Amber Archive Jan 2015 by subject
- [AMBER] [cpptraj] Problem with nativecontacts
- [AMBER] [MGMS-DS]: Molecular Modelling Workshop March 9-11, 2015 in Erlangen, Germany
- [AMBER] About amber parameters for free dioxygen in water solution
- [AMBER] ABOUT NPT and PMEMD.CUDA
- [AMBER] About statistical report of 'RMS deviation from ideal bonds/angles'
- [AMBER] About: AMBER Advanced Tutorial 22
- [AMBER] accelerated MD on 2 GPU cards
- [AMBER] AMBER 14 DPFP single energy calculations inconsistent
- [AMBER] AMBER 14 installation in cray machine : Problem related to parallel building
- [AMBER] Amber 14 Performance and Other Questions
- [AMBER] AMBER Digest, Vol 1109, Issue 1
- [AMBER] AMBER Workshop Announcement - Haifa Israel, Sun Apr 26th to 30th.
- [AMBER] Amber11: CUDA-enabled version does not work
- [AMBER] AmberTools 14
- [AMBER] ambertools14 fresh installation fails
- [AMBER] AmberTools14 MMPBSA CalcError with complex.prmtop and SA Bomb in use_sander=1
- [AMBER] aMD plot
- [AMBER] aMD plot (Daniel Roe)
- [AMBER] Atom type parameterization and prmtop file
- [AMBER] bad atom type: OA
- [AMBER] bcl script side chain optimization using Gaussian-Reg
- [AMBER] big cavity in the trajectory
- [AMBER] Calculating density during Radial distribution analysis
- [AMBER] cbrange in gnuplot
- [AMBER] chamber : psf to amber parmtop
- [AMBER] Checking bonds commanded with leap
- [AMBER] clustering in PC subspace
- [AMBER] Clustering molecule between copies (not between frames)
- [AMBER] clustering problem in ambertool14
- [AMBER] confusion about effect of number of solvent molecules on density
- [AMBER] Constant values in prmtop
- [AMBER] contacts with water
- [AMBER] could not find vdW (Na+) type IP
- [AMBER] cpptraj.MPI
- [AMBER] cpptraj: structures not aligned anymore after 'run' keyword
- [AMBER] CpptrajFile: error
- [AMBER] cuda version 5 using gnu V 4.9.1 issues
- [AMBER] diffusion coeficient
- [AMBER] diffusion time step
- [AMBER] energies too high
- [AMBER] Equilibration problem large system in explicit solvent
- [AMBER] Error during Adding Fragment(about MCPB )
- [AMBER] Error in Simulation of MN2+ containing complex
- [AMBER] Error while running tleap in AMBER
- [AMBER] Errors during Building Sidechain Model(MCPB program)
- [AMBER] ESP Charge for Fe
- [AMBER] extract torsion angle data
- [AMBER] Extracting multiple frames by cpptraj
- [AMBER] FATAL: Atom .R<RU5 13>.A<P 29> does not have a type.
- [AMBER] Fe(III)-OH2 vs Fe(II)-OH2 force constant
- [AMBER] FEP
- [AMBER] Force ramp pulling
- [AMBER] Free energy decomposing calculation time with MMPBSA.py
- [AMBER] Free Energy Workshop, Münster, March 9-11, 2015
- [AMBER] Fwd: Checking bonds commanded with leap
- [AMBER] Fwd: MMPBSA problem when using idecomp
- [AMBER] Fwd: NVE GPU question
- [AMBER] GBSA speeds for big molecules
- [AMBER] GPU error GTX card.
- [AMBER] Group defining heavy atoms
- [AMBER] harmonic restraint file
- [AMBER] HBond ANALYSIS
- [AMBER] Help in AMBER
- [AMBER] Help in AMBER+PLUMED interface
- [AMBER] help in analysis
- [AMBER] help in diffusion coefficient
- [AMBER] help in diffusion coefficient analysis
- [AMBER] help in force field
- [AMBER] help in minimization
- [AMBER] Help regarding potential surface scan using external interface
- [AMBER] how to choose the final binding mode
- [AMBER] How to defined a steered direction in SMD?
- [AMBER] How to fix 1-4 ELE error
- [AMBER] How to run an antechamber for ligands containing silver [Ag] atom?
- [AMBER] How to save structure at every minimisation/optimization cycle
- [AMBER] How to write the Amber code(s) to calculate pi-pi stacking interactions, polar contacts
- [AMBER] hydrogen bond charmm vs amber
- [AMBER] installation of AmberTools14
- [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch
- [AMBER] Lipid 14 format problem
- [AMBER] Matrix correl
- [AMBER] Matrix correlation
- [AMBER] max GPU cards per run
- [AMBER] Missing psi dihedral at cationic N-terminus of protein/peptide?
- [AMBER] MMGBSA of several MD trajectories
- [AMBER] MMPBSA Molsurf vs LCPO
- [AMBER] Need help in Targeted MD
- [AMBER] nocut MD SHAKE error
- [AMBER] NVE GPU question
- [AMBER] parameterization using antechember
- [AMBER] pbsa question
- [AMBER] PCA variance using Freq = 108.587 * sqrt( 0.6 / Eigenvalue )
- [AMBER] Periodic image of iwrapped structure
- [AMBER] PMEMD Error
- [AMBER] POPC membrane separation.
- [AMBER] Principal Axis
- [AMBER] Printer
- [AMBER] Printing out matrix labels
- [AMBER] Problem in creating prepin file
- [AMBER] Problem with Ambertools14
- [AMBER] problem with antechamber
- [AMBER] Problem with idecomp in MMPBSA
- [AMBER] problem with rdparm in amb2gmx.pl
- [AMBER] Proper output form of DCCM Analysis using ptraj
- [AMBER] Protein Drug explicit MD simulation
- [AMBER] pseudo F-statistic (pSF)
- [AMBER] Purchase second GPU for AMBER?
- [AMBER] Querry about puckering
- [AMBER] Question in Amber atom types
- [AMBER] Question of AM1-BCC
- [AMBER] R: Group defining heavy atoms
- [AMBER] Reading chemical bonds from par7 files
- [AMBER] Regarding MCPB
- [AMBER] RMSD calculation of a homodimer
- [AMBER] shell scripting within cpptraj input files
- [AMBER] Significantly different results between MMPBSA and MMGBSA
- [AMBER] Solvation free energy using soft core potential
- [AMBER] Targeted MD error
- [AMBER] The protein unfolded through the simulation
- [AMBER] Torsion restrain
- [AMBER] Trajectory processing using ptraj
- [AMBER] unusual structure after heating. why?
- [AMBER] Using DFTB parameters (Halorg) in Amber12
- [AMBER] Using restraints to get a complex
- [AMBER] Vector command CPPTRAJ
- [AMBER] Which papers should be cited for ff14SB
- [AMBER] Why there is a conflict between ibelly and igb in REMD?
- [AMBER] wrap warning
- [AMBER] xleap does not known when compiling with mpi
- [AMBER] ZN metal parametrization using MCPB -reg
- [AMBER] 回复: Errors during Adding hydrogen atoms to the PDB file(MCPB program)
- [AMBER] 回复: Errors during Building Sidechain Model(MCPB program)
- clustering problem in ambertool14
- Last message date: Sat Jan 31 2015 - 20:00:02 PST
- Archived on: Wed Dec 25 2024 - 05:55:07 PST