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AMBER Archive (2008) - By Subject
4909 messages sorted by: [ author ] [ date ] [ thread ]About this archive
Starting: Tue Jan 01 2008 - 19:53:35 CST
Ending: Wed Dec 31 2008 - 22:47:27 CST
- [Jmol-users] AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files
- About restart amber
- amber 10 and mpich2 (got eof on console error message from mpich2)
- AMBER 10 failure to run in UBUNTU
- Amber 9
- amber 9 compilation problem on IBM SP5
- Amber Force field for CNT: leaprc.ff23
- amber help
- AMBER Question
- amber tutorial A3
- AMBER vs Gaussian : zero VDW parameters?
- amber8 files in amber9
- Amber9 vs Amber10+MKL benchmark
- AMBER:
- AMBER: "Assuming uniform neutralizing plasma"
- AMBER: "Dumping RAW 2D RMS data is not yet implemented"?
- AMBER: "radius = 0.000"
- AMBER: # of ligands and receptors in mmpbsa
- AMBER: $AMBERHOME/dat/slko
- AMBER: (no subject)
- AMBER: .... RESTARTED DUE TO LINMIN FAILURE ...
- AMBER: 1.5ns rst file to PDB file Conversion Error
- AMBER: 100 short MD runs within a single Sander script?
- AMBER: 2'-5'-branched RNA
- AMBER: 2D RMS plot
- AMBER: 2D-RMSD
- AMBER: 3fe-4s cluster parameter file generation
- AMBER: 3rd Annual CMM Workshop on QM/MM Simulations
- AMBER: [amber/glycam] dealing with fucose...
- AMBER: [Fwd: failure to load box parameters]
- AMBER: [Fwd: segmentation fault in nmode]
- AMBER: [success] problem compiling Amber9 on Bull Linux
- AMBER: a link for Amber ff ported to Charmm
- AMBER: a minor bug in RESP
- AMBER: A new program for doing RESP
- AMBER: A problem about antechamber
- AMBER: A problem of dihedral angle
- AMBER: A problem of installing Amber10
- AMBER: A problem to loadup the molecular in the xleap
- AMBER: a question
- AMBER: a question about ff03ua
- AMBER: a question about matrix command?
- AMBER: a question about parameter b in the hyperbolic form of penalty function for RESP fit
- AMBER: a question of ptraj
- AMBER: A-prime RNA input file
- AMBER: about addles:¡°forrtl: severe (71): integer divide by z
- AMBER: about addles:¡°forrtl: severe (71): integer divide by zero¡±.
- AMBER: about AM1-BCC in antechamber
- AMBER: About antechamber and GAFF
- AMBER: About antechamber and GAFF [UPDATED]
- AMBER: about gaff.dat in ambeTools 1.0
- AMBER: about glycam06
- AMBER: about hydrogen bond in amber force field
- AMBER: About Hydrophobic Interactions.
- AMBER: about mmpbsa out data
- AMBER: about NMR refinement in explicit solvent
- AMBER: about QMMM output
- AMBER: About RAMD
- AMBER: About reading in heme and CO molecule together with myoglobin
- AMBER: about resp charges
- AMBER: about RMSD per residue
- AMBER: about SASA and AMBER
- AMBER: Ac-Co Parameters for Amber
- AMBER: Accessing Equilibration Results
- AMBER: acetone box
- AMBER: ACPYPI announcement
- AMBER: ACS COMP Division awards- deadline this week
- AMBER: adding missing residues
- AMBER: Adding New Parameters and Modifying Existing Parameters
- AMBER: adding new potential function
- AMBER: addions and addions2
- AMBER: AddIons approach
- AMBER: Addions in GB Mode?
- AMBER: addles
- AMBER: Adjust Force Field parameters
- AMBER: AdoMet parameterization with antechamber
- AMBER: Again: Installation problem of AMBER on cluster
- AMBER: aggregation or cluster detection
- AMBER: Alanine scanning
- AMBER: alascan error
- AMBER: alascan MUTANT_KEEP error
- AMBER: all & united atoms force field
- AMBER: amb2gmx for big systems
- AMBER: Amber 10 ambpdb bug?
- AMBER: amber 10 and mpich2 (got eof on console error message from mpich2)
- AMBER: Amber 10 on the BlueGene
- AMBER: amber 10 parallel cpu utlization
- AMBER: AMBER 10 PMEMD / SGI_MIPS
- AMBER: Amber 10 timing
- AMBER: AMBER 10: Fortran Runtime Error
- AMBER: amber 10: sander and pmemd performance
- AMBER: Amber 8 Equivalent of the Amber 5 - Edit program
- AMBER: Amber 8 on Redhat 4 X86_64
- AMBER: AMBER 8 problems on RHEL4/Opteron/PGF 7.0-7
- AMBER: amber 9 compilation error with mvapich and intel compilers
- AMBER: amber 9 compilation error with mvapich and intelcompilers
- AMBER: amber 9 compilation problem on IBM SP5
- AMBER: amber 9 install
- AMBER: Amber 9 installation
- AMBER: Amber 9 installation problems
- AMBER: amber 9 on Intel Harpertown
- AMBER: Amber 9 run error
- AMBER: AMBER 9 testing
- AMBER: Amber 9: Question regarding Test Failures and Compilers
- AMBER: AMBER : Inconsistent MD length and no of angles after ptraj
- AMBER: Amber : neutralizing without adding ions
- AMBER: amber :antechamber problem
- AMBER: Amber compilation with ifort
- AMBER: Amber compile
- AMBER: Amber dipole printout.
- AMBER: Amber DNA Model for X-ray Crystallography
- AMBER: AMBER entropy calculation
- AMBER: amber ff and how it deals with out-plane chiral C
- AMBER: AMBER file preparation for protein-carbohydrate complex
- AMBER: AMBER force field for glycolipid
- AMBER: AMBER forfield choose
- AMBER: Amber GB problems on PMEMD !!
- AMBER: Amber heme parameters
- AMBER: AMBER install problem
- AMBER: Amber installation
- AMBER: amber installation on cluster
- AMBER: AMBER installation problem
- AMBER: amber minimisation
- AMBER: AMBER minimization problems
- AMBER: Amber on Infiniband clusters: SDR vs DDR cables?
- AMBER: Amber on linux
- AMBER: AMBER Parallel test error
- AMBER: Amber parallel version on CPU power of 2 only
- AMBER: Amber Parameter Schema
- AMBER: AMBER parameters for Chlorophyll
- AMBER: AMBER PBSA
- AMBER: AMBER question: perturbed charge twice the unperturbed
- AMBER: Amber tools 1.2 test failure (installation)
- AMBER: amber tools installation
- AMBER: AMBER under cygwin on 64 bit Vista
- AMBER: Amber Workshop
- AMBER: AMBER-8 parallel installation - test run failure
- AMBER: AMBER10 AMBERTools antechamber
- AMBER: Amber10 Compilation
- AMBER: AMBER10 Compilation (SGI Altix)
- AMBER: amber10 compile gfortran question
- AMBER: AMBER10 compiling SANDER parallel problem
- AMBER: AMBER10 failing to compile PMEMD
- AMBER: amber10 installation
- AMBER: Amber10 installation error
- AMBER: Amber10 Installation error - incorrect file suffix
- AMBER: amber10 installation on sgi_mips
- AMBER: amber10 installation problem
- AMBER: amber10 installation problem in cygwin
- AMBER: AMBER10 installation question
- AMBER: amber10 make fails for static/parallel
- AMBER: Amber10 on Leopard with Intel compilers, "Undefined symbols" error
- AMBER: amber10 on SiCortex hardware
- AMBER: Amber10 testing problem
- AMBER: amber10/dat/leap/cmd/README need update
- AMBER: AMBER10: ambpdb problems
- AMBER: AMBER10: Fortran Runtime Error
- AMBER: amber10: pmemd gfortran
- AMBER: Amber10: Problem with tgtmd and ncsu testing
- AMBER: AMBER10: QMMM parallel test error
- AMBER: Amber10:Compiling with gcc 2.4.1
- AMBER: amber9 , ptraj vector commad issue
- AMBER: amber9 / difference of igb=0 and igb=6
- AMBER: AMBER9 Compilation
- AMBER: Amber9 fails test.parallel
- AMBER: amber9 hangas after job submission
- AMBER: amber9 install problem
- AMBER: Amber9 Installation Problem
- AMBER: AMBER9 installation problen with open mpi
- AMBER: Amber9 vs Amber10+MKL benchmark
- AMBER: Amber9 vs AmberTools 1.0: weird imaging problem with ptraj?
- AMBER: Amber9 with MPICH2 failure at runtime
- AMBER: amber: parameters for 5' nucleotide monophosphates
- AMBER: Amber: shared memory vs cluster
- AMBER: Amber:unsubscribe amber
- AMBER: AmberTools 1.0 installation error: x86_64
- AMBER: AmberTools on OS X fails tests
- AMBER: AmberTools on OS X Leopard with Intel compilers
- AMBER: AmberTools-1.1 port for FreeBSD
- AMBER: AmberTools1.1 (and 1.0) antechamber endless loop
- AMBER: ambertools: static linking of user binaries is not supported on Mac OS X
- AMBER: ambmask problem
- AMBER: AMD Opteron: compiler recommendations?
