AMBER Archive (2004) - Oct 2004 By Subject377 messages sorted by:
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Starting: Fri Oct 01 2004 - 09:30:53 CDT
Ending: Sun Oct 31 2004 - 13:39:48 CST
- AMBER 8 default is now HIS->HIE and not HIS->HID - typo?
- AMBER:
- AMBER: (no subject)
- AMBER: A question on AMBER8 installation
- AMBER: a question on ntwx and ntwr
- AMBER: A torsion parameter in AMBER2003 force field
- AMBER: about AM1-BCC charge method
- AMBER: about antechamber
- AMBER: About missing residues
- AMBER: About STD in NMODE
- AMBER: add charge error message: Number of electrons is odd
- AMBER: AddIons
- AMBER: AM1-BCC charges
- AMBER: Amber 8 - OS support.
- AMBER: AMBER 8 default is now HIS->HIE and not HIS->HID - typo?
- AMBER: amber 8 error
- AMBER: AMBER 8 installation - continued
- AMBER: AMBER 8 installation trouble
- AMBER: amber 8 parallel problem
- AMBER: amber with MPI
- AMBER: amber7 test on osx
- AMBER: Amber8 - Energy Calculations
- AMBER: Amber8 compilation in Dec-Alpha
- AMBER: amber8 compilation on AIX (regatta)
- AMBER: Amber8: ifort 8.0.046 Woo hoo!
- AMBER: Amber: what different?
- AMBER: Antechamber on cluster with queue?
- AMBER: antechamber, mopac RESTART
- AMBER: atoms out of bounds
- AMBER: BOND energy during minimisation
- AMBER: Box information from Amber
- AMBER: bugfix.17
- AMBER: building a small molecule
- AMBER: Calculating H-Bond networks using ptraj
- AMBER: Carnal & Radius of gyration
- AMBER: changepot
- AMBER: changepot & mol2 file
- AMBER: Comparison of simulation results on amber7 and amber 8
- AMBER: Compiling using pgf90
- AMBER: const-P MD at high T
- AMBER: continue for No radius for F atom in MM_PBSA
- AMBER: Continued:No skew or curtosis when zero variance in moment
- AMBER: Curves 5.3
- AMBER: difference in GBSOL in amber7 and amber8
- AMBER: distance between images
- AMBER: Distance Restraints
- AMBER: error in mm_pbsa
- AMBER: error in using AM1-BCC charge by antechamber
- AMBER: errors in SGI
- AMBER: exclusion list
- AMBER: file corruption with ptraj
- AMBER: frcmod_dmso
- AMBER: from gaussian to antechamber
- AMBER: generalized Born parameters
- AMBER: getting new box info
- AMBER: GIbbs : failure to start
- AMBER: H bond calculation of CHARMM trajactory using PTRAJ
- AMBER: Hot solvent/cold solute reference
- AMBER: how to neutralize the peptide
- AMBER: how to set up more than 3 groups constrain
- AMBER: hydrogen bonds
- AMBER: icc 8.0 built antechamber
- AMBER: Is AME equal to NME?
- AMBER: klambdas and Weights for Gaussian Quadrature
- AMBER: long minimization in sander
- AMBER: MAXATOM failure in ANTECHAMBER
- AMBER: MAXMASK problem
- AMBER: MD after partially solvated
- AMBER: MD problem (very long parhabs endless runtime)
- AMBER: mdinfo on amber6
- AMBER: mm-pbsa problem
- AMBER: MM_PBSA reproduction of literature values and accuracy
- AMBER: MMPBSA PB parameters - PARSE implementation in Amber
- AMBER: modes analysis in ptraj
- AMBER: More AMBER 8 compilation problems on OSF1 4.0F
- AMBER: More installation problems on Solaris 8
- AMBER: neutral Arg, charged Tyr ??
- AMBER: nmode error
- AMBER: No radius for F atom in MM_PBSA
- AMBER: No skew or curtosis when zero variance in moment
- AMBER: normal mode analysis after energy minimizaiton using sander
- AMBER: Note to all concerning filtering of messages posted to the amber list.
- AMBER: order parameter
- AMBER: parallel of sander_classic
- AMBER: parameter error for a ligand
- AMBER: Parameter for chlorophyll
- AMBER: Parameters for phosphorylated aminoacids
- AMBER: PBSA parameter question (Radii and Charges)
- AMBER: Phosphoserine
- AMBER: Plot B-factor extracted from PDB file
- AMBER: pmemd and ifort 8.1
- AMBER: PMF
- AMBER: Problem with AMBER/ANAL
- AMBER: problem with antechamber
- AMBER: Problem with EDIT (AMBER 5)
- AMBER: Problem with installing Amber8: Where are the MK libraries?
- AMBER: problem with protonate
- AMBER: problems with dihedrals
- AMBER: problems with dihedrals - extended information
- AMBER: process_mdout.perl
- AMBER: process_mdout.perl: work now
- AMBER: ptraj analyze modes question
- AMBER: ptraj and clustering
- AMBER: ptraj and PCA
- AMBER: ptraj questions
- AMBER: pure aromatic?
- AMBER: Question about Amino acid mutations
- AMBER: question about mm_pbsa and nmode
- AMBER: question about molsurf
- AMBER: question about nmode
- AMBER: question about ptraj's Mask
- AMBER: Question about restart MD
- AMBER: Question about Xleap
- AMBER: question on NAB
- AMBER: question on NMR restrain
- AMBER: Questions about MD sampling
- AMBER: questions regarding JTREE
- AMBER: recovering total force array
- AMBER: restrain one tosion angle
- AMBER: rms fluct and displacement in modes analysis
- AMBER: rms fluctuation units from ptraj
- AMBER: RSM & ptraj
- AMBER: RSM fluctuation & residues
- AMBER: RSM fluctuation by residues
- AMBER: Running on MPI
- AMBER: sander error
- AMBER: sander gets stuck
- AMBER: Sander-7 for Win32
- AMBER: sander8
- AMBER: Settings about frozen atoms in sander
- AMBER: small molecule simulation
- AMBER: solute leaving PBC box
- AMBER: solvation free energies using mmpbsa
- AMBER: Trajectory corruption
- AMBER: trajectory file question?
- AMBER: Use of intel compilers v8.1 for Amber 8.
- AMBER: Wich CPU?
- HIERARCHY OF INTERACTIONS"
- process_mdout.perl
- rms fluct and displacement in modes analysis
- RSM & ptraj
- sander8
Last message date: Thu May 05 2005 - 14:26:38 CDT
Archived on: Thu May 05 2005 - 14:30:04 CDT
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