AMBER Archive (2007) - Jan 2007 By Subject434 messages sorted by:
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Starting: Mon Jan 01 2007 - 04:16:12 CST
Ending: Wed Jan 31 2007 - 23:19:48 CST
- a request
- AMBER:
- AMBER: (no subject)
- AMBER: 22 improper torsions in old prep form
- AMBER: a question about analysis of DNA duplex after MD simulation with curves
- AMBER: about coordinates ****** and diffusion
- AMBER: About the problem of the PMEMD and cutoff
- AMBER: ADDIONS do not neutralize to ZERO
- AMBER: Amber 8.0 : how to represent EPS with VMD?
- AMBER: amber 9
- AMBER: AMBER citation questions
- AMBER: AMBER complile problem
- AMBER: amber parallel compile error with g95
- AMBER: amber9 installation error
- AMBER: amber9 parralel compiling
- AMBER: another sander bug?
- AMBER: Antechamber Charge Calculation Method
- AMBER: Antechamber esp calculation
- AMBER: assign atom hybrid
- AMBER: calcium parameter for GB
- AMBER: Can't run decompose energy in MM-PBSA
- AMBER: Can't run Normal Mode Analysis !!!
- AMBER: Charges in TI calculations and leap
- AMBER: convert pdb files to restart files
- AMBER: coordinates ******
- AMBER: CYX residue missing from Amber 9 ff03ua (?)
- AMBER: Deep energetics problem
- AMBER: Defining BOX INFO during TLEAP
- AMBER: deformation of DNA duplex after MD simulation (AMBER9)
- AMBER: dihedral angle by Ptraj
- AMBER: Dihedral FF parameters
- AMBER: Distance Restraints
- AMBER: Distance Restraints Problem
- AMBER: DNA structure analysis
- AMBER: Does amber use water density around 1 at room temperature
- AMBER: Drug bound to the protein
- AMBER: Drug Leads interaction with ds and Triplex DNA
- AMBER: entropy units
- AMBER: enzyme kinetics in silico
- AMBER: equilibration with amber5, production of MD with amber7
- AMBER: error when compiling Moilview
- AMBER: error when using sander.LES: exceeded MAXLES
- AMBER: evaluate expression
- AMBER: experimental phi-values as restraints
- AMBER: explicit implicit solvent
- AMBER: Fatal error: Command failed for target `test.sander.no_lmod'
- AMBER: fluctuations
- AMBER: format of .xyz files and pdb
- AMBER: Fwd: a request
- AMBER: G5 OSX serial compile error
- AMBER: Gas-phase energies (and more)
- AMBER: gaussian output to prepin problem
- AMBER: H-acceptors problem in ptraj
- AMBER: H-bond in each fram
- AMBER: H-bond in ptraj
- AMBER: HF/6-31G* ESP Charges do not match with ff02 charges
- AMBER: How are water molecules at cutoff being treated?
- AMBER: How many steps should be used for a MD calculation?
- AMBER: how much restraint ?
- AMBER: How to change the force field equation in amber by programming...
- AMBER: How to do minimization..
- AMBER: How to get a periodic box of modified water molecules
- AMBER: Hydrogen in a phosphate ion
- AMBER: I need some constant pressure MD help
- AMBER: image command
- AMBER: Improper angle by Antechamber
- AMBER: improper dihedral
- AMBER: improper torsions
- AMBER: Including Relevant Subject Lines
- AMBER: Installation help - SGI Altix 350
- AMBER: installing amber 8 on 5 nodes cluster PC
- AMBER: intra-molecular h-bonds in ptraj
- AMBER: Is there a pmemd machine file for OSX Intel
- AMBER: issues with restrt file
- AMBER: Leap adding 3 extra atoms
- AMBER: Leap adding extra atoms
- AMBER: Ligand-Protein Distance Restraints during MD Simulation
- AMBER: LJ potential
- AMBER: minimization using fcap
- AMBER: MM-PBSA doubt
- AMBER: MM-PBSA problem: Why
- AMBER: mm-pbsa, long distance free energy calculation problem
- AMBER: MM-PSBA decoupling
- AMBER: mm_pbsa Array reference error
- AMBER: mm_pbsa error
- AMBER: mm_pbsa problems
- AMBER: mm_pbsa vertex atom mismatch
- AMBER: mm_pbsa_statistics.pl
- AMBER: Molecular dynamic issues
- AMBER: MPI is slower than single processor with water
- AMBER: NH3 potential
- AMBER: nonpolar solvation energy
- AMBER: nuc.in file
- AMBER: NVT/NPT equilibration issue in GPCR-membrane simulation
- AMBER: organic solvent : hexan octan
- AMBER: output
- AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f
- AMBER: perturbed atoms are not bonded on using TIP5P wate
- AMBER: perturbed atoms are not bonded on using TIP5P water
- AMBER: pmemd install error
- AMBER: Preprocessor Error: _qmmm_module.f "Extra Characters..."
- AMBER: problem compiling Amber 7
- AMBER: problem with distance restraints
- AMBER: Problem with installation of the leap module of AMBER9 on Linux Suse 10.2
- AMBER: problems in energy minimization using TIP5P water model
- AMBER: problems trying to modify Amber8
- AMBER: ptraj
- AMBER: Ptraj: watershell and distance
- AMBER: question about the testing of AMBER9
- AMBER: questions about analysing LES results
- AMBER: Radii for water hydrogens are different
- AMBER: radius of gyration
- AMBER: Regarding energy of decomposition tutorials
- AMBER: RESP Charges for Charged Carboxylate in Organic Ligand
- AMBER: RESP charges for charged species
- AMBER: sander bug?
- AMBER: sander crashes during minimization
- AMBER: sanger
- AMBER: Section missing from AMBER 9 manual?
- AMBER: Simulation of a charged system
- AMBER: Simulations with GB models
- AMBER: solaris 10 and compilers on X86_64 hardware
- AMBER: solvation of protein using TIP3PBOX in amber 8
- AMBER: some questions about minimization and MD of DNA duplex with sander
- AMBER: test submission through PBS queue
- AMBER: The convergence criteria for the energy minimization of the DNA molecule (dodecmer duplux)
- AMBER: The unperturbed charge of the unit: -20.999999 is not zero.
- AMBER: torsion angle penalty calculation
- AMBER: torsion angle penalty calculationy
- AMBER: Unable to compile amber9
- AMBER: united atom parameters for -NH2 and -OH groups
- AMBER: unsubscribe
- AMBER: vdW parameters for chlorine atom
- AMBER: vertex atom mismatch
- AMBER: WARNING: Missing VDWNB for MM in 1 -> Taken from 0
- AMBER: Why there is a gap or jump if continue ntt=3 or ntt=1
- AMBER: xleap
- AMBER: yet another SANDER bug?
- Fwd: AMBER: Atoms overlapping
- Fwd: AMBER: Can't run Normal Mode Analysis !!!
- Fwd: AMBER: Improper angle by Antechamber
- Fwd: AMBER: mm_pbsa Array reference error
- help
- pmemd install error
- Re : AMBER: intra-molecular h-bonds in ptraj
- tree name generated by tleap is different from the input PREP parameter file
Last message date: Mon Dec 31 2007 - 15:27:41 CST
Archived on: Thu Jan 10 2008 - 17:13:08 CST
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