- AMBER: An enquiry about dynamic simulations of oxygen binding to myoglobin (Ann N Y Acad Sci. 1986;482:222-
- AMBER: ANAL
- AMBER: analysing normal modes
- AMBER: analysis REMD
- AMBER: anion and cation simulaton
- AMBER: anisotropic pressure scaling ntp=2
- AMBER: ANNOUNCE: Release of AmberTools, version 1.0
- AMBER: Announcement of ACS COMP Division CCG and HP award deadlines for Spring 2009 meeting
- AMBER: ANNOUNCEMENT: release of Amber 10
- AMBER: Another problem when trying to compile Sander in debug mode
- AMBER: antechamber
- AMBER: antechamber and charmm
- AMBER: antechamber and gaff for a homodimer
- AMBER: Antechamber and topology file
- AMBER: antechamber bug? produces incorrect NEWPDB.PDB file
- AMBER: antechamber cannot generate prep files
- AMBER: antechamber errors
- AMBER: antechamber generated input for gaussian error
- AMBER: ANTECHAMBER NAMING
- AMBER: antechamber problem
- AMBER: antechamber problems
- AMBER: Antechamber Question
- AMBER: antechamber run on charged system
- AMBER: antechamber test failure
- AMBER: Antechamber, net molecular charge
- AMBER: Antechamber/mopac am1-bcc charge
- AMBER: Antechamber/mopac query
- AMBER: anything wrong with this script
- AMBER: aromatic bent ligand
- AMBER: aromatic residues lost planarity during MD simulation
- AMBER: artifacts in ptraj avg output
- AMBER: ASSERTion ' ier == 0 ' failed in nmode.f
- AMBER: Atom names CL and four characters
- AMBER: atom type for carbon and nitrogen atoms
- AMBER: atom type in glycam06
- AMBER: Atom type with 10-12 and 6-12 interactions in Amber9
- AMBER: Atom types/parameters for chromene
- AMBER: atomic posiltional fluctuation
- AMBER: Atomic restraints
- AMBER: autodock pdb to obtain parm with tleap
- AMBER: Average structure
- AMBER: Azobenzene: AMBER+Gromos Force Field parameters
- AMBER: Azobenzene: dihedral angle CCNN force field parameter
- AMBER: B-factor
- AMBER: B-factor calculation from data with different write frequencies
- AMBER: Back on track
- AMBER: bacteriochlorophyll ff
- AMBER: bad nonbon in nmode (amber9)
- AMBER: BCC charges
- AMBER: bellymask for DNA backbone doesn't seem to work
- AMBER: benchmark walltime to ps/day calculation
- AMBER: Benchmarks on Fujitsu PrimePower 2500?
- AMBER: Bennett acceptance ratio with Amber10
- AMBER: Biased MD with Amber 10
- AMBER: big molecule numbers
- AMBER: big molecule numbers ( simulation with many formamide molecules )
- AMBER: Binary restart file !!
- AMBER: binding energy: high ELE
- AMBER: bis(trifluoromethylsulfonyl)imide (Tf2N)
- AMBER: bond breaking in proteins
- AMBER: bond command
- AMBER: Bond-angle-dihedral-improper-vdw energy terms for part of a system
- AMBER: Bonds getting shorter in sander
- AMBER: box shape changed at NVT
- AMBER: Br - ion defined ?
- AMBER: Buckingham potential
- AMBER: bugfix (imin=5) in amber9
- AMBER: Build a MPI NAB
- AMBER: build proline
- AMBER: build RNA by nucgen
- AMBER: Building Amber 10 with Intel MKL and compiler mini howto
- AMBER: building new ions
- AMBER: Building O-Ac modified monosaccharides consistent with Glycam force field parameters
- AMBER: Building ppc64 AMBER10 with xlf fortran 11.1
- AMBER: building quadruplex with nab
- AMBER: bye
- AMBER: Ca ions not recognized
- AMBER: caculating nonpolar solvation energies
- AMBER: Calcium and Magnesium LJ parameters
- AMBER: Calculate number of ions
- AMBER: Calculate the RESP charge Fe3+ of heme (p450)
- AMBER: Calculating the dielectrostatic constant from simulation?
- AMBER: calculating the energy from the restart file
- AMBER: calculating the enthalpy of evaporation
- AMBER: calibration of constant pH simulations
- AMBER: can amber read .xyz files?
- AMBER: Can sander provide ESP with PBC?
- AMBER: can't make antechamber work for regular nucleotides
- AMBER: cannot read big .pdb files
- AMBER: capping with non charged residues
- AMBER: CAVITY_SURFTEN & CAVITY_OFFSET default params
- AMBER: cfortran.h error with xlf90 compiler
- AMBER: CG and HC atoms partial charges in AMBER
- AMBER: change in secondary structure during MD
- AMBER: Changes in the Amber web site
- AMBER: changing pdb structure
- AMBER: charge derivation for modified amino acids
- AMBER: Charge derivation: RESP vs. antechamber
- AMBER: Charge neutralization, GlcNac & GalNac improper torsional angles from old PREP
- AMBER: Charge scheme for simulating protonated adenine
- AMBER: check COM velocity
- AMBER: Chloride anion ligands leave the protein during MD
- AMBER: Choline chloride salt
- AMBER: chromophore parameters for Molecular Dynamics
- AMBER: cis - trans isomerization
- AMBER: Clarification on error message
- AMBER: Clarification re qmmask
- AMBER: Cluster analysis
- AMBER: cluster for running amber10
- AMBER: cnstph test case failure or expected divergence?
- AMBER: cntrl namelist error
- AMBER: Collect dihedral angles
- AMBER: collision with surface
- AMBER: COM RESTRAINT
- AMBER: Combine mdcrd
- AMBER: Combine mdcrd files
- AMBER: Combine mdcrd while stripping WAT problem
- AMBER: Combining multiple structures into single pdb
- AMBER: Comment: constant pH, non-integer charge -> weird error
- AMBER: Compailation problum in Amber 10
- AMBER: comparison of MD trajectories recorded with pmemd and sander
- AMBER: Compilation of amber8 patched with ramd
- AMBER: Compilation of PMEMD
- AMBER: compilation problem
- AMBER: compilation problem with AMBER10
- AMBER: Compile AMBER 9 on TACC Ranger super computer
- AMBER: compile amber10 on Mac
- AMBER: Compile amber10 parallel with suppied LAM
- AMBER: compile Amber9 on 64bit AMD Opteron
- AMBER: Compile Error
- AMBER: Compiler issues with Altix450
- AMBER: compiling amber 10
- AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC
- AMBER: Compiling Amber10 PMEMD with MVAPICH, InfiniBand support
- AMBER: Compiling amber10 with xlf90 fortran compiler
- AMBER: compiling AMBER9 with bintraj option on AMD64
- AMBER: compiling ambertools with intel compilers
- AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90
- AMBER: compiling PMEMD with MKL10.0
- AMBER: concerning force fields
- AMBER: concerning force fields ( to Karl Kirschner )
- AMBER: configure_amber (10) for pg compilers
- AMBER: Conformation search...
- AMBER: connectivity lose during the minimizations
- AMBER: connectivity problem
- AMBER: constant ph (cpinutil file)
- AMBER: Constant pH dynamics
- AMBER: Constant pH simulation force field
- AMBER: Constant pH with new parameters (amber10)
- AMBER: Constat area simulation
- AMBER: constph
- AMBER: Constrained group
- AMBER: Contacts
- AMBER: convergence of free energy calculations
- AMBER: Conversion between truncated octahedron and orthorohombic box
- AMBER: conversion from crd to netcdf returns almost identical file!
- AMBER: convert AMBER format input files into DL_POLY format input files?
- AMBER: Convert dcd to mdcrd
- AMBER: converting from CNS file format
- AMBER: coordinate change of pdb structure using xleap
- AMBER: coordinate file question
- AMBER: Coordinated Zinc
- AMBER: coot mutation
- AMBER: Correlation functions from iRED analysis
- AMBER: corrupted restart file
- AMBER: Critical patch for pmemd 10 extra points code
- AMBER: cross correlation function using iRED matrix
- AMBER: cross time correlation function
- AMBER: Cutoff list exceeds largest sphere in unit cell
- AMBER: Cysteine sulphonic acid parameters
- AMBER: D2O
- AMBER: DCCM correlation analysis
- AMBER: Debugf AMBER9
- AMBER: definition of dihedral in amber
- AMBER: Deleting solute from box
- AMBER: Dell 2 Quad Core System Performance
- AMBER: Deriving Force Field Parameters
- AMBER: DFTB parameters for O-P
- AMBER: DFTB QMMM parameters ambiguity in AMBER10 docs
- AMBER: DFTB/SCC-DFTB
- AMBER: diblock copolymer
- AMBER: difference between sander and NAB
- AMBER: Differentiating the force constant of distance restraints
- AMBER: Dihedral Angle Parameters
- AMBER: Dihedral Drive
- AMBER: dihedral energy calculation inconsistent with gaussian's result
- AMBER: dihedral energy in amber
- AMBER: dihedral potential with odd periodicity
- AMBER: Dihedral: ptraj
- AMBER: Dimension of the solvated box?
