AMBER Archive (2008) - Jul 2008 By Subject445 messages sorted by:
[ author ]
[ date ]
[ thread ]
About this archive
Starting: Tue Jul 01 2008 - 03:04:45 CDT
Ending: Thu Jul 31 2008 - 22:21:54 CDT
- amber 10 and mpich2 (got eof on console error message from mpich2)
- AMBER Question
- AMBER:
- AMBER: "radius = 0.000"
- AMBER: # of ligands and receptors in mmpbsa
- AMBER: 1.5ns rst file to PDB file Conversion Error
- AMBER: [amber/glycam] dealing with fucose...
- AMBER: a link for Amber ff ported to Charmm
- AMBER: about QMMM output
- AMBER: about RMSD per residue
- AMBER: ACPYPI announcement
- AMBER: adding missing residues
- AMBER: Alanine scanning
- AMBER: amb2gmx for big systems
- AMBER: amber 10 and mpich2 (got eof on console error message from mpich2)
- AMBER: Amber 10 on the BlueGene
- AMBER: AMBER 10: Fortran Runtime Error
- AMBER: amber 10: sander and pmemd performance
- AMBER: amber ff and how it deals with out-plane chiral C
- AMBER: Amber tools 1.2 test failure (installation)
- AMBER: AMBER10: ambpdb problems
- AMBER: AMBER10: Fortran Runtime Error
- AMBER: amber10: pmemd gfortran
- AMBER: amber9 / difference of igb=0 and igb=6
- AMBER: amber9 install problem
- AMBER: Amber9 vs AmberTools 1.0: weird imaging problem with ptraj?
- AMBER: AmberTools-1.1 port for FreeBSD
- AMBER: AmberTools1.1 (and 1.0) antechamber endless loop
- AMBER: analysing normal modes
- AMBER: antechamber and charmm
- AMBER: antechamber generated input for gaussian error
- AMBER: Atom type with 10-12 and 6-12 interactions in Amber9
- AMBER: bad nonbon in nmode (amber9)
- AMBER: bellymask for DNA backbone doesn't seem to work
- AMBER: big molecule numbers
- AMBER: big molecule numbers ( simulation with many formamide molecules )
- AMBER: bond command
- AMBER: calculating the enthalpy of evaporation
- AMBER: Charge neutralization, GlcNac & GalNac improper torsional angles from old PREP
- AMBER: compile amber10 on Mac
- AMBER: concerning force fields ( to Karl Kirschner )
- AMBER: configure_amber (10) for pg compilers
- AMBER: Constant pH with new parameters (amber10)
- AMBER: difference between sander and NAB
- AMBER: Distance diagnolization matrix plot
- AMBER: DMSOBOX
- AMBER: Does clustering involve fitting?
- AMBER: empty output
- AMBER: Energy analysis
- AMBER: Energy minimization of protein-ligand complex
- AMBER: Error when performing Alanine scanning
- AMBER: EVB tests failure
- AMBER: files in Amber directory ( to Junmei Wang )
- AMBER: For help: how to perform double decoupling thermodynamic integration calculation in AMBER10
- AMBER: For help: Thermodynamic Integration of solvation free energy using soft-core potential
- AMBER: for mask in rms
- AMBER: Force Field parameters : A new chemical compound
- AMBER: Force fields for REMD with GB solvent
- AMBER: fortran runtime error in "make test.serial" with gfortran
- AMBER: free energy
- AMBER: FreeBSD "port" for AmberTools-1.2
- AMBER: High force constant for MD ???
- AMBER: how to generate psf file using the AMBER topology file
- AMBER: how to get the potential energy of a protein from the system
- AMBER: How to obtain the oriented trajectories?
- AMBER: Hydroxyproline in AMBER
- AMBER: imin = 5 and PBC
- AMBER: improper dihedral in ff03 united atom forcefield
- AMBER: improper dihedrals in 03 united atom force field
- AMBER: Inconsistent types (INTEGER(4)/REAL(8)) - Is it serious ?
