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AMBER Archive (2007) - By Subject
4765 messages sorted by: [ author ] [ date ] [ thread ]About this archive
Starting: Mon Jan 01 2007 - 04:25:56 CST
Ending: Mon Dec 31 2007 - 15:27:41 CST
- A little question
- a request
- about ANTECHAMBER
- about deoxy- and oxy- heme
- amber mm-pbsa problem
- Amber query !!
- amber-developers: -y option in sander
- Amber9 compile problem
- AMBER9 Installation Help
- AMBER:
- AMBER: "Atom valence violated" from LEaP
- AMBER: "distance" command in ptraj
- AMBER: "FATAL: Atom xxx does not have a type."
- AMBER: $AMBERHOME on PATH
- AMBER: $AMBERHOME on PATH & compilations
- AMBER: $AMBERHOME on PATH)
- AMBER: $tleap is not normal
- AMBER: &dipole input and some questions on using polarizable force fields
- AMBER: &dipoles output in QM/MM simulations
- AMBER: &shf setup
- AMBER: (no subject)
- AMBER: ** No torsion terms for SNI-NI-SNI-CT
- AMBER: .lib files
- AMBER: .prmtop entries
- AMBER: 2 double bond in AMBER ffield
- AMBER: 22 improper torsions in old prep form
- AMBER: 31 integers in the first section of a prmtop file
- AMBER: 5 Ligands and 1 Protein
- AMBER: 64-bit pgf90 revisited
- AMBER: ????pig5678??????
- AMBER: [AMBER] QM/MM-DFTB
- AMBER: [chirality.c] Atom did not match
- AMBER: [Fwd: Tr: H bonds]
- AMBER: [rsachdeva@imtech.res.in: A query]
- AMBER: [rsachdeva@imtech.res.in: Pls help - REMD with torsional restraints]
- AMBER: [SOLVED] Problem with LEaP generating topology and coord files after double bond creation
- AMBER: a problem of surface area calulated by MM/PBSA
- AMBER: a question about analysis of DNA duplex after MD simulation with curves
- AMBER: A question about biomineral simulation, help!!
- AMBER: a question about xleap
- AMBER: a question of ptraj
- AMBER: A question related with periodic boundary condition
- AMBER: A test email
- AMBER: ab initio modeling using Amber
- AMBER: abnormal high temperature during NPT ensembles MD
- AMBER: abnormal termination of tleap
- AMBER: Abnormality in MM-PBSA result
- AMBER: About amber7
- AMBER: about coordinates ****** and diffusion
- AMBER: about define improper torsion in .frcmod file
- AMBER: about MD outputs
- AMBER: about parallelization in QM-MM
- AMBER: About protein-ligand binding
- AMBER: About RAMD
- AMBER: about restraining atoms
- AMBER: about shake
- AMBER: About TER records
- AMBER: About the problem of the PMEMD and cutoff
- AMBER: about wrap the trajectory
- AMBER: Add hydrogen and charge calculation
- AMBER: Addendum: Heat capacity calculations not coming out right
- AMBER: adding extra points to amber - how to?
- AMBER: adding organic molecule to polypeptide residue
- AMBER: adding polar hydrogens
- AMBER: adding water molecules in lipid bilayer model
- AMBER: addions
- AMBER: ADDIONS do not neutralize to ZERO
- AMBER: addles
- AMBER: addles segmentation fault
- AMBER: AIX 5 test failures: -NaNQ
- AMBER: Algorithm for integration of equations of motion
- AMBER: AM1-bcc
- AMBER: Amber 8 support of CHARMM ff?
- AMBER: Amber 8.0 : how to represent EPS with VMD?
- AMBER: AMBER 8: QMMM - molecule fluctuates wildly
- AMBER: amber 9
- AMBER: Amber 9 - bugfix.40 fails
- AMBER: AMBER 9 - Force Field Options - Question
- AMBER: amber 9 - output of forces
- AMBER: AMBER 9 - visualization of MD trajectory by MOE
- AMBER: Amber 9 compile on OS X
- AMBER: Amber 9 install on Debian Linux amd64
- AMBER: amber 9 install: patch reject
- AMBER: amber 9 installation: broken pipe
- AMBER: Amber 9 make parallel fails with mpich
- AMBER: amber 9 sander crashed with "forrtl: severe (174): SIGSEGV, segmentation fault occurred"
- AMBER: Amber 9 source code permissions (UNCLASSIFIED)
- AMBER: Amber 9 TI Details
- AMBER: Amber 9, sander imin = 5, -y flag
- AMBER: amber 9: fortran/test failures
- AMBER: Amber 9: Generating Input files for EVB simulations of the crosslinked structures (Hydrogels)
- AMBER: AMBER at WESTGRID
- AMBER: AMBER citation questions
- AMBER: AMBER complile problem
- AMBER: amber equation of ff99
- AMBER: AMBER ff in CHARMM format!!
- AMBER: Amber FF parameters for the Zinc-hydroxammate interaction
- AMBER: AMBER hydrophobic Box : script
- AMBER: Amber Installation Error
- AMBER: amber md movie using Chimera
- AMBER: amber md movie using Chimera. .
- AMBER: AMBER MINIMIZATION
- AMBER: amber on AMD opteron-250
- AMBER: amber parallel compile error with g95
- AMBER: AMBER parametrization (??) for OAA and Mg++
- AMBER: AMBER question: Combining Gaff and ff99 forcefields for a single molecule
- AMBER: AMBER sander
- AMBER: amber with periodic condition
- AMBER: Amber/ANAL and psf files
- AMBER: amber7 and xleap
- AMBER: AMBER7 Si atom type
- AMBER: AMBER8 compiler with intel 9.1 compiler
- AMBER: Amber9 analyze timecorr manual ambigous
- AMBER: amber9 compile problem
- AMBER: amber9 installation error
- AMBER: AMBER9 installation error on dual core AMD Opteron(tm) processor 275
- AMBER: Amber9 installation error on Mandriva 2007 linux
- AMBER: amber9 installation problem
- AMBER: amber9 leap installation error on sgi_altix
- AMBER: Amber9 parallel compilation openmpi issues
- AMBER: amber9 parallel compile problem
- AMBER: Amber9 parallel installation error (retry)
- AMBER: Amber9 parallel installation error (with openMPI)
- AMBER: amber9 parralel compiling
- AMBER: amber9 possible failure tgtmd
- AMBER: Amber9 Sander Error
- AMBER: Amber9's sander.MPI on x86_64
- AMBER: amber9/mmtsb
- AMBER: amber94 parameters for cholesterol
- AMBER: amber9: running parallel error
- AMBER: Amber: Number density profile, pucker..reg
- AMBER: Amber:PBSA&Extract_coords problem (Needed help)
- AMBER: ambpdb gives empty cpin
- AMBER: An enquiry about "Dynamics of ligand escape from the heme pocket of myoglobin (JACS, 1988, 110, 7690
- AMBER: anal
- AMBER: anal calculation error
- AMBER: anal calculatons
- AMBER: anal error
- AMBER: anal problem
- AMBER: angle between vectors
- AMBER: angle command in Ptraj
- AMBER: ANGVE/TORAVE
- AMBER: anneal algorthm
- AMBER: another sander bug?
- AMBER: Antechamber
- AMBER: antechamber --> sander problem
- AMBER: Antechamber Charge Calculation Method
- AMBER: antechamber error
- AMBER: Antechamber esp calculation
- AMBER: antechamber fails with large molecules
- AMBER: antechamber for topology file
- AMBER: Antechamber formal charges with Gasteiger method
- AMBER: antechamber problem
- AMBER: antechamber question
- AMBER: antechamber save prmtop inpcrd
- AMBER: Antechamber Warning
- AMBER: antechamber, how does it work
- AMBER: Antechamber--Boron Parameters
- AMBER: antechamber/charges/conformation
- AMBER: antechamber: mopac charges
- AMBER: antechamber: read in charges
- AMBER: Any experience on Dell two quad core system?
- AMBER: any general approach to create SiO2 wall
- AMBER: Applying bugfixes in Amber
- AMBER: applying restraints
- AMBER: articles
- AMBER: assign atom hybrid
- AMBER: assigning charges to a prepi file
- AMBER: assigning of head atom as null.
- AMBER: Atom type definition
- AMBER: Atom types
- AMBER: Atom types for polyunsaturated lipids
- AMBER: Atomic positional Fluctuations
- AMBER: atomicfluct
- AMBER: Atoms closer to 2 angstroms to each other
- AMBER: Atoms in conatct to a specific atoms during MD
- AMBER: Atoms in contact to a specific atoms during MD
- AMBER: Attaching capping groups
- AMBER: Average absolute value of cross velocity (Rate constant from PMF)
- AMBER: Average PDB - Unusual Bonds
- AMBER: Average potential energies and conformer ratios
- AMBER: Average structure
- AMBER: B or E Dihedral Labels in RDPARM output
- AMBER: Backbone atoms
- AMBER: Backbone flexibility/entropy
- AMBER: Backbone stability problems with parm94, glycam04 and AMBER 8
- AMBER: bad atom type errors in GB for halides?
