AMBER Archive (2006) - Apr 2006 By Subject289 messages sorted by:
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Starting: Sat Apr 01 2006 - 07:17:02 CST
Ending: Sun Apr 30 2006 - 23:09:35 CDT
- about the fix_numbering_pdb.csh in Amber Tutorial_eight
- AMBER:
- AMBER: "average" command in ptraj
- AMBER: "vector" command in ptraj
- AMBER: 7-Methylguanine force field parameters
- AMBER: a question
- AMBER: a question about "solvateoct" in AMBER 8
- AMBER: a quetion
- AMBER: about the decomposition energies using mm/pbsa
- AMBER: about the execuation of REMD with sander of amber9
- AMBER: about the shake with self-guide LD
- AMBER: Amber 9, sander imin = 5, -y flag
- AMBER: amber memory usage
- AMBER: amber7 compiling error
- AMBER: amber9 compilation error on SGI altix
- AMBER: AMBER9: MacG5 parallel sander.MPI
- AMBER: ambpdb and original PDB
- AMBER: An issue with the "multimolecule and multiconformational" resp fit
- AMBER: angle between planes
- AMBER: Announcement: Amber 9 is now available
- AMBER: Antechamber & atom types
- AMBER: Any difference about RESP or ESP with Chelpg or MK
- AMBER: Born igb =2
- AMBER: Calculation of g(r) from PTRAJ
- AMBER: compile error: can't locate file for: -lcrt1.o
- AMBER: compiling errors
- AMBER: Constant P for non-orthorhombic cells
- AMBER: Could not find atom type.
- AMBER: deviations from idealized geometry
- AMBER: Did these differences come from so-called "different machines" ?
- AMBER: Different result for serial and parallel sander with IREST=1 (AMBER 8) !
- AMBER: distance restraints for umbrella sampling
- AMBER: DNA structure
- AMBER: DNA tutorial, in vacuo minimization
- AMBER: Dual Xeon mpich compilation error
- AMBER: dual xeon mpich compilation problem: sorted
- AMBER: Entropy calculations with Nmode and ptraj
- AMBER: Error in the MD run
- AMBER: error propagation in MM-PBSA binding free energy calculation
- AMBER: Error when compiling amber9 ptraj
- AMBER: errors in mm_pbsa.in in AMBER 8 mannul ?
- AMBER: experiments with amber9 and fortran nag f95 on mac os x 10.4.3
- AMBER: Force field for DNA
- AMBER: Force Field Question
- AMBER: Fujitsu frt compiler
- AMBER: heating process
- AMBER: How I wasted a rainy Friday in San Diego
- AMBER: How to build 1,4-dimethyl benzene with amber9
- AMBER: How to evaluate the binding energy of a ligand?
- AMBER: how to perform parallel MD on a linux cluster with Platform LSF product
- AMBER: how to restrain the intramolecular hydrogen bond
- AMBER: ibelly & fix atom
- AMBER: increase in computational time with LES
- AMBER: Installing Delphi to perform mm_pbsa analysis?
- AMBER: internal coordinates
- AMBER: Langevin mode error??
- AMBER: LES copies
- AMBER: LES error
- AMBER: Mass wieghted Covariance Matrix
- AMBER: MM-GBSA decomposition
- AMBER: MM-PBSA problem
- AMBER: mm-pbsa: distant-dependent dielectric constant
- AMBER: mm_pbsa: "Missing values for MM ..."
- AMBER: MM_PBSA: “Found unknown atflag DELPHI”
- AMBER: modeling zinc binding site
- AMBER: molsurf or LCPO method in MM_GB/SA?
- AMBER: NGL error when creating snapshots for MM/PB(GB)SA
- AMBER: nmode different units
- AMBER: Nmode memory allocation error ?
- AMBER: Non-periodic simulations: How is the system kept together?
- AMBER: Obtaining an average structure from a trajectory
- AMBER: one question about mm_pbsa
- AMBER: organic molecule - from newbie :)
- AMBER: passwordless ssh stopped working
- AMBER: PB bomb in pb_atmlist(): MAXNEI too short
- AMBER: PCA
- AMBER: Performing Simulated Annealing?
- AMBER: POPC parameters
- AMBER: printing Amber VdW radii as separate column in pdb files
- AMBER: probable bug in antechamber
- AMBER: Problems compiling amber9
- AMBER: problems with saveamberprep command
- AMBER: protocols for NMR protein refinement with AMBER
- AMBER: Question about interpretation of sander.QMMM results
- AMBER: questions about mm_pbsa
- AMBER: reconstructing PMF
- AMBER: RESP problem
- AMBER: Respgen segemtation fault
- AMBER: Restarting constant pressure sims with restraints
- AMBER: RMS
- AMBER: RMS (fwd)
- AMBER: rmsd value for organic molecule
- AMBER: saltcon with explicit water?
- AMBER: Saving single coordinate set from Amber trajectory file as a restrt file.
- AMBER: Semi-empirical parameterization -- van der Waals and H-bonding?
- AMBER: separating LES copies in moil view
- AMBER: Setting box dimensions in leap
- AMBER: Test Failure during amber9 serial compilation
- AMBER: the best force field for DNA
- AMBER: timing estimates
- AMBER: two references
- AMBER: two references- I got them, thank you!
- AMBER: Umbrella sampling
- AMBER: Using XML for Amber files
- AMBER: VdW radii in the topology file
- AMBER: what is the integration scheme for langevin dynamic used in amber8
- AMBER: Which one is the best force field for DNA?
- AMBER:a problem in parallel compiler
- Respgen segemtation fault
- Respgen segemtation fault - debug attempt
Last message date: Sat Dec 30 2006 - 07:20:23 CST
Archived on: Wed Feb 21 2007 - 22:44:15 CST
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