Amber Archive Oct 2013 by subject
- [AMBER] [Amber]Question about softcore
- [AMBER] A problem with a specific input in pmemd.cuda.MPI. 4 GPU fails, 2 GPU works fine.
- [AMBER] About calculating entropy
- [AMBER] about error with "Must have more residues than processors!"
- [AMBER] About foundations of T-REMD
- [AMBER] About INP in case of MS=1
- [AMBER] about rms atomic fluctuation for protein crystal .thank you very much!
- [AMBER] About the Mg charge in AMBER FF
- [AMBER] acclerated molecular dynamics alphaP
- [AMBER] Amber 12 Updater error on Arch linux
- [AMBER] AMBER Digest, Vol 659, Issue 1
- [AMBER] AMBER ff99Sbildn
- [AMBER] Amber99SB force field
- [AMBER] ambertools patch 19 fails
- [AMBER] AmberTools13
- [AMBER] AmberTools13 and Amber11
- [AMBER] AMBERTOOLS13 test error: 01_Generalized_Born and 03_Alanine_Scanning
- [AMBER] AMBERTOOLS13 test error: 01_Generalized_Born and, 03_Alanine_Scanning (Jason Swails)
- [AMBER] Ambiguity in PMF calculated from umbrella sampling of a dihedral angle
- [AMBER] Block Averaging of Trajectory
- [AMBER] calculatie the energy between two groups of atoms from an MD trajectory, is it possible?
- [AMBER] changeLJ14Pair
- [AMBER] Constant pH with enzyme and substrate
- [AMBER] Constant pH with ligand
- [AMBER] CYM residue problem(MCPB)
- [AMBER] Difference between the .crd file format in AMBER-7 and AMBER-12
- [AMBER] Distributions of the phi and psi torsion angles during MD simulations
- [AMBER] DNA with NAB
- [AMBER] Doubt regarding the metadynamics simulation
- [AMBER] Erro in the Thermodynamic Intergration using soft core potentials"
- [AMBER] Error - PMEMD.MPI cannot understand line in rst file
- [AMBER] Error in antechamber Installation
- [AMBER] ERROR in DISTANCE RESTRAINT
- [AMBER] Error message from pmemd.cuda
- [AMBER] example of MTKpp on Ambertools 13
- [AMBER] Exceed character limit in bellyrestraint mask selection
- [AMBER] Free binding energy calculations for Zinc dependent ligands
- [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K.
- [AMBER] Fwd: requesting in executing CHAMBER
- [AMBER] Fwd: Shifting molecules by a box length
- [AMBER] GAFF angle term constants with phosphor or sulphur
- [AMBER] Generating reservoirs for non-Boltzmann T-RREMD
- [AMBER] Generating topology files for two proteins in a single input pdb
- [AMBER] Generation of melting curves
- [AMBER] Hbond analysis
- [AMBER] High energy in per-residue MMPBSA calculation
- [AMBER] High Temperature at NSTEP = 0
- [AMBER] How do I use MMPBSA.py for namd .dcd file?
- [AMBER] How to calculate the free energy change of a chemical reaction by the thermodynamic integration approach?
- [AMBER] How to deal with duplicate frames during MD?
- [AMBER] How to run npt simulation if IFBOX=0 in .prmtop file?
- [AMBER] How to use TIP4P/2005 water model
- [AMBER] huge values for the vibrational entropy from ptraj
- [AMBER] Hydrogen Bond Term in Amber ff99SB forcefield
- [AMBER] I/O errors while using CHARMM psf with CHAMBER
- [AMBER] idecomp does not work for canonical-residues
- [AMBER] igb=7, 8 incompatible with the ILDN modifications of ff99SB
- [AMBER] inquiry
- [AMBER] Installation error
- [AMBER] ionic strength conversion between MMPBSA.py and PBSA
- [AMBER] Iron(III)Hydroxide complexing with Enterobactin (quantum chemistry calculations?)
- [AMBER] ITN Marie Curie positions available for early-stage researchers
- [AMBER] Leap ff10 and Sodium ion
- [AMBER] Making Au surface using xleap
- [AMBER] mdcrd to dcd
- [AMBER] MMGBSA, Generalized Born, protein-nucleic acid complex
- [AMBER] MMPBSA calculation
- [AMBER] MMPBSA error
- [AMBER] MMPBSA problem with CHAMBER generated topology file
- [AMBER] MMPBSA, ligand sequence
- [AMBER] MMPBSA.py error
- [AMBER] MMPBSA.py MPI problem on TACC Stampede
- [AMBER] MMPBSA.py problem
- [AMBER] mmpbsa_py_energy and PBSA options
- [AMBER] MMPSA: PB Bomb in pb_aaradi(): ...