- AMBER: Discontinuous Constant pH Restarts
- AMBER: distance
- AMBER: Distance diagnolization matrix plot
- AMBER: Distance in z dimension
- AMBER: distance matrix command
- AMBER: distance restraint
- AMBER: distance restraint between non-bonded molecules
- AMBER: distance restraint between non-bonded molecules]
- AMBER: distance restraint in minimization
- AMBER: Distance restraints between com of two groups of residues
- AMBER: Distorsion in protein and ligand during MD
- AMBER: distorted aromatic rings
- AMBER: Distorted ring...
- AMBER: Disturb you for help !?=
- AMBER: Disturb you for help!
- AMBER: disulfide bridge with ff03ua FF
- AMBER: divcon
- AMBER: divcon.rst ??
- AMBER: DMSOBOX
- AMBER: DNA structure analysis
- AMBER: DNA-Gold parameters
- AMBER: DNA: GB solvent with salt
- AMBER: dockmolecules in examples directory of AmberTools-1.0
- AMBER: Does clustering involve fitting?
- AMBER: Does LEaP understant capping with ACE/NME?
- AMBER: Dose AMBER 10 pmemd support openmpi?
- AMBER: double strand DNA break up (imaging)
- AMBER: drawing repeated units
- AMBER: drug/protein interaction modeling setup
- AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2
- AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend)
- AMBER: Eigenmode dynamics - imaging traj
- AMBER: Eigenmode dynamics in Ptraj
- AMBER: el w-end en galicia!
- AMBER: ELAN_EXCEPTION @ --: 6 (Initialisation error) ELAN_EXCEPTION @ --: 6 (Initialisation error)
- AMBER: Electric field on atoms in equallibrium
- AMBER: Electrostatic Energy Components
- AMBER: Emperical Valence Bond
- AMBER: empty frcmod file but missing parameters
- AMBER: empty output
- AMBER: Energy analysis
- AMBER: Energy calculation and replica exchange in Amber9
- AMBER: energy decomposition vs ala scan
- AMBER: energy decomposition with sander?
- AMBER: energy leakage?
- AMBER: Energy minimization of protein-ligand complex
- AMBER: energy pairwise decomposition in GB/SA simulation
- AMBER: energy problems in simulation with restraints
- AMBER: energy terms in hybrid REMD calculation
- AMBER: Entropy calculation
- AMBER: Entropy calculations using NMODE
- AMBER: entropy of released water
- AMBER: equilibration
- AMBER: equilibration of peptide
- AMBER: Equilibration protocol for large protein
- AMBER: Equilibration/Heating - Protein fixed -Problem
- AMBER: Error during compilation of Amber8, /bin/sh: ./Makelist: not found, make[1]: *** [libobj] Error 127
- AMBER: error in compilation elsize.cc
- AMBER: Error in creating topology file
- AMBER: error in parallel amber 9 test
- AMBER: error in reading namelist cntrl
- AMBER: error message of xleap
- AMBER: Error message: Install Amber9 on fedora 9
- AMBER: Error runing Addles
- AMBER: Error when compiling and testing AmberTools
- AMBER: Error when performing Alanine scanning
- AMBER: error when read inpcrd
- AMBER: error when using tleap with leaprc.ff02EP
- AMBER: Error while compiling Amber
- AMBER: error while running REMD in amber9
- AMBER: Error with a binary restart file
- AMBER: Error- MM_PBSA calculation
- AMBER: Error: Bond: Maximum coordination exceeded -- setting atoms pert=true overrides default limits
- AMBER: Error: PB bomb in pb_reslist(): maxnbr too small
- AMBER: Error: tutorial one for md simulation of DNA
- AMBER: ESP on atoms (2)
- AMBER: Estimating dielectric constant
- AMBER: ESURF - SASA - isolate residues
- AMBER: EVB allocation problem
- AMBER: EVB tests failure
- AMBER: Ewald error estimate
- AMBER: Ewald PARAMETER RANGE WRONG
- AMBER: Ewald troubles when running very big boxes
- AMBER: Example .prepi file for nonstandard amino acids
- AMBER: Explanation of the energy unit ?
- AMBER: Extracting periodic box size deviation
- AMBER: Extracting the electric field (and its gradient) on particular solute atoms
- AMBER: F modified RNA is split in two parts when running sander simulated annealing
- AMBER: FAD and NAD parameters
- AMBER: FAD RESP charges and parameters
- AMBER: Failure of antechamber in amber10
- AMBER: ff02 in nmode gives error "too many dihedrals" ?
- AMBER: ff03-compatible parameters/charges for phosphothreonine and phosphotyrosine
- AMBER: ff94 vs. ff03
- AMBER: ff99 (PK/IDIVF)
- AMBER: ff99 and ff03 forcefield parameters
- AMBER: files in Amber directory ( to Junmei Wang )
- AMBER: fix for POL3 heating problem?
- AMBER: flexible molecule parameterization
- AMBER: Folate parameters
- AMBER: For help: how to perform double decoupling thermodynamic integration calculation in AMBER10
- AMBER: For help: Thermodynamic Integration of solvation free energy using soft-core potential
- AMBER: for mask in rms
- AMBER: for NMR refinement
- AMBER: force field
- AMBER: Force field equation
- AMBER: Force field for Gd (gadolinium)?
- AMBER: Force field for Gd3+ (metal ion)?
- AMBER: Force field in water and in vacuum ??
- AMBER: Force field Parameters
- AMBER: Force Field parameters : A new chemical compound
- AMBER: Force fields
- AMBER: Force fields for REMD with GB solvent
- AMBER: forrtl severe(174) error with minimization and md
- AMBER: fortran runtime error in "make test.serial" with gfortran
- AMBER: frcmod:attn needs revision
- AMBER: free energy
- AMBER: Free Energy Calculations - parameters for MM
- AMBER: Free energy landscape? HOWTO?
- AMBER: Free energy of dissociation
- AMBER: FreeBSD "port" for AmberTools-1.2
- AMBER: from dihe parameters to torsional energy
- AMBER: from Gromax to AMBER
- AMBER: Fully QM periodic runs
- AMBER: Further request answers from Dr. Junmei Wang
- AMBER: Fwd: Distorsion in protein and ligand during MD
- AMBER: Fwd: positive potential energy and large 1-4 EEL
- AMBER: Fwd: Welcome to amber
- AMBER: GAFF
- AMBER: GAFF atom types for flavin (again)
- AMBER: GAFF for organic crystals
- AMBER: gaff paramters
- AMBER: GAFF Schema
- AMBER: gasteiger is not working with ambertools 1.0
- AMBER: GB offset for proteins
- AMBER: GB versus explicit medium
- AMBER: Gbsa in NAB
- AMBER: GBSA SA calculation
- AMBER: general question
- AMBER: generate topology file for alanine scanning (mmpbsa)
- AMBER: Generating RESP charges
- AMBER: gigabit ethernet cards and switches
- AMBER: Glycam
- AMBER: Glycoprotein once again..........
- AMBER: glycoprotein setup
- AMBER: Gohlke in-house iRED Simulated Order Parameter Script
- AMBER: GPCR membrane simulation, setting surface tension
- AMBER: GPCR membrane simulation, setting surface tension - Message is from an unknown sender
- AMBER: Gradual releasing of position restraints
- AMBER: graphite
- AMBER: Group specification problem
- AMBER: H atom names in Amber
- AMBER: Happy holi
- AMBER: Harmonic Force Constant
- AMBER: Harmonic restraint between two atoms
- AMBER: Has anyone seen a protein fall apart due to PBCs?
- AMBER: hbonds in first solvation shells
- AMBER: Heating POL3 Box Troubles
- AMBER: Heating up
- AMBER: help can amber couple part of the system to different heat bath?
- AMBER: Help compiling Nab programs for AMBER tools
- AMBER: Help in radii
- AMBER: help MD running error
- AMBER: help me for filling a nanotube with water??
- AMBER: Help needed to analyze DNA Holliday Junction - Drug Binding MD simulations.
- AMBER: Help reg. input file
- AMBER: help regarding warning message
- AMBER: help to install AMBER9
- AMBER: Help with NMODE
- AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating
- AMBER: help... structure factors from amber trajectories?
- AMBER: help...ptraj does not output bounding box info
- AMBER: help...sander "segmentation fault" after 2hours of minimization
- AMBER: Help...which commands in ptraj does clustering by RMSD?
- AMBER: Heme cysteine
- AMBER: High Bfactor values for the terminal residues/atoms
- AMBER: High ESURF
- AMBER: High force constant for MD ???
- AMBER: hold atoms fixed
- AMBER: HOLD fixed vs restraint mask
- AMBER: How do you evaluate forces on a fixed atom?
- AMBER: how generate the final output file using mmpbsa
- AMBER: how to add new solvent type in Amber
- AMBER: How to add radius of an atom
- AMBER: How to adjust the problem of "Vlimit exceeded"
- AMBER: How to assign /make the ionion bond?