- AMBER: bad atom type:F
- AMBER: Bad residue/molecule data in prmtop
- AMBER: Basic AMBER question
- AMBER: basis set for RESP calculation
- AMBER: BELLY
- AMBER: BELLY issues
- AMBER: Belly Restraints and Distance Restraints
- AMBER: benchmarking pmemd and sander (pmemd segmentation fault problem follow up)
- AMBER: Beowulf cluster from PSSC Labs
- AMBER: Best Force field for protein, DNA, and organic compounds?
- AMBER: Best way to apply WC basepair restraints during MD
- AMBER: Binary file curiosities
- AMBER: binary restart file
- AMBER: binding energy_decomposition per residue
- AMBER: Binding free energy calculation - MM-pbsa
- AMBER: Binding free energy errors: Grid setting fail
- AMBER: Blue Gene, compile Amber9?
- AMBER: BOMB!
- AMBER: bondi radii problems
- AMBER: bound magnesium ions in proteins with GBSA
- AMBER: Box dimensions
- AMBER: Box problems in vacuum minimization with sander.serial 8
- AMBER: box size bomb in QMMM calculation
- AMBER: bug in nonbond_list.f (nee ew_setup.f)
- AMBER: Bug in ptraj mask processing?
- AMBER: bug in reprocessing with PB?
- AMBER: Bug report: a bug of xleap associated with NumLock
- AMBER: Bug report: iwrap failure in PMEMD with netCDF
- AMBER: BUG? Does TLEAP understand SPC/E water?
- AMBER: bugfix for impropers in parmchk
- AMBER: bugfix.all
- AMBER: Building parallel Amber 9.0
- AMBER: building water box with desired number of molecules
- AMBER: Bulk water simulation with centre of mass position restrain
- AMBER: Ca(2+) parameter
- AMBER: Calcium and peptides
- AMBER: calcium and zinc parameter
- AMBER: calcium ion force-fields
- AMBER: calcium parameter for GB
- AMBER: calcium parameters
- AMBER: Calculate force constants
- AMBER: calculate RMSD of only chain C
- AMBER: calculating charges to modified 4GA unit
- AMBER: Calculating cumulative average
- AMBER: Calculating dipole moments
- AMBER: calculating distance between two atoms
- AMBER: Calculating RMS for each residue?
- AMBER: calculation of angle between helices
- AMBER: Can a simulation run on AMBER 9 be compared with another from AMBER 8?
- AMBER: Can I measure improper torsion by ptarj?
- AMBER: Can I set harmonic constraints in SMD simulations ?
- AMBER: can open PDB file in xleap
- AMBER: Can t open PDB file in xleap
- AMBER: Can't open PDB file in xleap
- AMBER: Can't run decompose energy in MM-PBSA
- AMBER: Can't run Normal Mode Analysis !!!
- AMBER: carbohydrate-peptide
- AMBER: Charge not integral. Head-to-tail cyclic peptides
- AMBER: Charges in antechamber
- AMBER: charges in PBSA calculation
- AMBER: Charges in TI calculations and leap
- AMBER: CHARMM vs. AMBER ff literature
- AMBER: chem shift format
- AMBER: Chemical shift: simulation vs. experiment
- AMBER: chiral surfaces
- AMBER: choice of alpha carbons vs side chains
- AMBER: Citation for Langevin thermostat?
- AMBER: closest water molecules with 8 angstroms
- AMBER: Combining RESP with AM1-BCC
- AMBER: command line alternatives for teLeap
- AMBER: command tleap is not normal
- AMBER: Comparing explicit solvent/vacuum qmmm
- AMBER: Comparison of normal modes with ptraj?
- AMBER: compilation error in SGI Altix 4700 with Intel Fortran 10.1.008 and IMKL 10.0.1.014
- AMBER: compilation error in SGI Altix 4700 with Intel Fortran10.1.008 and IMKL 10.0.1.014
- AMBER: compile amber8 with mpich2
- AMBER: Compile Amber9 for MVAPICH
- AMBER: Compile openmpi
- AMBER: Compiling Amber 7
- AMBER: Compiling AMBER 8 on RHEL4 AMD64
- AMBER: Compiling Amber 8 on SuSE 10.2
- AMBER: compiling AMBER9 on Mac OS X Tiger (Intel)
- AMBER: Compiling openmpi/icc/icpc
- AMBER: Compiling parallel Amber9 on Linux cluster
- AMBER: Compiling single programs
- AMBER: Complexe Energy Analysis
- AMBER: Complexes
- AMBER: computational Ala scan
- AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2-
- AMBER: configure question
- AMBER: Confusion about Langevin dymamics
- AMBER: connect atom
- AMBER: connecting a non standard residue to the rest of an enzyme
- AMBER: Connecting two ethanes in LEaP
- AMBER: constant pH
- AMBER: constant pH with 25 titrable sites
- AMBER: Constant volume simulations
- AMBER: constant-pH MD with replica exchange
- AMBER: constraint pdb file
- AMBER: Constraint virial
- AMBER: contacts in ptraj (Amber 9)
- AMBER: Continuing an amber 8 simulation with amber 9
- AMBER: Convergence criteria in replica exchange simulations
- AMBER: convergence criterion not reached
- AMBER: convergence in classical MD
- AMBER: conversion of Macromodel substructure format to .frcmod file
- AMBER: convert pdb files to restart files
- AMBER: Converting AMBER-format force fields for tinker
- AMBER: coordinate changes using ptraj
- AMBER: coordinates ******
- AMBER: Copper and Chlorine parameters
- AMBER: corrected reaction field energy and PBCAL
- AMBER: correlation between PBTOT and GBTOT values in a MD trajectory
- AMBER: correlation time
- AMBER: Could not find cntrl namelist
- AMBER: Covert NOEs form Xplor to Amber
- AMBER: crd to pdb conversion
- AMBER: creating topology files for RNA DNA hybrid.molecule
- AMBER: CRESP charges in antechamber prepin
- AMBER: crg file
- AMBER: Criteria for classical md being OK to move to QM-MM
- AMBER: Cut off for cavities
- AMBER: cutoff & speed-up of GBSA
- AMBER: Cutoff list exceeds largest sphere in unit cell
- AMBER: cyclohexane and decalin on amber
- AMBER: Cygwin error
- AMBER: CYX residue missing from Amber 9 ff03ua (?)
- AMBER: decomposition energy
- AMBER: Deep energetics problem
- AMBER: deeper problem with the energetics
- AMBER: Defining BOX INFO during TLEAP
- AMBER: deformation of DNA duplex after MD simulation (AMBER9)
- AMBER: DelPhi
- AMBER: denaturing salt conditions
- AMBER: Density of a system in MD
- AMBER: Deriving constraint forces on water molecules based on SETTLE moves
- AMBER: DFTB email address
- AMBER: DHAS_10_12 compilation aborted for egb.f
- AMBER: dielectric constant in GB/SA
- AMBER: Difference in Equilibration & Production MD in Amber
- AMBER: dihedral angle by Ptraj
- AMBER: dihedral angles
- AMBER: dihedral angles restraint for DNA
- AMBER: dihedral driver
- AMBER: Dihedral FF parameters
- AMBER: dihedral parameters
- AMBER: dihedral simulation
- AMBER: dihedrals
- AMBER: Dihedrals in Sander
- AMBER: Dipolar and Inertia Moments
- AMBER: DISAVE value1
- AMBER: distance calculation!
- AMBER: Distance restraint to centre of mass
- AMBER: Distance Restraints
- AMBER: Distance restraints between center of mass of two molecules
- AMBER: Distance Restraints Problem
- AMBER: distance scan
- AMBER: distance.restraint for two groups of atoms (center of mass)
- AMBER: distcovar in ptraj
- AMBER: Disulfide Bonds
- AMBER: Disulfide Problem
- AMBER: divcon
- AMBER: DivCon calculation in Amber9
- AMBER: divcon missing in Antechamber 1.27
- AMBER: divcon on AIX using xlf 10.1
- AMBER: DNA and RNA computations
- AMBER: DNA base planarity restraint
- AMBER: DNA denatures during MD simulation
- AMBER: DNA Flat Angle Restraints
- AMBER: dna forcefield: PARMBSC0
- AMBER: DNA Helicoïdal Plots over time
- AMBER: DNA on Si surface
- AMBER: DNA RNA recognition problem
- AMBER: DNA structure analysis
- AMBER: docking ability
- AMBER: Docking with AMber
- AMBER: Does amber use water density around 1 at room temperature
- AMBER: Does Chimera support AMBER file formats?
- AMBER: Does Sander.MPI support coupling effect between different molecules at the same area at the same temperature in the mixture?
