Amber Archive Feb 2016 by subject
- [AMBER] 3DRISM: erratic values for partial molar volume
- [AMBER] [AMBER} nonpolar term for MMPBSA decomp showing up as 0
- [AMBER] A question about cpptraj autoimage
- [AMBER] accelerated MD - frequency of conformational change
- [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors
- [AMBER] AMBER Digest, Vol 1497, Issue 1
- [AMBER] Amber/tutorial/advanced/tutorial16/
- [AMBER] amber14 update
- [AMBER] aMD Secondary Structure
- [AMBER] antechamber run for FAD
- [AMBER] average 3D structure with condition
- [AMBER] Bounds command with GIst
- [AMBER] broken iodine bond problem in NEWPDB.PDB file.
- [AMBER] calculate ligand RMSD for MD simulations; nofit or not?
- [AMBER] cationic-pi interactions
- [AMBER] charge derivation
- [AMBER] charmmlipid2amber.py
- [AMBER] citrulline parameters
- [AMBER] Covariance Matrix in CPPTRAJ
- [AMBER] CPPtraj & ParmEd - delete atoms
- [AMBER] cpptraj command for pi-stacking or hydrophobic interactions.
- [AMBER] cpptraj nativecontacts.
- [AMBER] Dear all
- [AMBER] Defining Units in nastruct
- [AMBER] delta G computation (MMPBSA.py)
- [AMBER] Dihedral angles restraints from x-ray to NMR
- [AMBER] Dihedral parameters
- [AMBER] Downloading of Ambertools15
- [AMBER] draw vector along axis of an alpha helix
- [AMBER] Duration parmchk
- [AMBER] Energy decomposition error
- [AMBER] EPtot, Angle, Bond, Dihed
- [AMBER] Error atommask selectElemMask
- [AMBER] error in minimization whole system
- [AMBER] error in running rmsf command cpptraj
- [AMBER] error in sqm.out file
- [AMBER] Error: Bad > topology file.
- [AMBER] External library for leap
- [AMBER] free energy calculation of folding
- [AMBER] Fwd: cpinutil.py problem
- [AMBER] Fwd: Error with disulphide bonds in tleap
- [AMBER] Fwd: PC square fluctuations
- [AMBER] Fwd: Thermodynamic Integration
- [AMBER] Gaussian error with MCPB ion modeling calculation
- [AMBER] Getting and keeping ACPYPE updated
- [AMBER] Gist Installation in Amber12
- [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered
- [AMBER] gzip -9 heat.mdcrd Error
- [AMBER] Help to choose best-fit ion model
- [AMBER] Hg parameterization
- [AMBER] How to analyze mutational free energy difference?
- [AMBER] how to check protonation state
- [AMBER] How to separate a protein complex to its components
- [AMBER] How to transfer amino acid sequence to Xleap.
- [AMBER] Inquiry regarding amber installation
- [AMBER] interpret results
- [AMBER] Is the Force Constant in the Parm**.dat file derived from a mass-weighted Hessian
- [AMBER] Is there a way to compare trajectories?
- [AMBER] KeyError - MCPB.py
- [AMBER] Li & Mertz ion parameters
- [AMBER] Ligand Molecules Being Rejected in SHIFTS 5.0.1
- [AMBER] lmod & xmin in sander
- [AMBER] manually addition of parameters in frcmod file
- [AMBER] Maximum input value for the isothermal compressibility in AMBER
- [AMBER] membrane potential
- [AMBER] minimization error : segmentation fault
- [AMBER] minimization error : segmentation fault (AMBER Digest, Vol 1483, Issue 1)
- [AMBER] Minimization error using Sander
- [AMBER] MMGBSA error
- [AMBER] MMPB (GB) SA cpptraj failed with prmtop
- [AMBER] MMPBSA ImportError
- [AMBER] MMPBSA.py.MPI won't recognise mpy4pi
- [AMBER] more extra points needed
- [AMBER] Need Amber entropy calculated values
- [AMBER] No exe file in Amberhome
- [AMBER] Normalizing histogram with CPPTRAJ
- [AMBER] Nucleic acid builder
- [AMBER] Paradynamics with Amber
- [AMBER] parameter file for graphene oxide
- [AMBER] parameter file for isoaspartate acid
- [AMBER] Parameter for Aspartic Acid-Lysine Cyclic peptide
- [AMBER] Paramfit, negative bond parameters
- [AMBER] parmed/chamber problem recognizing atom types
- [AMBER] Pdb file to Mol2
- [AMBER] PDB to distance in AMBER
- [AMBER] Ph.D. position, Nancy, France
- [AMBER] Post-doctoral position in Computational Physics
- [AMBER] Preparing needed input files for TI
- [AMBER] problem running MD for diphosphoric acid anion
- [AMBER] problem with energy minimization (sander)
- [AMBER] Problem with HIS/HIE residue and ff14SB force field
- [AMBER] Problem with saving parameters for a complex having Heme group
- [AMBER] Problems with when using DFTB halorg .skf files in sqm
- [AMBER] Quasi-harmonic Calculations
- [AMBER] Query regarding extracting protons from coordinate/trajectory file
- [AMBER] Query: extracting protons from trajectory/coordinate file
- [AMBER] Question about AmberTools14/15 installation
- [AMBER] Question about mask command
- [AMBER] Question regarding protein-Dna binding free energy
- [AMBER] R: Fwd: cpinutil.py problem
- [AMBER] R: R: Fwd: cpinutil.py problem
- [AMBER] reading Amber trajectory files with chamber topology file
- [AMBER] Reg: problem in generating prmtop and crd files by using ff12SB of magnesium ions
- [AMBER] Regarding caution message in the out file with pmemd.cuda.MPI
- [AMBER] Regarding minimization in AMBER
- [AMBER] Regarding MMGBSA calculation
- [AMBER] Regarding trajectory analysis using CPPTRAJ
- [AMBER] Regaridng FIle preparation in AMBERTOOLS14
- [AMBER] Relabeling Atoms after a Run Trajectory
- [AMBER] REMD tutorial
- [AMBER] Replacement for xmgrace
- [AMBER] Restarting a heating simulation
- [AMBER] Segmentation fault when converting charmm to amber toppar using chamber
- [AMBER] Size of solvent box
- [AMBER] Size of solvent box, RDF
- [AMBER] SP3 Nitrogen planarity issue with ff14SB
- [AMBER] standard deviation of rmsd values
- [AMBER] Steered MD of membrane proteins
- [AMBER] summary.ETOT analysis
- [AMBER] summary.ETOT analysis and MMPBSA.py
- [AMBER] Technical problem running pH-REMD
- [AMBER] the angle between two axis
- [AMBER] Thermodynamic Integration
- [AMBER] tMD with ligand
- [AMBER] Typing {} in Xleap
- [AMBER] unable to generate Mercury parameter file
- [AMBER] Unable to run QM/MM with RNA and sodium ion
- [AMBER] Value of ntrx=7
- [AMBER] velocity auto correlation function
- [AMBER] want script for plotting graph on entropy
- [AMBER] want to ask you about PCA plotting
- [AMBER] waters inside cavity
- [AMBER] Wrong or no center in RdPar
- [AMBER] Wrong or no center in RdPar.
- [AMBER] Z-constraint PMF method
- [AMBER] Zero pressure with pmemd.cuda
- Hg parameterization
- Nucleic acid builder
- Last message date: Mon Feb 29 2016 - 23:30:07 PST
- Archived on: Fri Sep 06 2024 - 05:55:18 PDT