- AMBER: How to build a cubic box of a newly synthesized compound?
- AMBER: How to build a dimer using amber
- AMBER: How to calculate deformability by PTRAJ ?
- AMBER: how to calculate delta G from IC50
- AMBER: How to calculate RMSIP after PCA analysis by PTRAJ?
- AMBER: how to calculate the interaction energy
- AMBER: How to change default radius assigned to an atom
- AMBER: how to change the force field parameters inside the prmtop file?
- AMBER: how to choose the appropriate ensemble for a given problem
- AMBER: How to confirm atom types of small molecule perceived by antechamber
- AMBER: How to convert a CHARMM trajectory to AMBER format?
- AMBER: How to create *.top & *.crd file with hexagonal lattice
- AMBER: How to create average structure?
- AMBER: how to derive torsional angle parameters in gaff
- AMBER: How to determine the basic parameters of a Replica Exchange Molecular Dynamics(REMD?
- AMBER: how to enlarge the TIP3PBOX size
- AMBER: how to extract energy
- AMBER: How to extract solvent box information from .rst or .mdcrd files?
- AMBER: how to extract x,y,z of a set of atoms from an MD trajectories
- AMBER: how to generate psf file using the AMBER topology file
- AMBER: how to ger resp charge for a residue?
- AMBER: How to get all eigenvalues by "analyze matrix"
- AMBER: how to get the potential energy of a protein from the system
- AMBER: how to link two different atoms in xLeap
- AMBER: How to manually adjust periodic boundary conditions (PBC)
- AMBER: How to obtain the oriented trajectories?
- AMBER: how to overcome theunusual bonds formation
- AMBER: How to print out the improper dihedral angles/wilson angles?
- AMBER: how to remove counter ions ( K+ / Cl- ions) using rdparm?
- AMBER: How to set a ZN atom radius for PB calculations
- AMBER: How to set up a water slab in Amber?
- AMBER: How to solve - Missing BELE for MM in 1 in amber.
- AMBER: How to transfer unformatted coordinates into formatted ones
- AMBER: Huge difference between pbtot and gbtot in mm-pbsa calculations
- AMBER: Hybrid REMD amber10
- AMBER: hybrid remd imaging
- AMBER: Hydration free energies of charged ions using PME
- AMBER: Hydrogen bond energies in explicit solvent.
- AMBER: hydrogens are flying in replica exchange simulations
- AMBER: Hydroxide ion in POL3 water
- AMBER: Hydroxyproline in AMBER
- AMBER: Hydroxyprolines!!!
- AMBER: idecomp=2 & RRES/LRES group specification
- AMBER: Identification of improper torsions in small molecules parameterized with GAFF by antechamber
- AMBER: igb and ibelly
- AMBER: IGB=10 in Amber10
- AMBER: Imaging before HBond analysis?
- AMBER: imaging problem
- AMBER: imem keyword using mmpbsa
- AMBER: imin = 5 and PBC
- AMBER: implicit energy calculations
- AMBER: improper dihedral in ff03 united atom forcefield
- AMBER: Improper dihedral parameters
- AMBER: improper dihedrals in 03 united atom force field
- AMBER: impropers over bonds between sidechains
- AMBER: improving GAFF sulfonamide parameters
- AMBER: Inconsistent types (INTEGER(4)/REAL(8)) - Is it serious ?
- AMBER: increasing temperature smoothly
- AMBER: Indentifying cluster center structures in trajectory
- AMBER: infinite polymers in CHARMM
- AMBER: initial command?
- AMBER: Initial Equilibration
- AMBER: Initial structure from NMR structures
- AMBER: Initial velocities based on date and time are NOT changing ?
- AMBER: initial velocities of MD
- AMBER: INPCRD error on open
- AMBER: input
- AMBER: Input file for Minimization
- AMBER: input options for replica exchange simulations
- AMBER: Inquiry on analyzing the amplitude from nmdout results
- AMBER: Inquiry on B-factor of NMR
- AMBER: Inquiry on nmode for alculate frequencies & thermodynamics analysis
- AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64)
- AMBER: install amber tools
- AMBER: Install problems
- AMBER: installation amber on suse11.0
- AMBER: installation amber9
- AMBER: installation amber9 in fedora9
- AMBER: installation amber9 in fedora9 using bash shell
- AMBER: Installation Error
- AMBER: Installation error on IBM cluster
- AMBER: Installation of Amber 10 on Dual-Core Intel Mac
- AMBER: Installation on Mac OSX G5 dual processor
- AMBER: Installation problem of AMBER on cluster
- AMBER: Installation Problem of AMBER10
- AMBER: installing amber on new linux
- AMBER: Installing OpenMPI
- AMBER: Installing PMEMD with Amber10
- AMBER: installing pmemd with fftw
- AMBER: interaction energies
- AMBER: interaction energies in Amber
- AMBER: interaction energies in Amber and VMD/NAMD
- AMBER: interaction energies in Amber and VMD/NAMD (SOLVED)
- AMBER: internal energy INT is not zero from MM_GBSA
- AMBER: IRED to time correlation
- AMBER: Iron-Sulfur Cluster
- AMBER: is amber workshop available this summer??
- AMBER: Is boiling point a good way to validate solvent paramters?
- AMBER: Is G_disp calculated in MM_PBSA now?
- AMBER: is in vacuo simulation neccessary?
- AMBER: Is it possible to recover the umbrella file in ABMD simulation after hard disk failure?
- AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10?
- AMBER: is that possible fix box size in constant pressure MD
- AMBER: Is there a way to cluster frames of a trajectory?
- AMBER: Is there an easy way to calculate the electric field at the center of a group of atoms
- AMBER: Is there any way I can extract the potential energy of the solute with the solvent instead of the total energy in Amber?
- AMBER: Jarzinsky relationship
- AMBER: Jarzynski
- AMBER: JavaGenes
- AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files
- AMBER: join two units in amber9 or amber10
- AMBER: large number of solvent molecules were added for protein with 221 AA residues
- AMBER: lastrst problem
- AMBER: latest update on residuegen
- AMBER: launching a job works with sander.MPI and fail with pmemd.MPI
- AMBER: ld: cannot find -lgcc_s
- AMBER: leap - using default radius 1.500000 for HO3
- AMBER: Leap atoms CL and OXT do not have a type
- AMBER: LEap error message for parmBSC0 force field
- AMBER: LEaP problem with LEU first residue?
- AMBER: LEAP: solute concentration
- AMBER: leaprc help
- AMBER: Lennard-Jones parameters
- AMBER: LES
- AMBER: LES trajectories
- AMBER: LEU as first residue
- AMBER: ligand complexed simulation
- AMBER: Ligand energy minimization
- AMBER: Ligand force field generation, and its consistency with the force field of the protein.
- AMBER: ligand partial charge and conformation question
- AMBER: ligand slips out of pocket
- AMBER: ligand unit charge is not zero
- AMBER: linear interaction energy
- AMBER: LINMIN error in geometrically constrained minimization @ MM-PB/SA conditions
- AMBER: Liquid/Gas Phase
- AMBER: LJ parameters
- AMBER: load opls force field
- AMBER: loading pdb in leap to create parameter files
- AMBER: loadPdb returns extra atoms
- AMBER: local coordinate system question
- AMBER: Location of vdw radii and partial charges for ff99SB
- AMBER: Lone pairs in antechamber
- AMBER: looks like I have problem with "make clean" command
- AMBER: makeDIST_RST computation of r3 value with IAT < 0
- AMBER: makeDIST_RST error -- no map function for HH TYR
- AMBER: mask for oligosaccharide
- AMBER: mass weighted rms fit
- AMBER: massively parallel computation
- AMBER: Materials and methods
- AMBER: matrix correl
- AMBER: matrxi dist command
- AMBER: MAXAT can not be changed for AMBERTool 1.0
- AMBER: mbondi radii for gaff atom types
- AMBER: MD at a given pH
- AMBER: MD goes wrong
- AMBER: MD of protein-ligand comlex
- AMBER: MD simulation crashed
- AMBER: MD with NMR restraints
- AMBER: mdout file details
- AMBER: measuring contacts: error "glibc detected"
- AMBER: meet problem in adding ions and waterbox
- AMBER: meet problems in adding ions and waterbox
- AMBER: Membrane simulations
- AMBER: memory limitation of Amber 9
- AMBER: memory usage
- AMBER: Metal parameter values
- AMBER: Microcannonical MD Reference
- AMBER: Minimisation and heating under GB conditions
- AMBER: Minimisation: cis-azobenzene parameters
- AMBER: minimization
- AMBER: Minimization in Octahedric Box
- AMBER: Minimization methods
- AMBER: minimization stops or does not write anything
- AMBER: Minimizaton stops after Ncyc steps only
- AMBER: misplacement of TER by leap
- AMBER: Missing gaff angle parameters for dimethyl esters
- AMBER: missing gaff parameters
- AMBER: missing torsion parameters
- AMBER: MKL libraries/Amber10
- AMBER: MM-GBSA with very positive GB value
- AMBER: MM-PBSA
- AMBER: MM-PBSA -energy decomposition error
- AMBER: mm-pbsa / sander.MPI ?