- AMBER: Drug bound to the protein
- AMBER: Drug Leads interaction with ds and Triplex DNA
- AMBER: DUMBFREQ
- AMBER: During the Sander process, does the pH of the solution change orr not
- AMBER: edit.out amber version 9
- AMBER: effective step period for constant pH simulations
- AMBER: ele vs van der Waals
- AMBER: electric field calculation
- AMBER: electron density difference
- AMBER: Electron density profile
- AMBER: Electrostatic Energy in MD Simulation (GB)
- AMBER: Employing SCC-DFTB with a periodic boundary condtion
- AMBER: energy calculation
- AMBER: Energy calculation by Anal
- AMBER: Energy calculations.
- AMBER: energy minimization parameter
- AMBER: Energy minimization problem
- AMBER: Energy minimization problem of -SO3H group
- AMBER: Energy outputs in TI Approach
- AMBER: Energy Spread using GB & Langevin Dynamics (NAB)
- AMBER: Entropy in MM_PBSA
- AMBER: entropy units
- AMBER: entropy with ptraj
- AMBER: environment variables
- AMBER: enzyme kinetics in silico
- AMBER: equilibration
- AMBER: equilibration in explicit solvent
- AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated
- AMBER: equilibration with amber5, production of MD with amber7
- AMBER: equilibrium constants via MMPBSA
- AMBER: Error - must define AMBERHOME environment variable
- AMBER: Error at Equilibration....
- AMBER: error due to exceeding left-hand side digital numbers in restart output
- AMBER: Error during compilation on a SGI Irix machine
- AMBER: Error in installing amber8 on Ubuntu
- AMBER: Error in MMPBSA Calculation
- AMBER: error in modified PNA -DNA simulation..
- AMBER: error in modified PNA DNA simulation
- AMBER: Error in protonating
- AMBER: Error in reading number of frame in PTRAJ
- AMBER: Error in running replica exchange MD
- AMBER: Error in running Replica Exchange MD with amber9
- AMBER: error in running sander
- AMBER: Error on compile amber8
- AMBER: Error on compiling AMBER8
- AMBER: Error reading radii of Cu during ESP caculation.
- AMBER: error when compiling Moilview
- AMBER: Error when doing a TI simulation: "vlimit exceeded
- AMBER: error when using sander.LES: exceeded MAXLES
- AMBER: error while Running TMD
- AMBER: error with amber9 production run.
- AMBER: Error- MM_PBSA calculation
- AMBER: Error: "Suspended (tty input)" & "Unit 6 Error on OPEN: md.out"
- AMBER: Errors in amber9 parallel installation
- AMBER: errors in SHIFTS execution
- AMBER: Essential ions and water molecules in MMPBSA computations
- AMBER: evaluate expression
- AMBER: EVB Calculations
- AMBER: Ewald BOMB....... what is this..
- AMBER: Example needed for addAtomType command
- AMBER: EXCEEDED MAXLESADJ in sander.LES.MPI (amber9)
- AMBER: experimental phi-values as restraints
- AMBER: explanation to edit and use the script
- AMBER: explicit implicit solvent
- AMBER: Explicit water in implicit enviornment?
- AMBER: Explicit water opinion
- AMBER: Extra Points... How to Deal with Them
- AMBER: Extra points... virial computation
- AMBER: Extra-term to the Energy function !!
- AMBER: EXTRA_PTS: frtype 2 Should not be here
- AMBER: extract protein energy from MD trajectory
- AMBER: extracting coordinate from crd file
- AMBER: extracting coordinates from crd file
- AMBER: Extracting Coords&MMPBSA&ambpdb
- AMBER: extracting starting structures from equilibration trajectory
- AMBER: Fails to load libraries present in /leap/lib/
- AMBER: Failure to recompile antechamber
- AMBER: Failure to SCF convergence
- AMBER: Failure to SCF convergence & parallelization and memory
- AMBER: Fatal error: Command failed for target `test.sander.no_lmod'
- AMBER: FATAL: Atom .R<CYF 17>.A<N 1> does not have a type.
- AMBER: Fe bonds in HEME !
- AMBER: ff02 + POL3 - polar interactions !!
- AMBER: FF02: sander problem with irstdip=1
- AMBER: ff99 vs ff99SB for RNA
- AMBER: ff99SB and the N- and C- charged terminal residues
- AMBER: Finding x-displacement
- AMBER: five-coordinated phosphorus
- AMBER: FLAG LENNARD_JONES_ACOEF NAN
- AMBER: fluctuations
- AMBER: follow-up
- AMBER: for makeDIST_RST
- AMBER: for NMR restrains files
- AMBER: force field for hydrogels
- AMBER: force field for irregulate DNA ends
- AMBER: Force field for RNA with U-turn motif
- AMBER: Force Field Parameters
- AMBER: force field question
- AMBER: force fields
- AMBER: Force fields for iron
- AMBER: format of .xyz files and pdb
- AMBER: FORTRAN code for calculating ENERGY of all the four terms (bonds, angles, dihedrals, nonbanded pairs) of Amber8's sander
- AMBER: fragment parametrization tutorial?
- AMBER: frcmod
- AMBER: frcmod file
- AMBER: frcmod file and NONB for dummy atoms
- AMBER: Free Energy Calculations
- AMBER: Free energy for part of the system
- AMBER: Fwd: [chirality.c] Atom did not match
- AMBER: Fwd: a request
- AMBER: Fwd: About TER records
- AMBER: Fwd: Amber9 parallel compilation openmpi issues
- AMBER: Fwd: antechamber save prmtop inpcrd
- AMBER: Fwd: Comparing explicit solvent/vacuum qmmm
- AMBER: Fwd: help me out...
- AMBER: Fwd: problem regarding water handling in explicit simu
- AMBER: Fwd: ptraj with protein-ligand
- AMBER: Fwd: QM region + cutoff larger that box
- AMBER: Fwd: SCC convergence failure in QM-MM DFTB
- AMBER: Fwd: Schedule for QM-MM with Amber9/Amber10
- AMBER: Fwd: Serial "make" failure with xleap
- AMBER: Fwd: System extending beyond of (non existent) virtual box
- AMBER: Fwd: unable to save prmtop/inpcrd for chcl3box
- AMBER: g(r)
- AMBER: g(r) in mixtures?
- AMBER: G5 OSX serial compile error
- AMBER: GAFF atom typing for flavin
- AMBER: Gaff Charge
- AMBER: Gas-phase energies (and more)
- AMBER: gaussian output to prepin problem
- AMBER: GB Energy Spreads for MD Structures
- AMBER: gb minimization using nab
- AMBER: GB vs. Invacuo Energies
- AMBER: GBSA or PBSA: GPB or GGB are +ve or -ve?
- AMBER: GBSA: NMODE ERROR
- AMBER: GDP UNKNOWN ATOM TYPE: O3 warning
- AMBER: General AMBER questions
- AMBER: generating a .rst file from an .mdcrd file
- AMBER: Generating structure of polyethylene glycol in AMBER
- AMBER: generating topology files for PBSA
- AMBER: Generation of ESP(ind) within atomic charges derivation for polarizable force field
- AMBER: Getting prmtop and inpcrd
- AMBER: getting same box dimension
- AMBER: gibbs problems
- AMBER: Glycam
- AMBER: grid output: bulk water density
- AMBER: Group declaration question
- AMBER: Group input for restrained atoms
- AMBER: H bond
- AMBER: H-acceptors problem in ptraj
- AMBER: H-Bond
- AMBER: H-bond in each fram
- AMBER: H-bond in ptraj
- AMBER: H-bond ptraj dilemma
- AMBER: Hardware recommendations please
- AMBER: Harmonic constraints
- AMBER: hbond analysis output
- AMBER: hbond ptraj
- AMBER: hbond ptraj pls help.
- AMBER: Hbonds
- AMBER: Heat capacity calculations not coming out right
- AMBER: Heat capacity, diffusivity way off in this simulation of SPC/E water?
- AMBER: Heat of Vaporization
- AMBER: Heating the system prior to production run
- AMBER: heating up system
- AMBER: heical content in simulations
- AMBER: Hello
- AMBER: help in QM/MM simulation
- AMBER: help me out...
- AMBER: Help WARNING: The unperturbed charge of the unit
- AMBER: help with phosphotyrosine
- AMBER: Help!! I cannot perform the ambpdb
- AMBER: Help: 1 ns for implicit solvent (GB) calculations, enough?
- AMBER: HELP: Are there anybody have used AMBER to simulate glucose chain?
- AMBER: Heme and CYS !!
- AMBER: heme force field
- AMBER: heme force-field (2)
- AMBER: heme forcefield atom types
- AMBER: hey
- AMBER: HF/6-31G* ESP Charges do not match with ff02 charges
- AMBER: HG atoms in CYX residues
- AMBER: hi
- AMBER: hi..
- AMBER: high energy with mm_gbsa igb=5
- AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa
- AMBER: hii
- AMBER: Holding NA Base syn during annealing
- AMBER: How are water molecules at cutoff being treated?
