quantifying pi-pi interactions
- AMBER: question about the topology file
- AMBER: Radius of gyration
- AMBER: reading psf file
- AMBER: resp
- AMBER: respin file
- AMBER: Restarting with new topology
- AMBER: Restraints of the strand-endings?
- AMBER: saltconc for explicit solvent calculation.
- AMBER: sander error: rst file crash
- AMBER: SHAKE problem after minimization
- AMBER: simulating a small chain protein in water box
- AMBER: Simulation a small chain of amino acids - error in MD simulation
- AMBER: Snapshots (pdbs) from a trajectory.
- AMBER: Solvation Energies
- AMBER: Some warning !!! during SANDER ?
- AMBER: strange temperature behavior when changing to constant pressure
- AMBER: the energy and temperature both increasing during the simulation with NTT=0
- AMBER: The plc.frcmod file in the old version tutorial
- AMBER: too big EEL values in the minimisation output
- AMBER: top2mol2.c scanf format string bug
- AMBER: trajout script
- AMBER: Unable to find mopac charges in divcon.out
- AMBER: Unable to find solution for an error - "cannot successfully assign bond type"
- AMBER: Unit of force
- AMBER: vlimit exceeded for step 0, vmax = infinity
- AMBER: watershell and image commands
- AMBER: watershell command
- AMBER: what to do with the counter ions when minimizing average structure of DNA?
- AMBER: xleap
- AMBER: Xleap woes
- AMBER: Zn metal library
- AMBER: ZN prepin
- Amber: ZN-complex file
- AMBER: ZN-CYS prepin and frcmd file
- antechamber:tutorial
- Fluorine and Bromine Parameters in Amber 9
- Fwd: AMBER: sander error: rst file crash
- I got the error meassage in testcase of QMMM
- installation instructions
- top2mol2.c scanf format string bug
- Unit of force
Last message date: Sat Dec 30 2006 - 07:20:23 CST
Archived on: Wed Feb 21 2007 - 22:44:16 CST
495 messages sorted by:
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