- [AMBER] Modified Cysteine
- [AMBER] Monte Carlo Method/Simulation in AMBER 12
- [AMBER] MPI install with openmpi
- [AMBER] NAB : Orienting a molecule
- [AMBER] namelist input > 80 columns
- [AMBER] optimization using gaussian and RESP using antechamber
- [AMBER] output of diffusion data doesn't show two columns for big number values
- [AMBER] Parameter Discrepancy in Walker Tutorial B1?
- [AMBER] parmchk doesn't recognize the changes made in leaprc.ff99SB and parm.99
- [AMBER] parmed.py bug when using the "parmout" command ?
- [AMBER] PCA analysis and amber prmtop file
- [AMBER] Phenyl-boronic acid derivatives lacking of parameter in Mol2 file
- [AMBER] PMEMD trajectory and MMPBSA
- [AMBER] PMF for 2 Arginines
- [AMBER] Predicting druggable hotspots
- [AMBER] Problem about water Cap with igb=10
- [AMBER] problem after minimization of pure DMF
- [AMBER] problem for prmtop and inpcrd file generation
- [AMBER] Problem in antechamber execution Problem in antechamber execution problem in antechamber execution
- [AMBER] Problem in creating .mol2 and .frcmod files
- [AMBER] Problem in deriving RESP charges with RED-3.52 tools
- [AMBER] PROBLEM IN QM/MM RUN
- [AMBER] problem in saving prmtop file in ff12SB force field
- [AMBER] PROBLEM USING ANTECHAMBER
- [AMBER] problem using the R.E.D server output
- [AMBER] problem with addIons in tleap
- [AMBER] problem with heme parameters bound to HIS
- [AMBER] Protein-DNA covalent bond
- [AMBER] ptraj - loading list of frames
- [AMBER] PTRAJ - Problem with inserting TER card
- [AMBER] Python script to reweight aMD simulations
- [AMBER] QM/MM interfacing Gaussian
- [AMBER] QM/MM MMPBSA
- [AMBER] Questions about softcore part
- [AMBER] Questions about VDW process of thermodynamic integration method
- [AMBER] Questions about VDW process of thermodynamic integration method
- [AMBER] Questions regarding AMBER
- [AMBER] ratio between frames for MM/PBSA and frames for normal mode calculations
- [AMBER] Reading NetCDF file
- [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file
- [AMBER] Regarding addition of DL_Poly Inversion and three body potential in Amber
- [AMBER] Regarding addition of DL_Poly Inversion potential in Amber
- [AMBER] Regarding radial distribution function
- [AMBER] Replica exchange umbrella sampling
- [AMBER] RESP charge calculation problem for SO4 -2 group
- [AMBER] rotational diffusion error
- [AMBER] running MMPBSA.py on an NMR ensemble
- [AMBER] Running simultaneously AMBER jobs in CPU and GPU
- [AMBER] Sander error
- [AMBER] Sander error (AmberTools 13 & Amber10)
- [AMBER] Scaling of multi GPU runs
- [AMBER] Script?
- [AMBER] Segmentation fault in tleap
- [AMBER] SHAKE flucatuation
- [AMBER] Shifting molecules by a box length
- [AMBER] Single quotes in AMBER manual
- [AMBER] Soft-core questions for TI method
- [AMBER] solvate box
- [AMBER] strange behavior of MCPB
- [AMBER] Stuck on AmberTools bugfix.23
- [AMBER] Stuck on AmberTools12 bug fix.23
- [AMBER] sumit.saurav.jain.gmail.com has indicated you're a friend. Accept?
- [AMBER] Temperature based trajectory in REMD
- [AMBER] Terachem tests with trial version
- [AMBER] The Error when I run MdoutAnalysizer.py
- [AMBER] TI soft-core parameters
- [AMBER] tleap cannot handle dummies in the middle?
- [AMBER] Trajectory determination and directionality in TI with softcore potentials
- [AMBER] unique atoms in TI softcore
- [AMBER] Update 21 for Amber 12: EXTERN QM/MM interface
- [AMBER] Use of Langevin Thermostat with Amoeba force field
- [AMBER] why are pres_X, pres_Y, and pres_Z different?
- Fwd: DMPC GAFF lipid membrane is freezing at 303 K.
- Last message date: Thu Oct 31 2013 - 15:00:03 PDT
- Archived on: Mon Dec 02 2024 - 05:54:52 PST