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AMBER Archive (2004) - By Subject
4314 messages sorted by: [ author ] [ date ] [ thread ]About this archive
Starting: Thu Jan 01 2004 - 04:51:48 CST
Ending: Thu May 05 2005 - 14:26:38 CDT
- 1cbn
- : AMBER: basis set
- [pradipta_b@mail.jnu.ac.in: AMBER: Software to visualize normal modes!]
- a new question
- about PME in Amber6
- About RESP Calculation
- Amber
- AMBER 8 default is now HIS->HIE and not HIS->HID - typo?
- AMBER:
- AMBER: "ATTN, need revision"
- AMBER: "closestwater" algorithm
- AMBER: "matrix" in ptraj
- AMBER: "No radius found for F" error and vdw radii for F in MMPBSA
- AMBER: "Total vdw box size" information is gone
- AMBER: %GIBBS-F-MISMATCH, The parm and coord files disagree on the number of atoms
- AMBER: (no subject)
- AMBER: -p4pg problem
- AMBER: .crg file for Delphi
- AMBER: .lib file error in tleap
- AMBER: 1-4 EEL
- AMBER: <dV/dL> fluctuations in TI
- AMBER: [0] MPI Abort by user Aborting program !
- AMBER: [Fwd: KLAMBDA in amber7]
- AMBER: [Fwd: No timings from jac test on opteron quad]
- AMBER: A few questions in the protein unfolding simulations using GB model
- AMBER: A general question
- AMBER: a general question about the mmpbsa method
- AMBER: A parm file suit for half beta and half alpha structure
- AMBER: A problem about a sander parallel run
- AMBER: a problem about alanine scan of proline
- AMBER: A problem for compiling amber8 parallel version
- AMBER: A problem regarding constant pH calculation in Amber 8
- AMBER: a question
- AMBER: a question about anal
- AMBER: A question about pheTI in AMBER8 test.
- AMBER: A Question about RESP
- AMBER: A question about RMSD calculation
- AMBER: a question about Van der waals radius
- AMBER: A question on AMBER8 installation
- AMBER: a question on MM-PBSA and Delphi
- AMBER: a question on ntwx and ntwr
- AMBER: a quick question about carnal
- AMBER: A tool for building coordinates of huge macromolecules
- AMBER: A torsion parameter in AMBER2003 force field
- AMBER: about AM1-BCC charge method
- AMBER: about amber8, replica exchange
- AMBER: about antechamber
- AMBER: About binding energy
- AMBER: about correlation calculation in ptraj
- AMBER: About DelPhi and GRASP
- AMBER: About Disulfer bond
- AMBER: about FEP
- AMBER: about glycam 04
- AMBER: about GLYCAM prep files in AMBER
- AMBER: About glycam2004
- AMBER: About Hbond calculations using ptraj
- AMBER: About missing residues
- AMBER: about MM-PBSA
- AMBER: About MM/PBSA, PB Calculation
- AMBER: about mm_pbsa parameter
- AMBER: about PARALLEL run on SGI.
- AMBER: about RDF calculation in action.c
- AMBER: About RESP Calculation
- AMBER: about running ptraj in ambber8 (re-post)
- AMBER: about running ptraj in amber8
- AMBER: About STD in NMODE
- AMBER: About the Amber constraint constant
- AMBER: About the calculation of non-bond list
- AMBER: About the free energy difference in vacuum with GIBBS.
- AMBER: About the parameter names
- AMBER: about the parameter of the cystein pair in MD simulation
- AMBER: About TI with sander
- AMBER: About tree structure of TRP residue
- AMBER: About umbrella sampling in Amber 8
- AMBER: add charge error message: Number of electrons is odd
- AMBER: add dummy atoms
- AMBER: Add Hydrogen bond through xLeap?