- AMBER: MM-PBSA : bad atom type: ZN
- AMBER: MM-PBSA and delphi
- AMBER: MM-PBSA and trajectory input
- AMBER: MM-PBSA calculation problem
- AMBER: MM-PBSA error in Amber10: possible bug?
- AMBER: MM-PBSA for carbohydrates
- AMBER: MM-PBSA in AMBER 10
- AMBER: MM-PBSA Issue in Amber 10
- AMBER: mm-pbsa multiple trajectory approach?
- AMBER: MM-PBSA multiple trajectory problem
- AMBER: MM-PBSA problem
- AMBER: MM-PBSA problem : Missing PBCAV for PB
- AMBER: MM-PBSA problem : Use of uninitialized value in multiplicatiom with Amber10
- AMBER: MM-PBSA/NMODE in Amber 10
- AMBER: MM/GBSA Error during deccomposition
- AMBER: mm/pbsa and saltcon effect
- AMBER: MM_PBSA - SASA - Question
- AMBER: MM_PBSA binding error
- AMBER: MM_PBSA doesn't terminate
- AMBER: mm_pbsa error
- AMBER: mm_pbsa error : Scale paremeter for PBSA
- AMBER: mm_pbsa incorrect complex prmtop file
- AMBER: MM_PBSA output file
- AMBER: mm_pbsa positive ELE
- AMBER: mm_pbsa problem
- AMBER: MM_PBSA problem in binding_energy
- AMBER: mm_pbsa problem: bad atom type: IP
- AMBER: MM_PBSA problems in AMBER9
- AMBER: MM_PBSA snapshot statistic calc problem
- AMBER: mm_pbsa.pl and Amber10
- AMBER: mm_pbsa.pl not reading parameters for nmode
- AMBER: mm_pbsa: vertex atom mismatch
- AMBER: mm_pbsa_statistics / 3 traj
- AMBER: mmpbsa
- AMBER: mmpbsa binding energy
- AMBER: MMPBSA error
- AMBER: mmpbsa errors in redoing the tutorial A3:MMPBSA
- AMBER: mmpbsa INSTRNG error?
- AMBER: mmpbsa molsurf.c error
- AMBER: mmpbsa with gromacs trajectory
- AMBER: Mn2+ parameters in AMBER
- AMBER: MNDO parameters for Mg+2
- AMBER: Model of deoxyadenosine in Cornell 95 paper
- AMBER: modified parmtop file from ptraj?
- AMBER: MOIL-View is for SGI. How do we analyze LES trajectories?
- AMBER: MOIL-View: is there a command line version?
- AMBER: mol2 save
- AMBER: mol2, xleap, Segmentation fault
- AMBER: Molecular dynamics simulation of large-scale domainmovement in a protein
- AMBER: molecular structure
- AMBER: molecule drift out of water box?
- AMBER: molsurf
- AMBER: molsurf fails
- AMBER: MOLYBDENUM
- AMBER: More on tweaking a topology file
- AMBER: mpd error in submitting parallel job
- AMBER: MPI run problem
- AMBER: mpirun Permission denied.
- AMBER: mulliken charges in QM/MM calculation
- AMBER: multiple dihedral restraints using group
- AMBER: multiple dihedral restraints using group (in Amber 10)
- AMBER: multiple heat baths in a single simulation?
- AMBER: mwcovar limit?
- AMBER: N(CN2)- ion
- AMBER: nab
- AMBER: NAB conjgrad returns error?
- AMBER: NAB documentation
- AMBER: NAB documentation for programmers
- AMBER: NAB examples
- AMBER: NAB parameter: wcons
- AMBER: NAB to calcuate entropy
- AMBER: NAB to calcuate entropy. .
- AMBER: NAB: getseq_from_pdb()
- AMBER: NAD parameters
- AMBER: NAD+ parameters problem using tleap
- AMBER: NAN errors in Etot, EPtot, EKtot and EELEC
- AMBER: NAN errors still exist
- AMBER: Need help with force field parameters for Lipopolysaccharide (LPS)
- AMBER: Need help... High energies for complex...
- AMBER: Negative dihedral coefficients in amber99 - Possible?
- AMBER: Negative ligand
- AMBER: Negative ligand (Peroxide)
- AMBER: net charge
- AMBER: netcdf configure returned 1
- AMBER: netcdf configure returned 1 - PROBLEM SOLVED
- AMBER: neutral C-terminus and N-terminus parameters for amber
- AMBER: new residues in AMOEBA
- AMBER: Newbie question: partial minimization in implicit solvent
- AMBER: nfft1-3 too large
- AMBER: NMA
- AMBER: nmode
- AMBER: nmode "Atom out of bounds" for min of multiple ligands
- AMBER: Nmode - entropy calculation of receptor - should I apply restraint?
- AMBER: nmode analysis
- AMBER: Nmode entropy calcs
- AMBER: nmode output
- AMBER: nmode problem
- AMBER: Nmode segmentation fault
- AMBER: nmode units
- AMBER: NMODE units and hrmax value for Langevine modes
- AMBER: nmode/nab entropy calculations memory issues
- AMBER: nmode/nab entropy calculations without hydrogens
- AMBER: nmode: number of atoms limitation
- AMBER: NMR average structure
- AMBER: NMR optimization with group averages (IGR1 / IGR2)
- AMBER: NMR refinement
- AMBER: NMR restraints
- AMBER: NMR structure as initial structure
- AMBER: NMROPT=1 in minimisation
- AMBER: No bond and angle parameters for - -?????
- AMBER: Non aqueous implicit solvation
- AMBER: Non bond list error
- AMBER: NON-BONDED parameters
- AMBER: Non-polar Parameters For MM_PBSA Calculation
- AMBER: Nonbonded FE parameter missing in frcmod.
- AMBER: nonbonded parameters for titanium
- AMBER: NONBONDED_PARM_INDEX
- AMBER: normal-vector of a plane with 'corrplane'
- AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER?
- AMBER: Not integral charge increasing with number of lipids
- AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error
- AMBER: NPRO net charge in amber10/dat/leap/lib/all_aminont03.lib is 0.900026, why?
- AMBER: NPT to NVT
- AMBER: nscm code
- AMBER: NTC and NTF
- AMBER: NTR Restraints
- AMBER: Nudged Elastic Band initial heating problem
- AMBER: Number of Hydrogen Bonds?
- AMBER: NVE energy and temperature drift
- AMBER: Oct 6 deadline for ACS computational chemistry awards
- AMBER: offset residue numbering
- AMBER: Once again, with feeling --- Support for intel mpi in pmemd 10; better support for intel MKL
- AMBER: OPLS force field
- AMBER: opls/aa in Amber status
- AMBER: Optimal compiling of amber on XT3
- AMBER: organic solvents
- AMBER: Origin of periodic box
- AMBER: output effective Born radii
- AMBER: output file AMBER9_MPI
- AMBER: output file format in SANDER.MPI & PMEMD
- AMBER: Packing density calculation
- AMBER: pairwise interaction energies
- AMBER: parallel amber 10 sander.MPI (low cpu utilization)
- AMBER: parallel error : undefined reference to `MAIN_'
- AMBER: parallel installation
- AMBER: Parallel Self-guided Langevin simulation
- AMBER: parallel test / libmpi_f90.so.0
- AMBER: parameters
- AMBER: Parameters for alkali cations and halogen anions
- AMBER: Parameters for chloride ion in contact with a protein
- AMBER: parameters for Fe coordinated to four CYS ?
- Amber: parameters for Silicon
- AMBER: parameters for silicon atom
- AMBER: parameters in ff03 and ff99
- AMBER: parameters of nonbonded potentials
- AMBER: paricular atom coordinates?
- AMBER: parmbsc0
- AMBER: parmbsc0 parameters for RNA.DNA systems
- AMBER: Parrallel computing
- AMBER: PB Bomb in pb_atmlist(): maxnba too short
- AMBER: PB Radii
- AMBER: PBC in 2D
- AMBER: PBCAL in MM_PBSA
- AMBER: PCA - analysis
- AMBER: PCA analysis
- AMBER: PCAL and polar contribution in the output file
- AMBER: pdb file ??
- AMBER: PDB files in Amber10
- AMBER: PDB standards
- AMBER: pdb structure is only half the molecule.
- AMBER: PEO-PLA/PCE
- AMBER: peptide at the box center during NVT-MD
- AMBER: peptide MD
- AMBER: Performance issues on Ethernet clusters
- AMBER: periodic bondary condition
- AMBER: periodic boundary
- AMBER: periodic boundary condition
- AMBER: PF6 parameters
- AMBER: PGI amber9 problems
- AMBER: PKa calculation
- AMBER: Playstation 3 Benchmarks
- AMBER: Plea for REMD tutorial
- AMBER: pmemd
- AMBER: pmemd 10 output
- AMBER: pmemd 9.0 compilation error
- AMBER: PMEMD and polarized force field ff 02
- AMBER: PMEMD and sander.MPI
- AMBER: PMEMD installation problem.