- AMBER: How can i calculate generalized order parameters using ptraj.
- AMBER: How can I modify the frcmod file of ligand with a nonstandard guanidine
- AMBER: How do I make and enter new ff parameters into AMBER
- AMBER: how is the standard deviations calculated in mm-pbsa?
- AMBER: How many steps should be used for a MD calculation?
- AMBER: how much restraint ?
- AMBER: How precise is a MD simulation?
- AMBER: How precise is a MD simulation? Which strcutures should be reported?
- AMBER: How to add semi-experience parameter in divcon?
- AMBER: How to apply psuedo-bonds for restraints
- AMBER: How to build organic compound in Amber
- AMBER: how to calculate energy of the peptide
- AMBER: HOW TO CALCULATE FREE ENERGY OF A DNA DUPLEX USING MMPBSA
- AMBER: How to calculate S2 from P2 using ptraj ?
- AMBER: how to calculate the ps/day of md simulation using using my cluster system in amber7
- AMBER: How to calculate the time-dependent transmission coefficient for rate constant esimation from PMF ca
- AMBER: How to carry out drug-dna complex simulations
- AMBER: How to change the force field equation in amber by programming...
- AMBER: how to combine two molecules
- AMBER: How to couple only one residue to the temperature bath?
- AMBER: how to create an O linked N-acetylglucosamine in a protein
- AMBER: How to decide extra-helical or intra-helical bulge conformation by PTRAJ ?
- AMBER: How to delete particular frame from mdcrd file (not with ptraj).
- AMBER: How to delete particular frame from mdcrd file (not with ptraj).]
- AMBER: How to do minimization..
- AMBER: How to extract energy of molecule from the system with explicit water molecules
- AMBER: How to fix the distance between two atoms.
- AMBER: How to fix two angle but do umberlla sampling for distance?
- AMBER: How to get a periodic box of modified water molecules
- AMBER: How to get sane package
- AMBER: how to include mpirun in this script
- AMBER: how to incorporate ismem =1 into mm_pbsa
- AMBER: How to intergrate the area under a curve.
- AMBER: how to modify map.DG-AMBER file?
- AMBER: How to modify the velocity of a water molecule?
- AMBER: How to parameterize frcmod for NA
- AMBER: How to perform MD simulation in NVT ensemble?
- AMBER: How to place torsion restraint
- AMBER: How to reimage the trajectories of LES calculations?
- AMBER: how to simulate a ligand bound to a residue
- AMBER: how to solvate the protein with different solvents
- AMBER: how to stop ptraj atom renumbering
- AMBER: How to use AMBER Parameter Database ?
- AMBER: How to use antechamber properly?
- AMBER: How to use loadpdbusingseq command to load branched structure?
- AMBER: hybrid remd
- AMBER: hybridization in Amber, pertaining to resonant structures, ions
- AMBER: Hydration points
- AMBER: hydrogen bond
- AMBER: Hydrogen in a phosphate ion
- AMBER: I need some constant pressure MD help
- AMBER: I need some help in PTRAJ
- AMBER: I'm sorry ... please ignore the junk !!
- AMBER: IFVARI parameter
- AMBER: Ignore my reply to Amber protonate!
- AMBER: image command
- AMBER: imin=5 and inptraj
- AMBER: implementation of GB model in AMBER
- AMBER: implicit minimization
- AMBER: implicit solvent free energy calcs
- AMBER: Implicit solvent simulation is too slow.
- AMBER: implicit solvent simulations
- AMBER: implicit solvent simulations with calcium ion
- AMBER: Implicit/Explicit solvation
- AMBER: Improper angle by Antechamber
- AMBER: improper dihedral
- AMBER: Improper torsion terms
- AMBER: improper torsions
- AMBER: Improving pmemd parallel scaling
- AMBER: Including crystal water when using united-atom forcefield leaprc.ff03ua
- AMBER: Including Relevant Subject Lines
- AMBER: incoherent intermediate scattering function
- AMBER: inconsistency between PBSA and GBSA
- AMBER: inconsistency between PBSA and GBSA - help
- AMBER: Information about Amber 9
- AMBER: Input files for the Potential of mean force.
- AMBER: Input required for RESP
- AMBER: installation
- AMBER: Installation help - SGI Altix 350
- AMBER: installation of amber9 on suse linux 10.3
- AMBER: Installation Question
- AMBER: installing amber 8 on 5 nodes cluster PC
- AMBER: Installing AMBER v9 in Linux
- AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine
- AMBER: Installing amber9 in IBM P5?
- AMBER: installing LMOD error
- AMBER: Installing on windows
- AMBER: Integrating the alpha-helix bias correction into ff94
- AMBER: Intel Fortran Compiler 9.1, MPICH, and AMBER 8
- AMBER: interaction energy calculations
- AMBER: Interactive Molecular Dynamics with Amber?
- AMBER: interior dielectric constant
- AMBER: Internal dielectric and MMPBSA
- AMBER: intra-molecular h-bonds in ptraj
- AMBER: invalid digit '*' in the input file
- AMBER: Ionic strength in pbsa
- AMBER: iRED and corrired
- AMBER: is possible to compile pmemd using scali MPI?
- AMBER: Is the simulation reasonable ? (SMD : dissocation antibody-antigen)
- AMBER: Is there a pmemd machine file for OSX Intel
- AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj
- AMBER: Is this system too large?
- AMBER: isolated NTP
- AMBER: issues with restrt file
- AMBER: junk in `Noshake mask` output section
- AMBER: Keq computations
- AMBER: Known residue, unknown error in teLeap
- AMBER: Langevin dynamics in NAB
- AMBER: large RMS fluctuations in turning off VDW interactions by TI
- AMBER: Leap adding 3 extra atoms
- AMBER: Leap adding extra atoms
- AMBER: LEaP bond problem
- AMBER: LEaP crashes
- AMBER: leap problem
- AMBER: leap restrainTorsion
- AMBER: LeaP: Mol2 files
- AMBER: leaprc.ff02polEP.r1into xleap
- AMBER: LES
- AMBER: Les analyse
- AMBER: LES problem
- AMBER: les/nudged elastic band
- AMBER: Less error
- AMBER: Ligand-Protein Distance Restraints during MD Simulation
- AMBER: Ligand-Residue interaction tracking
- AMBER: Limitation in number of atoms/residues
- AMBER: Link to Modified NA bases files
- AMBER: LINMIN Failure vs Parallelization
- AMBER: Linux install
- AMBER: lipid bilayer
- AMBER: LJ parameters for alkynes
- AMBER: LJ potential
- AMBER: loading a crystal PDB file
- AMBER: Lone Pairs
- AMBER: Machine environment to install AMBER 8
- AMBER: MacOSX installation help
- AMBER: make serial failure for xleap
- AMBER: make test serial
- AMBER: make test.parallel
- AMBER: make test.parallel not complete
- AMBER: Making movies in VMD
- AMBER: manganese ion
- AMBER: Math libraries
- AMBER: MAXGRP error message
- AMBER: MAXPR
- AMBER: MD at constan pH
- AMBER: md output file
- AMBER: md potential energy
- AMBER: MD simulation error
- AMBER: MD simulations with Pt atom - how to keep square planar geometry?
- AMBER: MD temperature and MM_pbsa temperature
- AMBER: MD_model
- AMBER: mdfil.f
- AMBER: mdfil: Error unknown flag: -p4pg
- AMBER: MDGRAPE and AMBER
- AMBER: Measuring Bond Angle over simulation
- AMBER: membrane simulation
- AMBER: Membrane Simulation: NPT Issues
- AMBER: metal ions
- AMBER: Metal ions in GBSA
- AMBER: metalloprotein dynamics
- AMBER: methods to approach two atoms
- AMBER: Minimization
- AMBER: minimization + simulation
- AMBER: Minimization amber9 segmentation fault
- AMBER: Minimization and MD input files
- AMBER: minimization energy query
- AMBER: Minimization increases energy
- AMBER: minimization not running
- AMBER: minimization using fcap
- AMBER: Minimization with heme group
- AMBER: Minimum energy tolerance gradient setting for minimization
- AMBER: Missing 'yacc' command
- AMBER: Missing BELE for MM in 1
- AMBER: Missing BELE for MM in 1 (residue 47)
- AMBER: missing impropers for nitros?
- AMBER: Missing Value for MM ELE
- AMBER: Missing values for MM ELE (MM-PBSA)..help!!
