AMBER Archive (2007) - Jul 2007 By Subject479 messages sorted by:
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Starting: Sun Jul 01 2007 - 08:10:09 CDT
Ending: Tue Jul 31 2007 - 16:34:12 CDT
- A little question
- amber-developers: -y option in sander
- AMBER: $AMBERHOME on PATH
- AMBER: (no subject)
- AMBER: ????pig5678??????
- AMBER: About amber7
- AMBER: about wrap the trajectory
- AMBER: adding organic molecule to polypeptide residue
- AMBER: adding water molecules in lipid bilayer model
- AMBER: amber7 and xleap
- AMBER: Amber9 analyze timecorr manual ambigous
- AMBER: Amber9 parallel compilation openmpi issues
- AMBER: antechamber
- AMBER: antechamber save prmtop inpcrd
- AMBER: antechamber: mopac charges
- AMBER: Atoms in conatct to a specific atoms during MD
- AMBER: Atoms in contact to a specific atoms during MD
- AMBER: Average potential energies and conformer ratios
- AMBER: Bad residue/molecule data in prmtop
- AMBER: Basic AMBER question
- AMBER: Belly Restraints and Distance Restraints
- AMBER: bound magnesium ions in proteins with GBSA
- AMBER: bug in nonbond_list.f (nee ew_setup.f)
- AMBER: Bug report: a bug of xleap associated with NumLock
- AMBER: can open PDB file in xleap
- AMBER: Can t open PDB file in xleap
- AMBER: Can't open PDB file in xleap
- AMBER: computational Ala scan
- AMBER: Convergence criteria in replica exchange simulations
- AMBER: convergence criterion not reached
- AMBER: convergence in classical MD
- AMBER: corrected reaction field energy and PBCAL
- AMBER: Could not find cntrl namelist
- AMBER: crg file
- AMBER: Cutoff list exceeds largest sphere in unit cell
- AMBER: DNA denatures during MD simulation
- AMBER: DNA RNA recognition problem
- AMBER: Error during compilation on a SGI Irix machine
- AMBER: errors in SHIFTS execution
- AMBER: extract protein energy from MD trajectory
- AMBER: FLAG LENNARD_JONES_ACOEF NAN
- AMBER: Fwd: Amber9 parallel compilation openmpi issues
- AMBER: Fwd: antechamber save prmtop inpcrd
- AMBER: Gaff Charge
- AMBER: GDP UNKNOWN ATOM TYPE: O3 warning
- AMBER: General AMBER questions
- AMBER: Generation of ESP(ind) within atomic charges derivation for polarizable force field
- AMBER: help with phosphotyrosine
- AMBER: heme force field
- AMBER: how to create an O linked N-acetylglucosamine in a protein
- AMBER: How to extract energy of molecule from the system with explicit water molecules
- AMBER: How to use antechamber properly?
- AMBER: incoherent intermediate scattering function
- AMBER: Input required for RESP
- AMBER: Known residue, unknown error in teLeap
- AMBER: large RMS fluctuations in turning off VDW interactions by TI
- AMBER: Linux install
- AMBER: manganese ion
- AMBER: md potential energy
- AMBER: MD simulation error
- AMBER: methods to approach two atoms
- AMBER: mm_pbsa and energy decomposition (missing BELE for MM in 1)
- AMBER: modelling substrate binding
- AMBER: Molecular Dynamic Simulations using TIP4P water - Please Help
- AMBER: MPI error message
- AMBER: MPI Quiescence problem in REMD
- AMBER: MPI script
- AMBER: Multiple residues position
- AMBER: Ne van del waals potential
- AMBER: netcdf support needed (Amber 9, sander imin = 5, -y flag)
- AMBER: Non bond list overflow
- AMBER: Non-standard amino acid residue
- AMBER: not getting topology and restraint file
- AMBER: Nucleic acid : nonplanarity
- AMBER: Nudget Elastic Band query
- AMBER: O-acetylated sugar
- AMBER: offending restraint
- AMBER: parallel compilation
- AMBER: PCA with ptraj
- AMBER: potential energy calculation
- AMBER: problem in compiling amber with suse 9.1 i686, finally in leap
- AMBER: problem in compiling amber9 and running amber9
- AMBER: problem in installing amber9
- AMBER: Problem while creating input files in antechamber
- AMBER: Problem while saving .top and .crd files.
- AMBER: Problem with leaprc
- AMBER: Problem with running Sander
- AMBER: Problems during compilation
- AMBER: Problems simulating a big system
- AMBER: program bug?
- AMBER: ptraj error
- AMBER: ptraj: RMS per residues and per time
- AMBER: QM-MM output interpretation
- AMBER: QM/MM LJ parameters
- AMBER: QMMM to follow reaction involving water
- AMBER: question about formatted mdrcrd files...
- AMBER: question about iwrap
- AMBER: Question about NAB (Nucleic Acid Builder)
- AMBER: Question on TIP4P model
- AMBER: RE Amber: Simulated Annealing
- AMBER: refc error
- AMBER: regarding distance restraints
- AMBER: related to new amber force field
- AMBER: resp
- AMBER: RESP charge generation
- AMBER: RESP_compilation
- AMBER: RESP_compilation_IT_WORKS
- AMBER: rmsd residue wise
- AMBER: running_RED-III
- AMBER: Sander Error
- AMBER: Saving (.)prepin file
- AMBER: secstruct command
- AMBER: Setting nonbonded cutoff to 1
- AMBER: SHAKE failure in TI calculation of zero sum model system of "ethane-to-ethane" in water
- AMBER: Simulated Annealing - Best way to create randomness
- AMBER: Simulated annealing - Nudget Elastic Band
- AMBER: Slight_error_on_Compiling_Replica_Exchange
- AMBER: Slow Processor Loads when Using PMEMD
- AMBER: Specific/Non-specific dihedral issue in Amber
- AMBER: Stirp command in ptraj
- AMBER: Substitute for GAFF
- AMBER: surface area over the trajectory
- AMBER: temperature fluctuation in REMD
- AMBER: testing amber9 for parallel use
- AMBER: tgtrmsmask and tgtfitmask
- AMBER: thermodynamic data for conformers
- AMBER: TIP4P MD simulations
- AMBER: Truncated Octahedron box volume
- AMBER: using amber to minimize structure obatined from cyana
- AMBER: Verifying Bond Angles
- AMBER: what's the problem of "Missing BELE for MM in 1 (residue 246)" in MM-GBSA?
- AMBER: Who has the structure file of beta-chitin?
- AMBER: xleap and amber7
- AMBER: À´×Ôpig5678µÄÓʼþ
- AMBER:charge file
- Contact TSRI: Ross Walker
- help:- regarding "perl" in analyzing the simulation
- how to create an O linked N-acetylglucosamine in a
- how to create an O linked N-acetylglucosamine in a protein
- MPI error message
- Problem with sander.MPI
- Query
- RED problem
- SV: AMBER: Atoms in contact to a specific atoms during MD
Last message date: Mon Dec 31 2007 - 15:27:41 CST
Archived on: Thu Jan 10 2008 - 17:13:09 CST
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