Amber Archive Nov 2003 by subject
- [Fwd: AMBER: MM_PB/GB/SA]
- AM1-BCC in Amber7
- AMBER water mediated contacts
- AMBER: 1 fs timestep for GB?
- AMBER: a problem with antechamber and leap
- AMBER: a problem with memory size
- AMBER: about some of the cards in Sander 7
- AMBER: absolute vs. relative binding free energy
- AMBER: AM1-BCC in Amber7
- AMBER: amber on mac cluster
- AMBER: antechamber mopac7 parameters
- AMBER: antechamber test failure
- AMBER: Any correct way to image a molecule ?
- AMBER: atmtypenumbers for halogens
- AMBER: atomtypenumber
- AMBER: average coordinates
- AMBER: Can use mm_pbsa_statistics.pl to calculate each snapshot's Delta Delta G, then give the SD
- AMBER: change force constants
- AMBER: charge fitting
- AMBER: Compaq Tru64 Unix
- AMBER: compiling amber using gcc on SGI Unix machines
- AMBER: Compiling AMBER7 on Suse
- AMBER: Correction [Separation of a Water molecules]
- AMBER: Cutress %cmass error
- AMBER: Diffusion constant
- AMBER: distrance restraints for alpha carbons
- AMBER: dual processor
- AMBER: fix some area
- AMBER: Fluorine in GBSA
- AMBER: Freezing of water with TIP3P potential.
- AMBER: gaff errors?
- AMBER: GB/SA
- AMBER: GIBBS - PMF problem: Lambda has not changed
- AMBER: handling non neutral systems
- AMBER: Hello
- AMBER: high temperature, 498K, unfolding simulations
- AMBER: How to estimate SD of the delta delta G between two mm_pbsa runs
- AMBER: image question
- AMBER: infinitely long DNA (to Yong Duan)
- AMBER: intermolecular force
- AMBER: large file for carnal
- AMBER: Lone pairs and resp
- AMBER: make clean doesn't clean leap
- AMBER: MD Equil
- AMBER: mgbjsb radii in GBSA
- AMBER: missing of VdW Parameters for N3
- AMBER: MM_PB/GB/SA
- AMBER: MM_pbsa
- AMBER: mm_pbsa and antechamber
- AMBER: molsuf failure with too many intersecting cusps
- AMBER: mpich problem
- AMBER: ndfmin in belly runs
- AMBER: Nmode problem
- AMBER: parmchk on MAC
- AMBER: PMEMD 3.1 Release - High Scalability Update to PMEMD
- AMBER: Pressure during MD
- AMBER: Problem with MPI_Finalize
- AMBER: Problems restarting with sander
- AMBER: protein MD - problem
- AMBER: Protein Rotation
- AMBER: Pseudouridine force field parameters
- AMBER: ptraj and charmm files
- AMBER: question about input files for small molecule with fluorine
- AMBER: RESP charge
- AMBER: RESP fitting limit?
- AMBER: Restart a simulation
- AMBER: restart MD program
- AMBER: restarted MD and ptraj
- AMBER: Restarting MD amber7
- AMBER: restrain
- AMBER: Restraints
- AMBER: restraints and reordering water
- AMBER: RMSd per residue
- AMBER: RNA and Protein questions (also some general questions)
- AMBER: rotation removal in sander GB
- AMBER: sander lastist
- AMBER: saveamberparm
- AMBER: Separation of a Water molecules
- AMBER: shake constraint on all bonds
- AMBER: structure refinement using CNS vs. AMBER
- AMBER: torsion problems of dummy atoms
- AMBER: update of BOX dim.
- AMBER: water mediated contacts
- AMBER: water prep file needed
- AMBER: Why I get the same TSTRA for different strucutures from Nmode calculation?
- AMBER: Zinc parameters
- AW: AMBER: Problem with MPI_Finalize
- Nmode problem
- Last message date: Wed Jan 14 2004 - 15:53:02 PST
- Archived on: Mon Feb 03 2025 - 05:53:16 PST