- AMBER: Missplaced TERs
- AMBER: MM-GBSA residues decomposition comparison
- AMBER: MM-GBSA: pairwise decompose energy calculation can't read snapshot_com.all.out
- AMBER: MM-PBSA calcuation for drug dna complex in 2:1 ratio
- AMBER: MM-PBSA calculation with GB dynamic
- AMBER: MM-PBSA calculations of entropy within the sphere
- AMBER: MM-PBSA doubt
- AMBER: mm-pbsa error with nm = 1
- AMBER: MM-PBSA POPC/TIP3P/GPCR/LIGAND
- AMBER: MM-PBSA problem: Why
- AMBER: MM-PBSA questions/clarifications
- AMBER: mm-pbsa, long distance free energy calculation problem
- AMBER: MM-PBSA: Can't finish the binding energy process
- AMBER: MM-PBSA: decompose energy error
- AMBER: MM-PBSA_binding energy script error
- AMBER: MM-PSBA decoupling
- AMBER: MM/GBSA error message
- AMBER: mm_pbsa and energy decomposition (missing BELE for MM in 1)
- AMBER: mm_pbsa Array reference error
- AMBER: MM_PBSA calcultion- help me
- AMBER: mm_pbsa continue run
- AMBER: mm_pbsa error
- AMBER: mm_pbsa individual contributions of residues
- AMBER: MM_PBSA No radius found for Br!!
- AMBER: mm_pbsa problems
- AMBER: mm_pbsa vertex atom mismatch
- AMBER: MM_PBSA with complex plus Ion
- AMBER: mm_pbsa: missing values in ras-raf tutorials
- AMBER: mm_pbsa_statistics.pl
- AMBER: MMPBSA
- AMBER: mmpbsa calculation
- AMBER: mmpbsa decomposition error
- AMBER: mmpbsa free energy pairwise decomposition
- AMBER: MMPBSA NOT Getting results
- AMBER: MMPBSA with water molecule in active site
- AMBER: MMPBSA-nmode .top question
- AMBER: MMTSB Toolset
- AMBER: mobile proton algorithm
- AMBER: modelling substrate binding
- AMBER: modifications to force field for Fe4S4 cubane
- AMBER: modified leaprc for glycoproteins
- AMBER: Modified Nucleic Acid Problem
- AMBER: Modified nucleotides
- AMBER: Modified nucleotides-ATOM TYPES
- AMBER: mol2 format
- AMBER: Molecular dynamic issues
- AMBER: Molecular Dynamic Simulations using TIP4P water - Please Help
- AMBER: Molsurf error
- AMBER: momentum and periodic boundary condition
- AMBER: MPI
- AMBER: MPI error message
- AMBER: MPI is slower than single processor with water
- AMBER: MPI Quiescence problem in REMD
- AMBER: MPI script
- AMBER: multi chain simulations
- AMBER: multichain simulations
- AMBER: Multiple Bonds to one Atom
- AMBER: multiple excecution of sander
- AMBER: Multiple residues position
- AMBER: NAB Average Structure
- AMBER: NAB MD Output
- AMBER: NAB normal mode output
- AMBER: NAD parameters
- AMBER: NAN and vlimit exceeded errors in restrained MD.. using IBELLY
- AMBER: Nanopore simulation
- AMBER: native contact analysis!
- AMBER: Ne van del waals potential
- AMBER: neb for path between binding sites
- AMBER: NEB tutorial
- AMBER: NEB tutorial and addles
- AMBER: Need help in Analysis
- AMBER: need help to calculate IR spectra from amber trajectory
- AMBER: Needed help regardng Simulated Annealing
- AMBER: needing more detailed knowledge of tautp than the manual
- AMBER: NETCDF
- AMBER: netcdf support needed (Amber 9, sander imin = 5, -y flag)
- AMBER: neutral terminals
- AMBER: Neutralize charges for simulated annealing?
- AMBER: New 2 the board
- AMBER: newby question on converting xyz format to pdb format after energy minimization
- AMBER: NH3 potential
- AMBER: nmode
- AMBER: nmode ntrun=2
- AMBER: NMR refinement
- AMBER: NMR violations increase in explicite water
- AMBER: NMR vs. X-ray structures
- AMBER: No radius found for K+ (MM_PBSA)
- AMBER: NOC 3.0 is released
- AMBER: Non bond list overflow
- AMBER: Non-standard amino acid residue
- AMBER: nonpolar solvation energy
- AMBER: Normal Mode Analysis
- AMBER: not getting topology and restraint file
- AMBER: nscm in simulation annealing
- AMBER: ntt parameter in vacuum
- AMBER: ntt=1 or ntt= 3?
- AMBER: NTX=7 ?............lastist= ?...........lastrst= ?????
- AMBER: nuc.in file
- AMBER: Nucleic acid : nonplanarity
- AMBER: Nucleic acid analyse : base pair parameters, backbone torsions...
- AMBER: nucleic acid electrostatic energy
- AMBER: Nudget Elastic Band query
- AMBER: NVE energy and temperature drift
- AMBER: NVT/NPT equilibration issue in GPCR-membrane simulation
- AMBER: O-acetylated sugar
- AMBER: Octahedral box orientation
- AMBER: offending restraint
- AMBER: Offending restraints????
- AMBER: Once again, "distance" command in ptraj
- AMBER: oops
- AMBER: OpenMPI on MacBook Pro -- problems
- AMBER: organic solvent : hexan octan
- AMBER: output
- AMBER: ow to split MDCRD file using ptraj
- AMBER: pair distribution function
- AMBER: paper request
- AMBER: Parallel Amber compilation problems !!
- AMBER: parallel compilation
- AMBER: parallel implementation of Amber 9
- AMBER: Parallel scaling
- AMBER: Parallel test error with shared libraries
- AMBER: Parallelizin antechamber?
- AMBER: Parameter file for Dipeptide
- AMBER: parameter file for Fe-S cluster
- AMBER: parameterization for copper
- AMBER: Parse charges for small molecules
- AMBER: parse radii
- AMBER: PB Bomb
- AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f
- AMBER: PB warning in pb_miccg(): CG maxitn exceeded!
- AMBER: PBradii
- AMBER: PBSA Error
- AMBER: PBSA generate snapshots
- AMBER: pbsa installation problem
- AMBER: PCA with ptraj
- AMBER: PDB file format for AMBER
- AMBER: pdb file produced by vmd
- AMBER: PDB file with charge and size in mm_pbsa calculations
- AMBER: PDB files
- AMBER: pdb flie format
- AMBER: PDB problems
- AMBER: PDBs
- AMBER: Performance of polarizable model simulations
- AMBER: performance with implicit solvent
- AMBER: personal computer configuration for parallel computing
- AMBER: perturbed atoms are not bonded on using TIP5P wate
- AMBER: perturbed atoms are not bonded on using TIP5P water
- AMBER: pH effect on protein folding
- AMBER: phe-phe molecule
- AMBER: phe-phe prep file
- AMBER: phe-phe simulation
- AMBER: phosphorylated residues
- AMBER: phosphorylation
- AMBER: pi-pi interactions
- AMBER: planarity restraints for NA
- AMBER: Please check the total charge and your -nc flag
- AMBER: Please Disregard My Last E-mail: Missing 'yacc' command
- AMBER: plotdat: Amber Data Plotting Program
- AMBER: PM6?
- AMBER: PME and counter ions
- AMBER: PME memory requirement
- AMBER: PMEMD and restart files
- AMBER: PMEMD compilation problems !!
- AMBER: PMEMD configuration and scaling
- AMBER: pmemd install error
- AMBER: PMEMD internals !!
- AMBER: pmemd segmentation fault
- AMBER: pmemd source issues
- AMBER: pmemd with openmpi
- AMBER: pmemd: same rst, different result?
- AMBER: pmend vs sander.MPI
- AMBER: PMF along 1D axis or every axis
- AMBER: PMF calculation
- AMBER: PMF calculation - minimum conformer
- AMBER: PMF define dehedral angel and distance restrainst for center of mass of domains.
- AMBER: PMF for DG calculation.
- AMBER: PMF: WHAM result
- AMBER: Polarizable Force Field: Ligand Parameterization et al.
- AMBER: Polarizable potential
- AMBER: Polarizable potentials
- AMBER: polarizable water models.
- AMBER: polarization and water density
- AMBER: polymer
- AMBER: poor performance of sander on a quad-core linux machine
- AMBER: POPS Lipid Bilayer: Full Parameter/Topology File
- AMBER: Portland Group vs. Intel Compilers.
- AMBER: positive binding energy
- AMBER: Positive binding free energy!
- AMBER: Positive EPtot in QM-MM
- AMBER: potential energy calculation
- AMBER: Potential of mean force, how to calculate rate of dissociation?
- AMBER: Potential of mean force.
- AMBER: Potential of mean force: how to extract the min structure?
- AMBER: Prblm rgrdng Simulated Annealing
- AMBER: Pre-ABMER Installation Prob w/ MPICH2
- AMBER: Pre-requisites for AMBER software
- AMBER: predictive NOE generation
- AMBER: prep file limit exceeding
- AMBER: prep file new residue
- AMBER: Prepgen
- AMBER: Prepin error (?) in xleap
- AMBER: prepin file format description; pointers on parameterization
- AMBER: prepin for metal centre
- AMBER: Preprocessor Error: _qmmm_module.f "Extra Characters..."
