Amber Archive Jul 2011 by subject
- [AMBER-Developers] [AMBER] Antechamber trouble with COA-acyl chain
- [AMBER] (NAB issue) wc_helix : Problem in creating RNA structures
- [AMBER] /bin/sh /bin/dash
- [AMBER] /dat/slko DFTB files
- [AMBER] About extracting partial atoms from a Amber trajectory file
- [AMBER] About visualizing amber trajectory (periodic box) in VMD
- [AMBER] adiabatic conformational map of carbohydrates
- [AMBER] Ala double mutation scans
- [AMBER] alpha 2-3 Sialyllactose in GLYCAM
- [AMBER] alpha 2-3 Sialyllactose in GLYCAM,
- [AMBER] AMBER
- [AMBER] Amber help
- [AMBER] Amber test failure
- [AMBER] AMBER/sander parallel performance problem
- [AMBER] AMBER10 pimd failure on =>16 cores
- [AMBER] Amber11
- [AMBER] amber11 forcefield
- [AMBER] amber11 openmpi installation problem
- [AMBER] Amber11 Tests fail
- [AMBER] Amber11 using MPICH (parallel install problem)
- [AMBER] AMBER9- error in LEaP while learning MMPBSA tutorial
- [AMBER] Amber_CygWin_installation
- [AMBER] AmberTools
- [AMBER] AmberTools compilation problem
- [AMBER] AmberTools installation -
- [AMBER] AmberTools installation error
- [AMBER] AmberTools1.5 &ff10
- [AMBER] Analysis the changes of secondary structure in MD trajectory
- [AMBER] Antechamber trouble with COA-acyl chain
- [AMBER] APBS
- [AMBER] Aromatic bonds disappear during sdf creation with sleap
- [AMBER] atom mapping in leaprc.parmCHI_YIL.bsc
- [AMBER] belly energies
- [AMBER] breaking down amber parameter file to create fragments of original molecule using tleap
- [AMBER] Cannot find MMPBSA.MPI
- [AMBER] CHAMBER: problems reading bond parameters in charmm parameter file
- [AMBER] Changing the L-J parameter does not work?
- [AMBER] CHARMM format to Amber format
- [AMBER] CHARMM in AMBER
- [AMBER] chiral restraints in AMBER
- [AMBER] cluster MD trajectory by attribute
- [AMBER] configure_error
- [AMBER] confusions about some thermodynamic properties
- [AMBER] confusions about some thermodynamic properties of TIP3P water
- [AMBER] continuing an mmpbsa run
- [AMBER] converting amber8 prmtop to amber11
- [AMBER] Count number of frames in any trajectory file
- [AMBER] create walls
- [AMBER] Creating hoogsteen basepaired DNA using NAB
- [AMBER] CUDA 4.0
- [AMBER] Cuda compilation problem
- [AMBER] cudaMemcpy GpuBuffer::Upload failed invalid argument
- [AMBER] deletion of one water molecule from .rst and prmtop files
- [AMBER] Different trajectories with different RMSD with changing the parameters of gamma_ln, taup, timesteps and extend of density equilibration
- [AMBER] Different trajectories with large difference in RMSD with changing the parameters values of gamma_ln, taup, timesteps and extend of density equilibration
- [AMBER] Diffusion
- [AMBER] Discrepancy in Ca++ Vdw parameters ?