- AMBER: pmemd iwrap trouble
- AMBER: PMEMD with AMOEBA parms including a lone pair site
- AMBER: pmemd: "undefined reference to `mpi_(name-varies)'"
- AMBER: PMEND 9 compilation problems
- AMBER: PMF calculation for binding constant or rate constant?
- AMBER: PMF calculation for rate constant or binding constant?
- AMBER: point charges
- AMBER: Points on a Sphere
- AMBER: POL3 with gaff and ff02EP
- AMBER: Polarizable force field for divalent ions?
- AMBER: Position: Postdoctoral Fellow
- AMBER: potassium ion
- AMBER: potential of mean force: Unit of PMF energies and min path
- AMBER: prep files ATP-MG++ and for phosphorylated threonine
- AMBER: prepare an initial structure in Amber
- AMBER: Preparing peptides with D-amino acids
- AMBER: Prepgen
- AMBER: Prepgen does not give correct result?
- AMBER: pressure component
- AMBER: pressure regulation methods
- AMBER: pressure varies in constant pressure membrane simulation
- AMBER: principal component analysis
- AMBER: print distance between atoms during simulation within sander itsself
- AMBER: printing dipoles in Amber10 (and earlier)
- AMBER: prmtop spec trivia
- AMBER: problem
- AMBER: Problem about antechamber
- AMBER: problem bull linux compiling
- AMBER: Problem compiling Amber with Intel 10 compilers - "undefined reference" errors
- AMBER: Problem in .parmtop file
- AMBER: Problem in calculation of resp charges using RED III
- AMBER: Problem in EVB and Trajectory analysis
- AMBER: problem in installing parallel version of amber10 with lam
- AMBER: problem in neturalization
- AMBER: Problem In Paralklel Amber
- AMBER: problem in starting sander
- AMBER: Problem installing PMEMD with intel mpi, ifort
- AMBER: Problem loading the leaprc.amoeba force field file in Amber 10.
- AMBER: Problem of "Too many dipole-dipole interactions allocated" when using amoeba.
- AMBER: problem of install amber9
- AMBER: Problem of Ptraj analyze matrix
- AMBER: problem of use MPICHI2 to run RMED on amber10
- AMBER: Problem running implicit minimization
- AMBER: Problem running NEB in AMBER10
- AMBER: problem to compile PMEMD?
- AMBER: problem when running energy minimization with polarizable potential
- AMBER: Problem While Installing Amber
- AMBER: Problem with "trajout pdb"
- AMBER: problem with amber8 installation
- AMBER: problem with ambmask
- AMBER: problem with AMOEBA
- AMBER: problem with antech amber
- AMBER: problem with antechamber
- AMBER: Problem with box dimension in AmberTools ptraj
- AMBER: problem with cartesian restraints with NTP simulations
- AMBER: problem with Dihedral angle potentials
- AMBER: problem with distance restrain
- AMBER: problem with distance restraints
- AMBER: problem with editing with xleap
- AMBER: Problem with energy decomposition in MMPBSA
- AMBER: Problem with evaporating water over longer simulation times
- AMBER: problem with group input
- AMBER: problem with group input and NMR restaints
- AMBER: problem with Mg2+ during MD
- AMBER: problem with minimization
- AMBER: Problem with MMPBSA
- AMBER: problem with nmod
- AMBER: problem with parmchck
- AMBER: problem with prep file generation
- AMBER: problem with rdparm
- AMBER: problem with restraints
- AMBER: problem with running mm-pbsa
- AMBER: Problem with running refinement of NMR structures with RDCs
- AMBER: Problem with setting the NMR restraints
- AMBER: Problem with the prmtop file generated by sleap and leaprc.amoeba in Amber 10.
- AMBER: problem with toturial A3 (MM-PBSA)
- AMBER: problem with traj and strip waters
- AMBER: problem with zMatrix in tleap
- AMBER: Problem with: Increase lastrst in the &cntrl namelist
- AMBER: PROBLEM: AmberTools Installation using Ubuntu
- AMBER: problem:capping
- AMBER: Problem:neturalization
- AMBER: Problems compiling Amber with MKL
- AMBER: Problems compiling leap on Altix Cluster
- AMBER: Problems for use manganese molecules
- AMBER: problems form the pdb to the mol2
- AMBER: Problems in execution of Replica Exchange calculations Amber 9.0
- AMBER: Problems in restrained minimization
- AMBER: Problems installing Amber Tools for Amber 10
- AMBER: problems of antechamber
- AMBER: Problems of MM/MM-GBSA calculations
- AMBER: Problems simulating a protein-ligand complex
- AMBER: problems with 10-12 potential in amber8 sander
- AMBER: Problems with Frozen atoms
- AMBER: Problems with neglected restaints
- AMBER: problems with ptraj and strip waters
- AMBER: problems with Replica Exchange
- AMBER: problems with restart of MD
- AMBER: problems with sleap
- AMBER: Problems with sleap and amoeba
- AMBER: Problems with the charge (membrane simulation)
- AMBER: process_mdout modify
- AMBER: program to calculate rmsd
- AMBER: Protein rotating out of box
- AMBER: protein-ligand complex problem
- AMBER: Proton Parameters
- AMBER: protonate in Amber10
- AMBER: protonated guanine, cytosine parameters
- AMBER: protonated histidine ( charges in parm file versus all_a mino03.lib ). . .
- AMBER: protonated histidine ( charges in parm file versus all_amino03.lib )
- AMBER: protonated histidine ( charges in parm file versus all_amino03.lib ).
- AMBER: Protonated Phosphate Problem
- AMBER: Protonation states in Constant pH Simulations
- AMBER: ptraj
- AMBER: ptraj & imaging of velocities
- AMBER: ptraj - closest command
- AMBER: ptraj - read in part of trajectory
- AMBER: PTRAJ - Segmentation Fault
- AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory
- AMBER: ptraj / covariance / quasiharmonic approximation / entropy
- AMBER: ptraj analyze matrix
- AMBER: ptraj analyze modes from nmode
- AMBER: ptraj and netcdf with AmberTools1.2 ?
- AMBER: ptraj and non-bonded contacts
- AMBER: ptraj average structure
- AMBER: ptraj center problem
- AMBER: ptraj closest command
- AMBER: ptraj has trouble with x-plor psf file from VMD
- AMBER: ptraj imaging issue
- AMBER: ptraj mask not working with psf file
- AMBER: ptraj new mask parser: differences from ambmask and core dumps
- AMBER: Ptraj Normal Mode Analysis
- AMBER: ptraj problem with centering in the box
- AMBER: ptraj problem with imaging
- AMBER: Ptraj pucker for pyranose
- AMBER: ptraj rmsd calculation
- AMBER: ptraj selection
- AMBER: Ptraj | Multiple trajout commands?
- AMBER: ptraj, hbond and non-bonded contacts
- AMBER: ptraj: how to select all non-hydrogen atoms
- AMBER: ptraj: new mask parser
- AMBER: ptraj: projection command missing in dispatch.c (AMBER 10)
- AMBER: Pulling using restraintmask
- AMBER: Q: ntc = 3 parallel runnable not compiled in Amber 9?
- AMBER: QM/MM
- AMBER: QM/MM and unpaired spin
- AMBER: QM/MM Heating
- AMBER: QM/MM simulation
- AMBER: QM/MM: input conversion error
- AMBER: QMMM with printcharges
- AMBER: qmmm_DFTB problem
- AMBER: Querry
- AMBER: Querry about simulating a glycopeptide
- AMBER: Query
- AMBER: query about Generalized Born simulation
- AMBER: Query about the charge of atoms in the parmtop file
- AMBER: Query on MM-PBSA
- AMBER: Query on restart file
- AMBER: query regarding energy minimization
- AMBER: query regarding loadpadb
- AMBER: Query related to implicit solvent EXTDIEL
- AMBER: Question
- AMBER: question - gaff and leaprc.ff03ua
- AMBER: question about antechamber
- AMBER: question about dihedral angles
- AMBER: Question about loading frcmod.ionsjc_tip3p in xleap
- AMBER: question about pression
- AMBER: question about ptraj
- AMBER: Question about resp charges for a charged molecule...
- AMBER: question about simulation box
- AMBER: question about the charge
- AMBER: question about the improper torsion
- AMBER: Question for how to get all eigenvalues by "analyze matrix"
- AMBER: Question fot Amber 10 Benchmarks
- AMBER: Question on AMBER MD Implications
- AMBER: question on antechamber: jaguar ouput
- AMBER: Question on Urea box
- AMBER: Question: GAFF
- AMBER: Question: tweaking topology files to add SHAKE-constrained bonds
- AMBER: questions about gaff
- AMBER: Questions about Locally enhanced sampling (LES) and Replica exchange
- AMBER: questions about previous posts
- AMBER: questions about run MD at different pH
- AMBER: Questions on TIP4P model?
