AMBER Archive (2005) - Nov 2005 By Subject310 messages sorted by:
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Starting: Tue Nov 01 2005 - 02:15:23 CST
Ending: Wed Nov 30 2005 - 23:43:55 CST
- AMBER:
- AMBER: About WHAM program
- AMBER: addition to the last mail (lahey F95) !
- AMBER: AMBER 8 compilation with lahey F95 !
- AMBER: AMBER compilation with -DREM
- AMBER: anal and periodic boundary conditions
- AMBER: ANAL problem
- AMBER: antechamber charge methods
- AMBER: Antechamber error
- AMBER: Antechamber/Leap, problem with Improper angles
- AMBER: Any way to get different charge on same type atom
- AMBER: Ask for helpf to get examples for MM-PBSA with AMBER8
- AMBER: average struct without solvent
- AMBER: bug report
- AMBER: bugfix 49
- AMBER: calculating end-end distance
- AMBER: calculating time correlation functions with ptraj
- AMBER: CD spectrum
- AMBER: Cluster - input files
- AMBER: cluster analysis
- AMBER: Comparing EELEC from amber and that calculated in the trivial fashion.
- AMBER: constant pressure vs. constant volume heating
- AMBER: Density of Cyclohexane box
- AMBER: DNA simulations
- AMBER: EEL and EAMBER values
- AMBER: Error message
- AMBER: ESP exceeds the MAXESP(20000),
- AMBER: ew_legal.h
- AMBER: FATAL error with ATP and MG2 - fixed
- AMBER: FATAL error with ATP, MG2 residue
- AMBER: fedora installation problem
- AMBER: Fluorine in MM-PBSA (AMBER8)
- AMBER: gaff sugar residue instability
- AMBER: GRID program used to add ions and solvate AMBER minimized structures
- AMBER: How to check for water mediated hydrogen bonds?
- AMBER: how to extract the residues of first solvation shell from the simulated system after the production?
- AMBER: How to generate a RMSd-residue number graph using AMBER8 ptraj?
- AMBER: How to use XLEAP to link one atom in a monomer to another atom in ano
- AMBER: How to use XLEAP to link one atom in a monomer to another atom in another monomer? (where both the 2 monomers are in a same pdb file)
- AMBER: How to wrap a truncated octahedron water box into the primary box?
- AMBER: ifort compiling problem
- AMBER: Improper Torsional Parameters
- AMBER: input for mm_pbsa
- AMBER: iwork array for nmr
- AMBER: just one more try:) xleap, opteron, pgi and segmentation fault. (fwd)
- AMBER: Leap error: Could not find atom type: CE
- AMBER: Leap handling crystallographic waters
- AMBER: Leap task
- AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list
- AMBER: Making movie from AMBER trajectory
- AMBER: Making movie from AMBER trajectory using UCSF Chimera
- AMBER: Metals with Amber
- AMBER: Mg2+ issues of using MM-PB/GBSA
- AMBER: MM-PBSA: plot the "Ggas+Gsol" vs time
- AMBER: MM/PBSA basic questions
- AMBER: mm_pbsa
- AMBER: MM_PBSA problem
- AMBER: MM_PBSA problem---Illegal division by zero at ...
- AMBER: MM_PBSA question
- AMBER: MM_PBSA stopped at some snapshot
- AMBER: MM_PBSA_parameter
- AMBER: more data points on the parmchk problem
- AMBER: My model loses its motion in MD
- AMBER: need clarification on EWALD BOMB error
- AMBER: Parameters for S-substituted nucleic acids
- AMBER: PARM-99
- AMBER: parmchk segfaulting
- AMBER: pH=1 MD simulation
- AMBER: PMEMD limitation on NFFT
- AMBER: Polarization & energy analysis
- AMBER: ptraj distance mask
- AMBER: ptraj Hbond analysis
- AMBER: Quantifying DNA perterbation
- AMBER: Question about PB bomb
- AMBER: Question about PDB format
- AMBER: Question about using MM_PBSA
- AMBER: question convert crd files to pdb files
- AMBER: Question of PB bomb
- AMBER: Questions about MM-PBSA in Amber8
- AMBER: rdparm bug
- AMBER: recent Chimera MD enhancements
- AMBER: RED and EP from GAMESS
- AMBER: RED&GAMESS: sorry ... my mistake
- AMBER: RED: extra variable definition
- AMBER: REM difficulties
- AMBER: reordering atoms after antechamber
- AMBER: Residual Dipolar Refinement
- AMBER: Resp install problem
- AMBER: Resp install problem, again
- AMBER: RESP problem RESP
- AMBER: restart coordinate file
- AMBER: restart file and crd file
- AMBER: rounding in xleap when using saveoff command...
- AMBER: Solvation in trifluoroethanol
- AMBER: some problems with Antechamber
- AMBER: sp0 console message after using addAtomTypes
- AMBER: Targeted MD
- AMBER: temprature and restraint in constant volumm MD
- AMBER: Time Correlation Functions with Amber
- AMBER: tkbc2
- AMBER: tRNA's modified bases in the Amber parameters database
- AMBER: Using OPLS atom types
- AMBER: using periodic boundary conditions to create infinite double helix
- AMBER: Will Amber 9 available?
- AMBER: XRED II error while initializing
- gaff sugar residue instability
Last message date: Sat Dec 31 2005 - 12:51:27 CST
Archived on: Sat Dec 31 2005 - 12:51:46 CST
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