- AMBER: pressure tensor in a slab configuration
- AMBER: Pressure Variation for NPT simulation of TIP5P water
- AMBER: Pressure Variation for NPT simulation of TIP5P water (fwd)
- AMBER: Pribelm with Minimization & MD
- AMBER: principal axis calculation in Ptraj
- AMBER: principal mask dorotation
- AMBER: Print individual free energies in MD trajectories using MM_PBSA
- AMBER: printcharges option when using QM/MM simulation
- AMBER: Problem about prepare the model when running antechamber
- AMBER: problem about the coordinates out the box
- AMBER: problem compiling Amber 7
- AMBER: Problem compiling AMBER 9 on ppc64
- AMBER: problem compiling Amber9 on 64-machine
- AMBER: problem compiling amber9 on IBM 64 bit machine with xlf90_suse compiler
- AMBER: problem decomposing energies (MMPBSA)
- AMBER: Problem encountered during thermodynamic integration
- AMBER: Problem generating .prepin file in Antechamber
- AMBER: problem in compiling amber with suse 9.1 i686, finally in leap
- AMBER: problem in compiling amber9 and running amber9
- AMBER: problem in implcit simulation
- AMBER: problem in installing amber9
- AMBER: problem in installing amber9 SOLVED!
- AMBER: Problem in running CARNAL
- AMBER: problem in xleap
- AMBER: problem installing amber7
- AMBER: problem regarding implicit simulation
- AMBER: problem regarding water handling in explicit simu
- AMBER: Problem related simulation of dimer
- AMBER: problem related to visualizing of structure
- AMBER: problem running parallel jobs
- AMBER: Problem Solved
- AMBER: Problem using Ptraj
- AMBER: problem while analysing result
- AMBER: Problem while carrying out minimisation of drug molecule using sander
- AMBER: Problem while creating input files in antechamber
- AMBER: Problem while creating structure in xLeap
- AMBER: Problem while loading Pdb in xleap
- AMBER: Problem while running Antechamber
- AMBER: problem while running minimisation
- AMBER: Problem while saving .top and .crd files.
- AMBER: Problem while using antechamber
- AMBER: problem with AMBER8 installation
- AMBER: Problem with anisotropic pressure scaling
- AMBER: Problem with antechamber
- AMBER: Problem with Antechamber and point charges
- AMBER: problem with atom restraints
- AMBER: Problem with calcpka.pl and constant pH
- AMBER: problem with calculating RMSD
- AMBER: Problem with dacdif when using cygwin
- AMBER: problem with distance restraints
- AMBER: Problem with Getting SHAKE to work
- AMBER: Problem with installation of the leap module of AMBER9 on Linux Suse 10.2
- AMBER: Problem with LEaP generating topology and coord files after double bond creation
- AMBER: Problem with leaprc
- AMBER: Problem with minimization
- AMBER: Problem with MM-PBSA statistics
- AMBER: problem with mm_pbsa
- AMBER: Problem with modelling ammonium ion?
- AMBER: Problem with paralell installation
- AMBER: Problem with PCSHIFT module
- AMBER: problem with ptraj
- AMBER: problem with ptraj with calculating auto time correlation functions
- AMBER: problem with running rem on amber9
- AMBER: problem with running rem on amber9 (NOT A REMD PROBLEM)
- AMBER: Problem with running Sander
- AMBER: Problem with Sander
- AMBER: Problem with Sander restart file.
- AMBER: Problem with sander.MPI
- AMBER: Problem with SCC-DFTB parameter files
- AMBER: problem with starting REM on amber9
- AMBER: problem with Thermodynamic Integration
- AMBER: Problem with xLeap
- AMBER: Problem!!
- AMBER: problems compiling amber on mac OSX
- AMBER: Problems compiling Amber9 on IBM-AIX
- AMBER: Problems during compilation
- AMBER: Problems during compilation and test.
- AMBER: problems in adding ACE and NME group
- AMBER: problems in energy minimization using TIP5P water model
- AMBER: Problems installing Amber9
- AMBER: Problems loading parameter file in tleap
- AMBER: Problems loading pdb file including Mg ions
- AMBER: Problems simulating a big system
- AMBER: problems trying to modify Amber8
- AMBER: problems using TIP4PBOX
- AMBER: problems visualizing mdcrd in VMD
- AMBER: Problems with 'make'
- AMBER: Problems with AMBER8 on 32-bit FC6
- AMBER: problems with bonding disulfide linkages
- AMBER: Problems with Carbohydrate Non-standard Residue
- AMBER: Problems with cpin file
- AMBER: Problems with Machine file for sander.MPI
- AMBER: Problems with QMMM tests on Altix
- AMBER: problems with restart of smd simulation w/ jar=1 & nmr=1
- AMBER: process and plot matrix data
- AMBER: program bug?
- AMBER: Projecting trajectories onto normal modes
- AMBER: Protein containing iron.
- AMBER: protein-ligand binding affinity
- AMBER: protein-rna interaction & mmpbsa
- AMBER: protein_model
- AMBER: protocols for high pressure simulation
- AMBER: protonate
- AMBER: Protonation of Aspartate
- AMBER: protonation of His residue!
- AMBER: Protonation/deprotonation of terminal residues
- AMBER: Pseudo-CSA in Amber?
- AMBER: psi , phi angles
- AMBER: ptraj
- AMBER: ptraj and quasi harmonic analysis
- AMBER: ptraj average structure strip water
- AMBER: ptraj bug?
- AMBER: ptraj bug? -- doesn't like restart files from REMD
- AMBER: ptraj dipole calculation in QMMM simulation
- AMBER: ptraj error
- AMBER: ptraj error- glibc detected free(): invalid pointer: 0x0812bb38
- AMBER: ptraj frames maximum
- AMBER: ptraj hbond
- AMBER: Ptraj hbond analysis
- AMBER: ptraj hbond mask
- AMBER: ptraj hydrogen bonding defaults
- AMBER: PTRAJ problem
- AMBER: ptraj secstruct core dumped error
- AMBER: ptraj with protein-ligand
- AMBER: Ptraj: reading PDB files
- AMBER: ptraj: RMS per residues and per time
- AMBER: Ptraj: watershell and distance
- AMBER: ptraj:problems with time correlation calculation (comp. with NMR experiments)
- AMBER: ptray segfault: vector out
- AMBER: Puzzle with WAT
- AMBER: QM-MM output interpretation
- AMBER: QM/MM in reaction pathways?
- AMBER: QM/MM LJ parameters
- AMBER: QM/MM NPT Simulation
- AMBER: QM/MM simulation with SCC-DFTB
- AMBER: qm/mm ti
- AMBER: QM/MM Umbrella sampling
- AMBER: QM/MM-DRFTB
- AMBER: QMMM simulations
- AMBER: QMMM to follow reaction involving water
- AMBER: QMMM with printcharges
- AMBER: quasiharnomic analysis
- AMBER: query regarding parameter files for manganese
- AMBER: query regarding parameter files for manganese and mercuric ions
- AMBER: Question
- AMBER: question about a 20 kDa protein
- AMBER: question about ADDLES module
- AMBER: Question about Boron
- AMBER: question about charge of prmtop file
- AMBER: Question about determination of hydration points in binding sites
- AMBER: question about distance restraint on terminal WC of DNA duplex (AMBER9)
- AMBER: question about formatted mdrcrd files...
- AMBER: question about h bond
- AMBER: question about iwrap
- AMBER: Question about loadMol2
- AMBER: Question about MMPBSA v9
- AMBER: Question about MPI-IO
- AMBER: Question about NAB (Nucleic Acid Builder)
- AMBER: question about ntx=5
- AMBER: Question about ptraj matrix correl command
- AMBER: Question about separating bonded force
- AMBER: question about the testing of AMBER9
- AMBER: Question about translational and rotational degree of freedom in MM-PBSA v9 computations
- AMBER: Question on TIP4P model
- AMBER: question with ptraj loop
- AMBER: questions about analysing LES results
- AMBER: Questions about how ptraj calculates solvent shells
- AMBER: questions about smd of amber 9
- AMBER: Quick QUESTION
- AMBER: R.E.D.-III bug fixes
- AMBER: radial distribution by Ptraj
- AMBER: radial distribution function in ptraj
- AMBER: Radii for water hydrogens are different
- AMBER: radius of gyration
- AMBER: Rate of Dissociation
- AMBER: RDF of pure chloroform
- AMBER: Rdf question
- AMBER: RDF unit cell volume
- AMBER: RE Amber: Simulated Annealing
- AMBER: read the data
- AMBER: RED III
- AMBER: RED-vIII fails
- AMBER: REF file problem
- AMBER: refc error
- AMBER: refinement of NMR struture using AMBER
- AMBER: Reg COM restraint to DNA
- AMBER: Reg restraint value obtained during umbrella sampling
- AMBER: regarding anal calculations
- AMBER: Regarding conversion of CHARMM force field parameters to AMBER parameters.