- [AMBER] Discrepancy in Ca++ Vdw parameters considering two Amber data sources - please comment
- [AMBER] dist restraint
- [AMBER] distance and angle cutoff for hydrogen bond
- [AMBER] DNA simulation
- [AMBER] Edit prmtop file
- [AMBER] Element definition
- [AMBER] Energy Decomp with mm_pbsa.pl
- [AMBER] Energy or Temperature Fluctuation
- [AMBER] Energy output when using ibelly
- [AMBER] Error
- [AMBER] ERROR - No pdb file generated using NAB
- [AMBER] Error compiling amber cuda
- [AMBER] Error in ptraj trajin
- [AMBER] Error in unit 9 inpcrd file
- [AMBER] Error mmpbsa
- [AMBER] Error on installing AMBERTOOLS 1.5
- [AMBER] Error with na_anal.c
- [AMBER] error: GBSA with mm_pbsa.pl
- [AMBER] extra_pts.f
- [AMBER] Failure kReduceSoluteCOM with GPU
- [AMBER] Fatal error in MPI_Init: Other MPI error
- [AMBER] ff03 force field
- [AMBER] force field issues using AT15
- [AMBER] Fwd: cluster MD trajectory by attribute - solved
- [AMBER] Fwd: Cuda compilation problem
- [AMBER] Fwd: Periodicity in MD simulations
- [AMBER] glib(c) error in mmpbsa
- [AMBER] H++ protonation
- [AMBER] H-bond vs. time
- [AMBER] hbond analysis
- [AMBER] hbond vs time
- [AMBER] Heavy atom definition
- [AMBER] help
- [AMBER] How Kinetic energy is can be converted to Temperature under the SHAKE constraint?
- [AMBER] How to choose MMGBSA saltcon varaible value
- [AMBER] How to make the picture of secstruct and the analysis of Hbond
- [AMBER] How to use nonlin option of APBS in MMPBSA.py?
- [AMBER] idecomp and res card
- [AMBER] Imaging everything inside an octahedral box
- [AMBER] Inquiry about installing AMBER
- [AMBER] install DFTB plus with Amber 11
- [AMBER] INSTALLATION ERROR ON RED HAT LINUX
- [AMBER] installation of ambertools-- help
- [AMBER] Installation Problem
- [AMBER] Interaction - Constrain
- [AMBER] Intercalation site creation
- [AMBER] ions params for SPC/F water
- [AMBER] Kinetic energy in mdout file is not identical to that calculated from mdvel file.
- [AMBER] Large flcutions in the RMSD deviations upon changing the parameters values of gamma_ln, taup and timesteps ..How a small variation leads to such a larage change??
- [AMBER] ligand & protein with dist restraint
- [AMBER] Ligand parametrization
- [AMBER] Ligands and cofactors in enzymes
- [AMBER] Make_Gnu_Win_error
- [AMBER] minimization error
- [AMBER] Minimization Question
- [AMBER] Missing Na+ type in ff10 in maksing topolgy file
- [AMBER] MM-GBSA with QM data
- [AMBER] MM_pbsa
- [AMBER] MM_PBSA analysis warning
- [AMBER] MMGBSA of Mg-containing ligand
- [AMBER] MMGBSA.py error
- [AMBER] MMPBSA calculation in complex with Membrane
- [AMBER] MMPBSA yielding different values when processed with .prepin and .lib file
- [AMBER] MMPBSA.MPI running error problem
- [AMBER] MMPBSA.MPI running issue
- [AMBER] MMPBSA.py - cluster analysis
- [AMBER] MMPBSA.py is crashing
- [AMBER] MMPBSA_ERROR MAXNEI too short
- [AMBER] MPI cuda compilation error
- [AMBER] Multiple CPU and single GPU doubt
- [AMBER] NBONH is greater than number of hydrogen for protein.
- [AMBER] NETCDF Installation Error
- [AMBER] nmropt on dihedral angles, are half harmonic restraints possible?
