Amber Archive Oct 2003 by subject
- AMBER:
- AMBER: 'vlimit exceeded'
- AMBER: a problem with xleap
- AMBER: a question
- AMBER: Added water and mm_pbsa
- AMBER: addions/xleap question
- AMBER: Addles
- AMBER: amber 7 for industrial application
- AMBER: Amber charge problem
- AMBER: AMBER quasih question(s)
- AMBER: aminoacid mutation
- AMBER: antechamber
- AMBER: antechamber and bond type
- AMBER: Atomic charges and internal H-bond
- AMBER: calculation of LJ 12-6 from .dat file (fwd)
- AMBER: calculation of LJ 12-6 from .dat file (fwd)-CORRECTION!!!
- AMBER: carnal
- AMBER: carnal iteration deviation from original crd file
- AMBER: charmm force field in amber
- AMBER: comparing versions 6.0 and 7.0 of AMBER
- AMBER: Compiling AMBER
- AMBER: Compiling AMBER, ie, number of atoms limit
- AMBER: Compiling antechamber on amber 8
- AMBER: constant pressure in GB
- AMBER: correlated motion
- AMBER: density equilibrium & harmonic restrain
- AMBER: ECC vs non-ECC (non-amber issue)
- AMBER: force field for hybrid systems
- AMBER: Freezing the residues
- AMBER: frozen x unfrozen
- AMBER: frozen x unfrozen and the gibbs tragedy
- AMBER: H-bond analysis
- AMBER: how to measure the minor groove widths of a DNA?
- AMBER: how to mend the peptide with missing residues?
- AMBER: ibelly
- AMBER: ibelly in AMBER 6
- AMBER: ibelly problem
- AMBER: Implicit MD simulations in Amber7
- AMBER: Implicit precision in sander vs architecture
- AMBER: improper
- AMBER: infinitely long DNA & moil-view?
- AMBER: input/output error
- AMBER: Installation Problem, xleap can't load pdb files
- AMBER: is there a good program to quantitatively analyze hydration effect?
- AMBER: JAC on NCSA titan (Itanium 2 833MHZ)
- AMBER: large file for carnal
- AMBER: MD simulation: enzyme and its substrate
- AMBER: MD simulation: enzyme and its substrate!!
- AMBER: mddisplay
- AMBER: MeCNBOX & EWALD bomb
- AMBER: memory SC45
- AMBER: mgbjsb Radii in GBSA
- AMBER: minimize a covalently bounded protein-ligand complex
- AMBER: mm_pbsa crg file
- AMBER: mm_pbsa example
- AMBER: mm_pbsa rna/dna charges
- AMBER: mm_pbsa with amber7
- AMBER: monte carlo
- AMBER: mopac
- AMBER: more questions about igb
- AMBER: nmanal projection
- AMBER: Not getting restrt file on running sanders
- AMBER: nstlim
- AMBER: one more question
- AMBER: output frequency
- AMBER: PMEMD 3.1 Release - High Scalability Update to PMEMD
- AMBER: Pressure in NVT ensemble
- AMBER: prmtop file format
- AMBER: problem in tleap
- AMBER: problem with pdb files
- AMBER: Protein Rotation
- AMBER: question about ewald
- AMBER: Radius of Gyration and RMSD
- AMBER: reduce box and delete excess solvent
- AMBER: regarding trajectory input and output with ptraj or Carnal
- AMBER: Removal of Rotational and Translational Motion in AMBER6
- AMBER: Resp Problem
- AMBER: Restraints to maintain base pair planarity
- AMBER: Reverse TI run
- AMBER: RMSD and Radius of Gyration
- AMBER: RMSd per residue
- AMBER: running sander_classic on multiple processors
- AMBER: sander: vlimit problem
- AMBER: SC45
- AMBER: SHAKE for TIP4P!
- AMBER: SHAKE question
- AMBER: Simulation of small protein
- AMBER: Simulation of small protein (MD Display tips)
- AMBER: solute images
- AMBER: stable protein
- AMBER: STREAM problems : segmentation fault with CARNAL
- AMBER: surface code in Amber
- AMBER: torsional restraints for groups of atoms
- AMBER: tru64 alpha
- AMBER: Water as part of protein in mm_pbsa calculation
- AMBER: What does this error message mean?
- AMBER: what is the unit for the energy calculated from MM_PBSA?
- atomic charges and internal H-bond
- mm_pbsa problem
- Last message date: Tue Nov 11 2003 - 14:53:01 PST
- Archived on: Fri Apr 26 2024 - 05:53:21 PDT