- AMBER: Regarding counter ions
- AMBER: regarding distance restraints
- AMBER: regarding energy calculation
- AMBER: Regarding energy of decomposition tutorials
- AMBER: regarding frcmod file
- AMBER: Regarding free energy calculation and covalent bond
- AMBER: regarding implicit simulation
- AMBER: regarding non bonded energy caculations
- AMBER: Regarding Simulated Annealing
- AMBER: regrading interaction energy calculations
- AMBER: related to new amber force field
- AMBER: Release of the R.E.D.-III tools
- AMBER: REMD and mpiexec
- AMBER: REMD error
- AMBER: REMD error on first exchange
- AMBER: remd/rdc's
- AMBER: replacement of mutated atoms in protein structure
- AMBER: replica exchange
- AMBER: replica exchange out files continually overwritten
- AMBER: replica exchange problems with ifort >10.0.023
- AMBER: replica exchange simulation
- AMBER: Reply regarding PCA with ptraj and IED
- AMBER: reporting EPtot and EKtot separately for two molecules
- AMBER: reproducibility between software
- AMBER: Reproducing constant pH results !!
- AMBER: Request for addition of a useful command in ptraj module of AMBER
- AMBER: Request for addition of a useful command in ptraj module of AMBER #2
- AMBER: request for hardware recommendations
- AMBER: Request reg parameter for vitamin e
- AMBER: Residence time of WATER
- AMBER: residue types for GLY/high pH
- AMBER: resp
- AMBER: RESP calculation of modified nucleotides
- AMBER: RESP charge fitting using antechamber
- AMBER: RESP charge generation
- AMBER: RESP Charges for Charged Carboxylate in Organic Ligand
- AMBER: RESP charges for charged species
- AMBER: RESP question
- AMBER: RESP using antechamber
- AMBER: Resp: "Statistics of the Fitting"
- AMBER: RESP_compilation
- AMBER: RESP_compilation_IT_WORKS
- AMBER: Restart Files
- AMBER: Restart from restart file obtained from ptraj with added velocities
- AMBER: restarting REMD simulations
- AMBER: restrain center of mass of one domain
- AMBER: Restrained MD (amber9)
- AMBER: restrained md and mm pbsa
- AMBER: restraining atoms
- AMBER: Restraining valence angles
- AMBER: restraint command not taken
- AMBER: restraint in minimization
- AMBER: restraint value: written but none specified
- AMBER: restraint_wt and fixing chi
- AMBER: RESTRAINTMASK
- AMBER: Restraintmask syntax
- AMBER: Restraints and free energy
- AMBER: restraints during MD
- AMBER: Restraints on modified NA's
- AMBER: restraints to individual atoms
- AMBER: results from TI
- AMBER: rfree: Error input file
- AMBER: rigid epoxide substrate
- AMBER: rms and rms nofit
- AMBER: rms and rmsf in ptraj
- AMBER: rms in nmode
- AMBER: rmsd calculation in ptraj
- AMBER: rmsd calculation in ptraj II
- AMBER: rmsd residue wise
- AMBER: Rotations about center of mass of an isolated system
- AMBER: RST can not be opened
- AMBER: rst overflow for implicit REMD
- AMBER: running equilibration
- AMBER: Running Gaussian to get .out files
- AMBER: Running mpirun -np 1 on different processors
- AMBER: running_RED-III
- AMBER: S-nitrocysteine
- AMBER: sander (AMBER 9) and -y flag -- not working?
- AMBER: Sander (Amber 9) crash on cortex
- AMBER: sander and pmemd
- AMBER: sander bomb
- AMBER: Sander Bomb in subroutine nonbond_list
- AMBER: Sander BOMB.. simulation terminates by itself...
- AMBER: SANDER bug
- AMBER: sander bug?
- AMBER: sander core dumped during minimization
- AMBER: sander crashes during minimization
- AMBER: Sander Error
- AMBER: Sander error : Coordinate resetting (SHAKE) cannot be accomplished
- AMBER: SANDER error: 'angles are not correct'
- AMBER: sander MPI fails included tests
- AMBER: SANDER PMEMD ntpr ntwx discrepancy (?bug? report)
- AMBER: Sander slower on 16 processors than 8
- AMBER: Sander....
- AMBER: sander.MPI vs MPICH2 problem!!!
- AMBER: sander/topology problem
- AMBER: sanger
- AMBER: SASA per residue
- AMBER: Saving (.)prepin file
- AMBER: Saving a structuring from trajectory
- AMBER: Scaling for octahedral versus rectilinear boxes
- AMBER: SCC convergence failure in QM-MM DFTB
- AMBER: SCF convergence issues
- AMBER: Schedule for QM-MM with Amber9/Amber10
- AMBER: Scripts for md analysis
- AMBER: secstruct command
- AMBER: Section missing from AMBER 9 manual?
- AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9)
- AMBER: segmentation fault occured doing MD
- AMBER: Segmentation Fault when saving prmtop and inpcrd files in xleap
- AMBER: Serial "make" failure
- AMBER: Serial "make" failure with xleap
- AMBER: set up system solution with 3 different components, each with multiple copies
- AMBER: setbox command error
- AMBER: setting dimensions of truncated octahedron
- AMBER: Setting nonbonded cutoff to 1
- AMBER: SGI Altix Compilation Problems (Was: Error - must define AMBERHOME environment variable)
- AMBER: SHAKE failure in TI calculation of zero sum model system of "ethane-to-ethane" in water
- AMBER: shell model MD
- AMBER: short 2'OH-OP contacts in RNA
- AMBER: Should we just vary one parameter at a time only for PMF calculations?
- AMBER: side chain orientation
- AMBER: signal SIGSEGV(11)
- AMBER: Simulated Annealing
- AMBER: Simulated Annealing - Best way to create randomness
- AMBER: Simulated annealing - Nudget Elastic Band
- AMBER: Simulated Annealing - Start with Poor Structure
- AMBER: Simulating a section of a molecule
- AMBER: simulating part of a molecule with homology modeling
- AMBER: Simulation continuation problem. Cant read restart file!!!!!!
- AMBER: Simulation died due to lack of disk space
- AMBER: Simulation of a charged system
- AMBER: simulation of the phosphorylated protein
- AMBER: simulations stops in half way
- AMBER: Simulations with GB models
- AMBER: single phospholipid molecule in vacuo
- AMBER: single solvated glycine simulation - zwitterion, cation, anion parameters?
- AMBER: single solvated glycine simulation - zwitterion, cation, anion parameters? 2nd try
- AMBER: Slight_error_on_Compiling_Replica_Exchange
- AMBER: Slow Processor Loads when Using PMEMD
- AMBER: Small scale compute environments
- AMBER: SMD simulation
- AMBER: software to extract data from the output file??
- AMBER: solaris 10 and compilers on X86_64 hardware
- AMBER: Solution Structure Determination Protocols - Simulated Annealing
- AMBER: Solvate box
- AMBER: solvate shell
- AMBER: solvatebox vs solvateoct
- AMBER: solvateCap minin and mdin for qm-mm dftb
- AMBER: Solvation free energy
- AMBER: Solvation Issues
- AMBER: Solvation net forces
- AMBER: solvation of protein using TIP3PBOX in amber 8
- AMBER: Solved: Heat capacity calculations not coming out right
- AMBER: solvent accessible surface area (SASA)
- AMBER: solvent box pyridine
- AMBER: Solvent in closest contact with solute
- AMBER: Solvent models
- AMBER: some input problem
- AMBER: Some problems during the testing of Amber.
- AMBER: some questions about minimization and MD of DNA duplex with sander
- AMBER: Some questions on mm_pbsa
- AMBER: SPCFW water: angle problems in leap
- AMBER: Specific heat graph is a straight line
- AMBER: Specific/Non-specific dihedral issue in Amber
- AMBER: specifying psi and phi for a dipeptide
- AMBER: spring constant for restraint
- AMBER: Squished dimer during transition from NVT to NPT
- AMBER: Statictical significance of differences in energy mean values between different simulations
- AMBER: Statistical uncertainty estimation in Thermodynamic integration calculation..
- AMBER: Steered MD
- AMBER: Steered MD & Jarzynski's equality
- AMBER: Steered MD & Jarzynski's equality]
- AMBER: step-by-ste weight changes of dwt -- patch?
- AMBER: Still puzzled about this virial computation
- AMBER: Stirp command in ptraj
- AMBER: Strange behavior on g95 compile.
- AMBER: subroutine ephi !!
- AMBER: subscribe amber
- AMBER: Substitute for GAFF
- AMBER: Successful compile on Mac OSX + Intel compilers
- AMBER: supplement ptraj:problems with time correlation calculation (comp. with NMR experiments)
- AMBER: Surface
- AMBER: surface area over the trajectory
- AMBER: System extending beyond of (non existent) virtual box
- AMBER: Targeted MD
- AMBER: targeted MD problem
- AMBER: targetedMD problem
- AMBER: Targetted MD and ptraj analysis
- AMBER: temperature artifacts with andersen and GB?