- [AMBER] Non-Standard Residues Problems
- [AMBER] nonbond parameter for copper(Ⅱ) ion
- [AMBER] number of solvent molecule around solute
- [AMBER] old prmtop and prmtop 7
- [AMBER] Oxygen Gaff Atom Type
- [AMBER] Parm .dat format and frcmod
- [AMBER] PB calculation error when using MMPBSA.py
- [AMBER] Periodicity in MD simulations
- [AMBER] Please solve my problem
- [AMBER] pmemd trajectory for mm_pbsa/gbsa analysis on sander
- [AMBER] possible problem with periodic cell
- [AMBER] Proble related to with dipole-dipole correlation function
- [AMBER] problem installing amber 10
- [AMBER] Problem of creating trpcage TC5b amino acid sequence using "sequence" command
- [AMBER] Problem related to the Corelation Function
- [AMBER] Problem related to the Potential Mean Force
- [AMBER] Problem related to the residue template of zwiterionic state
- [AMBER] Problem related to the RMSD
- [AMBER] Problem related to the RMSD and Atomic fluctuation
- [AMBER] Problem related to the Velocity correlation function
- [AMBER] problem with addIons in tleap
- [AMBER] Problem with MMPBSA.py
- [AMBER] Problem with removing Hydrogen in trajectory file using prtaj
- [AMBER] problem with running MMPBSA.py on a single frame
- [AMBER] problem with type of pdb output.
- [AMBER] problem with unperturbed charge of the unit
- [AMBER] problem with xleap
- [AMBER] problem with ZAFF
- [AMBER] Problems installing AMBER 11
- [AMBER] Problems with density in aqueous solution
- [AMBER] protein-ligand-metal complex simulation
- [AMBER] ptraj analysis problems - protein leaving the box
- [AMBER] Ptraj and glibc error
- [AMBER] ptraj can not read NC file. and not succeed in apply patch.
- [AMBER] ptraj closest water
- [AMBER] Query about switch function using AMBER ff99SB forcefield and NAMD simulation code
- [AMBER] question about possible failures during Amber10 and AmberTools1.2
- [AMBER] reference for GLYCAM_06 force field
- [AMBER] Regarding "Total unperturbed charge: -0.507900" on CYP1A1
- [AMBER] regarding amber anal calculation
- [AMBER] regarding hydrogen bonding
- [AMBER] regarding per residue wise free energy decomposition
- [AMBER] Regarding umbrella sampling
- [AMBER] Registration open - AMBER Workshop in Shanghai, China, August 22-26, 2011
- [AMBER] Related to the correlation function
- [AMBER] REMD doubt : how to know the protein is not trapped in a conformation
- [AMBER] renum water
- [AMBER] reproducing a simulation
- [AMBER] Restrained MD
- [AMBER] Running Amber 11 simulations using pmemd.cuda.MPI
- [AMBER] Sander Compilation Problem
- [AMBER] sander job crashed
- [AMBER] sander problem
- [AMBER] sander.MPI is running on 8 nodes, but the output says it is running on 1 nodes
- [AMBER] sander11
- [AMBER] scee=scnb=1
- [AMBER] Script to run mm_pbsa.pl for ENTROPY calculation in parallel on workstation
- [AMBER] segmentation fault on tleap
- [AMBER] selective qmshake?
- [AMBER] sleap and ptraj output issue with terminal residues
- [AMBER] sleap cannot deal with lipids?
- [AMBER] Sorry
- [AMBER] Steered dynamics related questions
- [AMBER] Steered MD using pmemd.cuda ?
- [AMBER] SYBYL to GAFF atom types
- [AMBER] Thanks
- [AMBER] the picture of secstruct and the analysis of Hbond
- [AMBER] Tleap problem with save prmtop and inpcrd file. can someone give me advice?
- [AMBER] TR: Antechamber trouble with COA-acyl chain
- [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6
- [AMBER] Urea box: artifacts or just a special distribution?
- [AMBER] using Mg with ff99SB
- [AMBER] using sleap to load mol2 files
- [AMBER] using zaff parameters
- [AMBER] vdW issues during TI
- [AMBER] Volume of a Cavity
- [AMBER] When and how is leap re-numbering residues?
- [AMBER] XLEaP parameters for nonstandard residues
- [AMBER] xleap problem
- [AMBER] ZAFF parameters: non integral charge
- [AMBER] Zero values for gbsur
- [AMBER] zinc parameters
- Last message date: Sun Jul 31 2011 - 05:00:05 PDT
- Archived on: Wed Oct 09 2024 - 05:54:25 PDT