- AMBER: Radial Distribution Function
- AMBER: radial distribution function in ptraj
- AMBER: radius of calcium ion in MM_PBSA
- AMBER: Radius of Gyration
- AMBER: RDCs in AMBER 10
- AMBER: RDF in ptraj
- AMBER: RDF output file format
- AMBER: RDF: Segmentation fault
- AMBER: rdparm help
- AMBER: rdparm Segmentation fault
- AMBER: rdparm Segmentation fault on Ubuntu
- AMBER: re MD simulations of NMR structures: minimized average structure vs. ensemble member
- AMBER: Read trajectories generated by CHARMM
- AMBER: reading PDB trajectory
- AMBER: RED III execution problem
- AMBER: RED vIII-lack of charges in mol2
- AMBER: REDvIII_I_lack_of_charges_in_mol2
- AMBER: Reference for rmsd
- AMBER: Referencing AMBER
- AMBER: refine cyana structures!
- AMBER: Reg cysteine protonaitons states in pH constant MD
- AMBER: Reg cysteine protonation states
- AMBER: reg molecular dynamics
- AMBER: reg unstability of structure in md
- AMBER: reg-adding ions
- AMBER: reg-antichamber run
- AMBER: reg.building ions
- AMBER: reg.concentration of ions
- AMBER: reg.dnasaveparm&tcrd
- AMBER: regad-tutorial-dna-polyAT
- AMBER: regarding :scee
- AMBER: Regarding binding free energy calculation using MM_PBSA method
- AMBER: Regarding ff03 forcefield
- AMBER: Regarding force field ff02 and ion library
- AMBER: Regarding neutral Arginine unit
- AMBER: regarding rigid molecules
- AMBER: regarding segfault during energy minimization
- AMBER: Regarding SHAKE
- AMBER: Regarding sleap - documentation and output behavior
- AMBER: regarding:calculation of b factor using ptraj
- AMBER: Regarding:PME and neturalization
- AMBER: relative weight of RDC constraints
- AMBER: Release of version 1.2 of AmberTools
- AMBER: REMD Amber10 : error in reading namelist cntrl
- AMBER: REMD simulation error
- AMBER: REMD temperature profile
- AMBER: removing COM and rotation in explicit solvation
- AMBER: replica exchange : problem with sander
- AMBER: replica exchange with amber9
- AMBER: replicas trapped in a few low temperatures
- AMBER: reproducing http://amber.scripps.edu/tutorials/advanced/tutorial6/index.htm with explicit water
- AMBER: Res minimization
- AMBER: reset time and comments
- AMBER: residual dipolar couplings - alignment tensor energy
- AMBER: RESP
- AMBER: resp and 99999
- AMBER: RESP and Jaguar
- AMBER: RESP calculation on Copper containing molecule
- AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III
- AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems
- AMBER: RESP charges
- AMBER: RESP charges fitting for polarizable force fields
- AMBER: resp charges in parameterization
- AMBER: RESP charges of an unusual substrate
- AMBER: RESP GAUSSIAN AMBER
- AMBER: respgen -a charge groups function ineffective unless
- AMBER: Restart MD Simulation
- AMBER: restarting molecular dynamics
- AMBER: Restarting Problem in MD Simulation
- AMBER: Restraining with PMEMD 10
- AMBER: restraint box dimension
- AMBER: restraintmask - reference file is not working
- AMBER: Restraintmask and Restraint_WT : Question
- AMBER: Restraints
- AMBER: RESTRAINTS: no valid redirection found
- AMBER: Restricting the system to simulate
- AMBER: Ring flips
- AMBER: rms
- AMBER: RMS plot
- AMBER: RMSD calculation using AMBER7
- AMBER: RMSD of two different molecules
- AMBER: RMSD per residue
- AMBER: RMSD restraint in umbrella sampling
- AMBER: rmsd vs frame
- AMBER: running AMBER in NAMD Trucated Octahedron
- AMBER: Running Amber8 - Sander
- AMBER: Running md using glycam in AMBER
- AMBER: running minimisation on cis-azobenzene
- AMBER: running minimisation on cis-azobenzene----an electron-withdrew atom
- AMBER: Running patch "bugfix.at.all" with AmberTools 1.2
- AMBER: sander & imin=5
- AMBER: Sander *.top and *.crd file from PDB file
- AMBER: SANDER and PMEMD with openmpi
- AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd'
- AMBER: SANDER and PMEMD with openmpi. NO MORE failure 'make test.pmemd'
- AMBER: SANDER BOMB in subroutine nonbond_list
- AMBER: Sander crashes >99999 atoms
- AMBER: sander error on Make test.serial
- AMBER: Sander instead of PMEMD
- AMBER: SANDER Parallel
- AMBER: sander.MPI / openmpi on PBS
- AMBER: sander.MPI / parallel
- AMBER: sander.MPI setup with SGE
- AMBER: saveamberparm
- AMBER: saveamberparm error
- AMBER: saveAmberPrep in internal coordinates
- AMBER: Scale LJ parameters
- AMBER: SCC-DFTB for Zinc atom
- AMBER: scyld beowulf --amber10--openmpi
- AMBER: Seed for random number generator
- AMBER: seeking help regrading Zinc protein GBSA minimization
- AMBER: Segmentation fault
- AMBER: segmentation fault in SANDER
- AMBER: segmentation fault when restarting periodic structure
- AMBER: segmentation fault while generating the covariance matrix
- AMBER: Segmentation faults trying to run sander mpi
- AMBER: Select specific residues (leap)
- AMBER: self-diffusion coefficient and Berendsen
- AMBER: Set 251 is corrupted, ptraj error...
- AMBER: setBox command
- AMBER: setbox for solvateoct model
- AMBER: Setting GROUP for pmemd
- AMBER: setting periodic box
- AMBER: setting perioding box in AMBER
- AMBER: sgi4700 the time of MD simulation is 30 minute for 1ps about 2500 atom using 1cpu
- AMBER: shake the molecule
- AMBER: SHIFTS compile error
- AMBER: Short trajectory segments / frequent restarts causes explosion
- AMBER: Should the two phenyl rings of the trans-azobenzene on the same plane after minimisation?
- AMBER: Si parameters for MD (AMBER9)
- AMBER: SiCortex as an alternative to Ethernet and infiniband clusters
- AMBER: side chain expression
- AMBER: silhouette width/coefficient after clustering by PTRAJ9.9
- AMBER: silica slab
- AMBER: silica slab / FF
- AMBER: Silicon parameters
- AMBER: Simple Minimization - Error
- AMBER: simple sander
- AMBER: simulate dipole moment
- AMBER: simulated annealing
- AMBER: Simulating complexes with magnesium atoms
- AMBER: Simulating DNA Backbone in NAB
- AMBER: Simulating peptide linkers with AMBER
- AMBER: Simulating protein conformational changes?
- AMBER: simulating the pull out of Carbon Nanotube from polymer with AMBER
- AMBER: simulation with many formamide molecules
- AMBER: Single point energy calculations with explicit solvent.
- AMBER: single stranded DNA
- AMBER: size of pdb
- AMBER: SIZE.h problems
- AMBER: sleap - TER-card
- AMBER: sleap test failures
- AMBER: SMD pulling velocity
- AMBER: SMD RESTRAINTS
- AMBER: SMD using amber
- AMBER: SMD-related questions
- AMBER: solvate box : buffer list
- AMBER: solvate dna in TIP3PBOX 10.0
- AMBER: solvate with methanol
- AMBER: solvate without translating
- AMBER: solvatebox
- AMBER: solvatebox error
- AMBER: Solvatebox problem
- AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro
- AMBER: solvateBox/solvateDontClip
- AMBER: solvateOct produces strange residues compared to solvateCap
- AMBER: Solvent Accesible Surface Area (SASA) - Confused
- AMBER: solvent box again
- AMBER: solvent interaction in active site
- AMBER: Solvent mixture box
- AMBER: Some Problems With the Installation of Ambertools
- AMBER: something puzzled with mm_pbsa
- AMBER: Source FIles of SANDER
- AMBER: source of AMBER9
- AMBER: Sources of disruption during NVE
- AMBER: sp carbon notation?
- AMBER: SPARC benchmarks (was re Fujitsu PRIMEPOWER)
- AMBER: SPCFW problems
- AMBER: SPCFW temperature oscillations
- AMBER: standard residues
- AMBER: steered MD
- AMBER: Steered MD and Jarzynski in pulling simulations
- AMBER: steered MD initial state
- AMBER: stops writing trajectory
- AMBER: stripping water from a restart file
- AMBER: Structure comparison-NMR and X-ray structure using AMBER9
- AMBER: study of protein stability in different ion using AMBER
- AMBER: subroutine for torsional potential
- AMBER: subroutine Work : Jarynski work theorem
- AMBER: subscribe amber
- AMBER: suggestion for next amberTools 1.1
- AMBER: Support for intel mpi in pmemd 10; better support for intel MKL
- AMBER: Switching function in NAMD
- AMBER: syn and anti conformation
- AMBER: Systematic drift
- AMBER: tan luo radii
- AMBER: targeted MD
- AMBER: Temperature controlling method in AMBER
- AMBER: temperature error in md calculation
- AMBER: Temperature Range For REMD
- AMBER: Temperature regulation
- AMBER: temperature spikes
- AMBER: tempi in Replica Exchange
- AMBER: TERs
- AMBER: Test error in installing amber 10 using four threads on a single-cpu machine
- AMBER: Test failure with Amber 10
- AMBER: test of parallel sander 10 fail
- AMBER: test sander error in amber7
- AMBER: Test scripts
- AMBER: test.parallel.QMMM problem
- AMBER: The energy minimization of SIngle RNA chain
- AMBER: The forming of micelle
- AMBER: The forming of micelle (CMC)
- AMBER: the install problem
- AMBER: The list-directed or NAMELIST READ statement cannot be completed
- AMBER: the plot of the groove width versus time for RNA
- AMBER: the pmemd problem
- AMBER: the question about "RADIOPT" option in mm_pbsa
- AMBER: The size of the simulation box and the # of solute / water molecules?