- AMBER: Temperature Drift in MD (NAB)
- AMBER: Temperature fluctuation in NPT and NVE ensemble
- AMBER: temperature fluctuation in REMD
- AMBER: Test fails in Parallel version Amber9
- AMBER: test submission through PBS queue
- AMBER: TEST_FAILURES
- AMBER: testing amber9 for parallel use
- AMBER: testing protein stability
- AMBER: tgtrmsmask and tgtfitmask
- AMBER: the box vectors for a Leap generated truncated octahedron
- AMBER: The convergence criteria for the energy minimization of the DNA molecule (dodecmer duplux)
- AMBER: The number of the path atoms exceeds MAXPATHATOMNUM
- AMBER: The parallel test fails while sander.MPI seems to be installed correctly
- AMBER: The ring number exceeds MAXRING, increase MAXRING and recompile the programs, exit
- AMBER: The unperturbed charge of the unit: -20.999999 is not zero.
- AMBER: thermodynamic data for conformers
- AMBER: thermodynamic integration
- AMBER: Thermodynamic Integration (TI) error: "numgroup must be 2 if icfe is set"
- AMBER: Thermodynamic Integration for a CHARGED molecule
- AMBER: Thermodynamic Integration for conformational changes?
- AMBER: Thermodynamic Integration with Explicit Solvent
- AMBER: THF parameters
- AMBER: TI Approach - mass perturbation
- AMBER: TI calculation: charge is not zero in the perturbed state
- AMBER: TI calculation: the perturbed charge is not integral
- AMBER: Time step & non-bonded interactions updating
- AMBER: TIP4P MD simulations
- AMBER: TIP5P questions
- AMBER: TIP5P water Simulation
- AMBER: TIP5P water simulation using AMBER7
- AMBER: tleap crashing
- AMBER: TMD and "Current RMSD from reference"
- AMBER: Too big EEL energy in energy minimization
- AMBER: Too big EEL energy in energy minimization. .
- AMBER: Topology file problem in TI !
- AMBER: topology for postprocessed files?
- AMBER: torsion angle
- AMBER: torsion angle penalty calculation
- AMBER: torsion angle penalty calculationy
- AMBER: Torsion Restraint on Glycosidic Bond
- AMBER: Torsion terms in xleap
- AMBER: torsional restraints in a solvated MD simulation.
- AMBER: total energies during MM-PBSA
- AMBER: total energy in sander and nmode
- AMBER: trajectory problem
- AMBER: Transformation table
- AMBER: Trimannoside Problem
- AMBER: Trouble on wiki about GAFF
- AMBER: Troubles installing amber
- AMBER: Troubling with installing Amber8
- AMBER: Truncated Octahedron box volume
- AMBER: Tutorial 3: MM-PBSA.....implicit solvent for MD calculations?
- AMBER: Tutorial about SMD?
- AMBER: Tutorial for chemical shift calculation?
- AMBER: Tutorial of document about QM/MM in reaction pathways?
- AMBER: Tutorial protein-small-molecule-associates
- AMBER: umbrella sampling
- AMBER: Umbrella sampling - Tutorial
- AMBER: umbrella sampling and WHAM
- AMBER: umbrella sampling dihedral restraint question
- AMBER: Umbrella Sampling for the twist angle of a DNA base pairs
- AMBER: umbrella sampling: distance restraint
- AMBER: Unable to compile amber9
- AMBER: Unable to open MDCRD file using vmd
- AMBER: unable to run test
- AMBER: unable to save prmtop/inpcrd for chcl3box
- AMBER: Understading of mdcrd file and pdb file..
- AMBER: Unexpected Failure in XLeap
- AMBER: united atom parameters for -NH2 and -OH groups
- AMBER: units in hessian matrix
- AMBER: units of mwcovar matrix befor conversion
- AMBER: unres
- AMBER: unsubscribe
- AMBER: Use of Counter Ions in binding energy calculations
- AMBER: use of pucker function in ptraj
- AMBER: using amber for cyclic peptides
- AMBER: using amber to minimize structure obatined from cyana
- AMBER: Using charmm force field in amber
- AMBER: using glycam04 parameters
- AMBER: Using ntr=1 in xleap
- AMBER: Using position restraints during constant pressure equilibration
- AMBER: Using TLEAP to set up MD in the crystal lattice space?
- AMBER: Value of taup for bulk TIP5P water simulation(amber7)
- AMBER: van der Waals parameters and 6-12 potential parameters of NB in parm99.dat?
- AMBER: van der waals parameters.
- AMBER: vdW parameters for chlorine atom
- AMBER: vector corrplane
- AMBER: Verifying Bond Angles
- AMBER: vertex atom mismatch
- AMBER: Vlad has Tagged you! :)
- AMBER: vlimit error
- AMBER: vlimit exceeded for the step
- AMBER: vlimit exceeded, polarizable force field
- AMBER: vmd and amber
- AMBER: WARNING: Missing VDWNB for MM in 1 -> Taken from 0
- AMBER: Water cap MD error
- AMBER: water count
- AMBER: water density
- AMBER: Water density calculation
- AMBER: Water question
- AMBER: website problems
- AMBER: Weird restart file with ioutfm=0, iwrap=1 and ntwprt >0
- AMBER: What is the best computer for running AMBER simulations?
- AMBER: what's the problem of "Missing BELE for MM in 1 (residue 246)" in MM-GBSA?
- AMBER: Who has the structure file of beta-chitin?
- AMBER: Why there is a gap or jump if continue ntt=3 or ntt=1
- AMBER: Work with constand pH
- AMBER: work with constant pH on amber8
- AMBER: workaround for ibm xlf90 powerpc FORTRAN compiler: -q64 and -O3 yield Run.dhfr.min failure
- AMBER: working with Antechamber
- AMBER: Would amber work with Linspire 6.0?
- AMBER: xleap
- AMBER: xLeap "Could not find type" error
- AMBER: xleap and amber7
- AMBER: Xleap and Hydrogens
- AMBER: Xleap errors
- AMBER: xleap heme iron coordination error
- AMBER: xleap loading files
- AMBER: xleap on cygwin
- AMBER: xleap patch for xorg-7.3 ??
- AMBER: xleap patch for xorg-7.3 ??]
- AMBER: xleap question
- AMBER: xLeAP: TI calculation: the perturbed charge is not integral
- AMBER: yet another SANDER bug?
- AMBER: Zinc-Histidine force field
- AMBER: À´×Ôpig5678µÄÓʼþ
- AMBER:a question about RMSD
- AMBER:antechamber fails with large molecules
- AMBER:charge file
- AMBER:How to calculate the free energy of a series of conformations
- Amber_ifort_x86_64 test error
- antechamber
- antechamber problem
- Asking for help
- Asking for help about heating
- BOUNCE amber@scripps.edu: Non-member submission from [Taufik Al-Sarraj <taufik.alsarraj@utoronto.ca>]]
- Calculating Energies with imin=5
- Contact TSRI: Ross Walker
- dihedral term charge dependence
- divcon missing in Antechamber 1.27
- divcon on AIX using xlf 10.1
- ff02 and ff03 parameters
- FF94 or FF99?
- Fwd: AMBER: Atoms overlapping
- Fwd: AMBER: Can't run Normal Mode Analysis !!!
- Fwd: AMBER: Copper and Chlorine parameters
- Fwd: AMBER: Improper angle by Antechamber
- Fwd: AMBER: missing impropers for nitros?
- Fwd: AMBER: MM-PBSA: Can't finish the binding energy process
- Fwd: AMBER: mm_pbsa Array reference error
- Fwd: joshua
- help
- help:- regarding "perl" in analyzing the simulation
- how to create an O linked N-acetylglucosamine in a
- how to create an O linked N-acetylglucosamine in a protein
- IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031
- Minimization with heme group
- missing impropers for nitros?
- MM-PBSA amber script problem
- MPI error message
- Need your gudiance
- parameter
- pmemd install error
- Problem loading pdf into tleap
- Problem with sander.MPI
- process_mdout.perl
- Query
- Query regarding using tleap for preparing carbohydrate molecule
- RE : AMBER: Atom types for polyunsaturated lipids
- Re : AMBER: intra-molecular h-bonds in ptraj
- RED problem
- REMD with torsional restraints- Temperature swapping not occuring
- reporting EPtot and EKtot separately for two molecules
- SANDER error: 'angles are not correct'
- Strange shape in my MD simulations
- SV: AMBER: Atoms in contact to a specific atoms during MD
- tree name generated by tleap is different from the input PREP parameter file
- TUTORIAL B1 file polyAT_vac.prmtop
- tutorial file polyAT_vac.prmtop
- Tutorial5 -- sustiva and xleap
- using RESP
Last message date: Mon Dec 31 2007 - 15:27:41 CST
Archived on: Thu Jan 10 2008 - 17:13:08 CST
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