- AMBER: Indentifying cluster center structures in trajectory
- AMBER: Installation of Amber 10 on Dual-Core Intel Mac
- AMBER: Installation on Mac OSX G5 dual processor
- AMBER: interaction energies in Amber
- AMBER: interaction energies in Amber and VMD/NAMD
- AMBER: interaction energies in Amber and VMD/NAMD (SOLVED)
- AMBER: is amber workshop available this summer??
- AMBER: Ligand force field generation, and its consistency with the force field of the protein.
- AMBER: mask for oligosaccharide
- AMBER: mm_pbsa incorrect complex prmtop file
- AMBER: Model of deoxyadenosine in Cornell 95 paper
- AMBER: NMA
- AMBER: Nmode entropy calcs
- AMBER: NMR refinement
- AMBER: NONBONDED_PARM_INDEX
- AMBER: NPRO net charge in amber10/dat/leap/lib/all_aminont03.lib is 0.900026, why?
- AMBER: opls/aa in Amber status
- AMBER: parameters for Fe coordinated to four CYS ?
- AMBER: paricular atom coordinates?
- AMBER: parmbsc0
- AMBER: pmemd 10 output
- AMBER: PMEMD and polarized force field ff 02
- AMBER: PMEND 9 compilation problems
- AMBER: POL3 with gaff and ff02EP
- AMBER: Polarizable force field for divalent ions?
- AMBER: prepare an initial structure in Amber
- AMBER: Prepgen
- AMBER: Problem in .parmtop file
- AMBER: Problem with box dimension in AmberTools ptraj
- AMBER: problem with rdparm
- AMBER: problem with restraints
- AMBER: Problems in restrained minimization
- AMBER: Problems with Frozen atoms
- AMBER: protonated guanine, cytosine parameters
- AMBER: Protonated Phosphate Problem
- AMBER: ptraj problem with centering in the box
- AMBER: ptraj problem with imaging
- AMBER: ptraj selection
- AMBER: ptraj: projection command missing in dispatch.c (AMBER 10)
- AMBER: Q: ntc = 3 parallel runnable not compiled in Amber 9?
- AMBER: querry
- AMBER: Query
- AMBER: Query about the charge of atoms in the parmtop file
- AMBER: Question about loading frcmod.ionsjc_tip3p in xleap
- AMBER: question about the improper torsion
- AMBER: radius of calcium ion in MM_PBSA
- AMBER: RDF in ptraj
- AMBER: RED III execution problem
- AMBER: Regarding ff03 forcefield
- AMBER: Regarding force field ff02 and ion library
- AMBER: Release of version 1.2 of AmberTools
- AMBER: REMD temperature profile
- AMBER: replicas trapped in a few low temperatures
- AMBER: Res minimization
- AMBER: RESP calculation on Copper containing molecule
- AMBER: Restarting Problem in MD Simulation
- AMBER: RMSD per residue
- AMBER: Running patch "bugfix.at.all" with AmberTools 1.2
- AMBER: SCC-DFTB for Zinc atom
- AMBER: SHIFTS compile error
- AMBER: silhouette width/coefficient after clustering by PTRAJ9.9
- AMBER: simulation with many formamide molecules
- AMBER: size of pdb
- AMBER: sleap test failures
- AMBER: solvate dna in TIP3PBOX 10.0
- AMBER: targeted MD
- AMBER: test of parallel sander 10 fail
- AMBER: the install problem
- AMBER: The list-directed or NAMELIST READ statement cannot be completed
- AMBER: the plot of the groove width versus time for RNA
- AMBER: the pmemd problem
- AMBER: timing info output from pmemd
- AMBER: Trans proline
- AMBER: trouble interpreting <P2> time correlation function data
- AMBER: Tutorial 6
- AMBER: Volume of ucell too big
- AMBER: Where is ICO read from the ix array?
- AMBER: Which CO2 potential?
- AMBER: XLeap Problems
- AMBER:Some questions about replica exchan ge
- FreeBSD "port" for AmberTools-1.2
Last message date: Wed Dec 31 2008 - 22:47:27 CST
Archived on: Thu Jan 08 2009 - 16:01:48 CST
445 messages sorted by:
[ author ]
[ date ]
[ thread ]
About this archive
|