- AMBER: the SPCFW water model
- AMBER: thermodynamic integration with Amber9
- AMBER: Thermodynamic integration with positional restraint?
- AMBER: TI calculations in Amber10
- AMBER: TI: perturbation method
- AMBER: time autocorrelation: ??
- AMBER: Timing analysis on Ranger
- AMBER: timing info output from pmemd
- AMBER: Tinker 4.3
- AMBER: tip3p water and shake
- AMBER: TIP5P water simulation with AMBER7
- AMBER: tleap and Zn parameter
- AMBER: tleap error message
- AMBER: to prepare pdb file fro unusual amino acid.
- AMBER: to understand GAFF: about A and B coefficients
- AMBER: to understand how frcmod.ff99SB works
- AMBER: to unsubscribe email
- AMBER: top and crd files without hydrogen
- AMBER: topology file
- AMBER: Topology file format for Amber9
- AMBER: Torsion angle restrains and Jarzinsky
- AMBER: Torsion potential in GAFF / "statistic value of parm94"
- AMBER: Torsional Forcing to generate PES?
- AMBER: Tough time with antechamber
- AMBER: Tough time with antechamber (UPDATE, still need help)
- AMBER: trajectories into trajectory
- AMBER: Trajectory - Average Structure - Equilibration
- AMBER: Trajectory file ended and unit 24 error on open inptraj
- AMBER: Trajectory in "Sietraj"
- AMBER: trajout input
- AMBER: Trans proline
- AMBER: Trans-azobenzene and cis-azobenzene
- AMBER: trans-azobenzene under minimisation
- AMBER: Trouble compiling Amber 9 leap programs on SGI Altix system
- AMBER: Trouble installing Amber 9
- AMBER: trouble interpreting <P2> time correlation function data
- AMBER: trying ff99SP
- AMBER: Tutorial 6
- AMBER: tutorial A1, file missing readit.f
- AMBER: Tutorial B3- Section6
- AMBER: Tutorial B5
- AMBER: tutorial_8_section_6
- AMBER: twin cut-off radii
- AMBER: Umbrella Sampling for proteins
- AMBER: umbrella sampling for proton transfer
- AMBER: unable to compile AmberTools 1.0
- AMBER: Unable to create the top & crd files for a protein+ligand pdb structure
- AMBER: unable to open pdb file
- AMBER: uninstall of AMBER
- AMBER: united atom force field
- AMBER: united atom force field: antechamber
- AMBER: Units of atomicfluct
- AMBER: Units, units units
- AMBER: unsubscribe
- AMBER: unsubscribe amber
- AMBER: updating documentation
- AMBER: using "EP" for dummy atom
- AMBER: Using AMBER forces
- AMBER: using amber ports in Gromacs
- AMBER: Using antechamber without AMBER program
- AMBER: Using charmm force field in amber
- AMBER: using hydrogen bond facility to monitor ion pair interaction
- AMBER: Using mdcrd files to look at minor charge changes
- AMBER: Using Na+ ions as input to leap?
- AMBER: Using Na+ ions as input to leap? - solved
- AMBER: using NAB to calculate entropy
- AMBER: using NAB to calculate entropy. .
- AMBER: using NAB to calculate normal modes
- AMBER: using NAB to calculate normal modes. .
- AMBER: using packmol file in Amber
- AMBER: using ptraj
- AMBER: Using RDCs for structure refinement
- AMBER: Using restart files
- AMBER: using Velocity-Verlet algorithm
- AMBER: Using VMD to calculate end-to-end distance?
- AMBER: Vaccum Simulations in PMEMD !!
- AMBER: value of Pi in Amber
- AMBER: Variable PBCAL values in MM-PBSA calculations
- AMBER: varying restraint_wt with nmropt=1
- AMBER: vdw 6-9 potential
- AMBER: velocity autocorrelation function for SPC felxible water model
- AMBER: velocity units?
- AMBER: velocity-verlet algorithm and ensembles
- AMBER: Versions of mopac
- AMBER: vertex atom mismatch
- AMBER: Visualizing Electrostatic Potential
- AMBER: Visualizing Periodc box
- AMBER: vlimit exceeded
- AMBER: Vlimit Exceeded and inhomogeneous system !!!!!!
- AMBER: vlimit exceeded error
- AMBER: VLIMIT units; TGTFITMASK
- AMBER: vlimit-problems after image and restart
- AMBER: VMD file generation 4 - mdcrd analysis
- AMBER: VMD file generation 4 - mdcrd ptraj analysis
- AMBER: VMD Movie
- AMBER: VMD Movie .mdcrd file ptraj
- AMBER: VMD Movie 2
- AMBER: VMD Movie 3
- AMBER: VMD Movie 4
- AMBER: Volume of ucell too big
- AMBER: WARNING in readAmberTrajectory(): fsetpos() failed on when looking for box coordinates!
- AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-)
- AMBER: water in the binding site MMPBSA
- AMBER: Water residue tracking
- AMBER: Water Topology
- AMBER: Water tracking
- AMBER: watershell cero?
- AMBER: Weighting factors in RESP charge fitting
- AMBER: WHAM: how frequently do I need data on the system coordinates?
- AMBER: What's making my system lose total energy?
- AMBER: Where is ICO read from the ix array?
- AMBER: Which CO2 potential?
- AMBER: Which install compiler and flags?
- AMBER: Which is best temperature controlling method
- AMBER: who can give a sample input file regarding the energy decomposition with sander?
- AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ?
- AMBER: Whole System Equilibration & Pressure
- AMBER: Why LEap created a new H atom for CYM while generating TOPOLOGY file?
- AMBER: working with unformatted restart files in AMBER9
- AMBER: wrapping a restart file
- AMBER: wrapping w/ ptraj
- AMBER: writing a script in amber
- AMBER: writing out a distance between two atoms in sander
- AMBER: Writing pressure in md.out file in NVT simulation
- AMBER: XLEaP
- AMBER: xleap (draw using edit)
- AMBER: xleap (measureGeom)
- AMBER: xleap and Sirius on ubuntu 8.04
- AMBER: xLeap compilation issues
- AMBER: xleap error
- AMBER: xleap fails to savemol2
- AMBER: XLeap Problems
- AMBER: xleap screen output
- AMBER: xleap screen output SOLVED
- AMBER: xleap segmentation fault on SaveAmberParm
- AMBER: xLeap unit editor "seg fault"
- AMBER: XLF problem in compiling AMBER8 on IBM PPC64 SUSE
- AMBER: xmgr graphics display program
- AMBER: XMGRACE on Linux 64 Bit
- AMBER: Your "bellymask-patch"
- AMBER: Zn2+ Bondi radius value
- AMBER:Some questions about replica exchan ge
- AMBER:VMD Movie.mdcrd
- AW: AMBER: MM-PBSA
- AW: AMBER: tleap and Zn parameter
- bad atom type f(fluorine) in MM-PBSA
- bugfix 11 & 12
- Dell 2 Quad Core System Performance
- entropy of released water
- Force field parameter file for CNT
- Force Field Parameterizing
- FreeBSD "port" for AmberTools-1.2
- Fwd: AMBER: (no subject)
- Fwd: AMBER: lastrst problem
- Fwd: AMBER: LEaP problem with LEU first residue?
- Fwd: AMBER: Negative ligand (Peroxide)
- Fwd: AMBER: prepare an initial structure in Amber
- Fwd: AMBER: RESTRAINTS: no valid redirection found
- Fwd: AMBER: Restricting the system to simulate
- MD run time inquiry
- Personal favor
- Poly(A)-Poly(T) DNA Tutorial Query
- Problem with the NEB tutorial
- problems about TMD in your tutorial
- QUERRY?
- reaction coordinate in umbrella sampling
- reference paper - pls help
- Request
- rmsd vs frame
- solvating RNA in 8M urea box
- SV: AMBER: Correlation functions from iRED analysis
- SV: AMBER: ptraj, hbond and non-bonded contacts
- SV: SV: AMBER: Correlation functions from iRED analysis
- SV: SV: AMBER: ptraj, hbond and non-bonded contacts
- Systematic drift
- timestep problem
Last message date: Wed Dec 31 2008 - 22:47:27 CST
Archived on: Thu Jan 08 2009 - 16:01:46 CST
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