- AMBER: add Na+
- AMBER: adding ions to nucleic acids
- AMBER: Adding residues
- AMBER: AddIons
- AMBER: Additional note on ld.so.conf vs. LD_LIBRARY_PATH
- AMBER: address error
- AMBER: Aldo's PMEMD bug
- AMBER: algorithm used in AMBER
- AMBER: alignment problem using carnal
- AMBER: Alignment tensor for Sander RDCs
- AMBER: all_amino03.in discrepancy
- AMBER: all_nucleic02 and all_nucleic94
- AMBER: all_nucleic94 versus all_nucleic02
- AMBER: AM1-BCC charges
- AMBER: Amber
- AMBER: Amber & mutation
- AMBER: Amber 03 Forcefield discrepancy
- AMBER: AMBER 4 Manual?
- AMBER: AMBER 5 (sander) Parallel PME on IBM p630
- AMBER: AMBER 6 compilation problems!
- AMBER: Amber 7 (sander) use of PME
- AMBER: Amber 7 Compiling Problem
- AMBER: AMBER 7 Installation
- AMBER: amber 7 nmode on osx
- AMBER: Amber 7 on SGI: Sander MPI problem
- AMBER: amber 8
- AMBER: Amber 8 - Energy Minimization Parameters
- AMBER: Amber 8 - OS support.
- AMBER: Amber 8 compilation
- AMBER: AMBER 8 default is now HIS->HIE and not HIS->HID - typo?
- AMBER: amber 8 error
- AMBER: amber 8 error on installation
- AMBER: Amber 8 installation
- AMBER: Amber 8 Installation - C compiler?
- AMBER: AMBER 8 installation - continued
- AMBER: Amber 8 installation error
- AMBER: Amber 8 installation error on Xeon 2-CPU
- AMBER: AMBER 8 installation trouble
- AMBER: amber 8 parallel problem
- AMBER: Amber 8 ptraj segmentation fault
- AMBER: amber 8 under windows XP
- AMBER: Amber and Linux compilation
- AMBER: AMBER charges(Cornell et al JACS, 1995) and R.E.D
- AMBER: amber compilation
- AMBER: Amber compilation in IBM-SP4
- AMBER: Amber force field for protein-DNA system
- AMBER: Amber force field for protein-DNA system (again)
- AMBER: AMBER Gibbs Memory problem
- AMBER: Amber job submission using PBS
- AMBER: amber on AMD 64
- AMBER: AMBER on IBM SP cluster
- AMBER: Amber on RedHat 3.0
- AMBER: Amber on Redhat Enterprise
- AMBER: AMBER Parameter Database
- AMBER: Amber Transition State Output
- AMBER: amber with MPI
- AMBER: Amber-7:Bugfix.47
- AMBER: amber/pmemd with mpiexec
- AMBER: AMBER6 manual
- AMBER: Amber7 (8):FLUSH--FAILED:: Resource temporarily unavailable
- AMBER: Amber7 - mm_pbsa/molsurf
- AMBER: AMBER7 : Hybrid macromolecule
- AMBER: AMBER7 : update force field gaff.dat and parm99.dat
- AMBER: AMBER7 : update gaff and parm99 force field
- AMBER: Amber7 bugfix1
- AMBER: Amber7 compilation error
- AMBER: Amber7 installation error on Solaris 9
- AMBER: amber7 on digital unix
- AMBER: AMBER7 plastocyanin tutorial problem.
- AMBER: AMBER7 sander compiled on SGI R10000 fails to complete test suite
- AMBER: amber7 test on osx
- AMBER: Amber7 tleap problem
- AMBER: AMBER7 update force field
- AMBER: amber7, namelist, xlf and osx
- AMBER: Amber7:
- AMBER: Amber7: pdb format file
- AMBER: Amber8 - Energy Calculations
- AMBER: Amber8 - Floating point
- AMBER: Amber8 - LAM MPI Compilation problems
- AMBER: amber8 compilation
- AMBER: Amber8 compilation error
- AMBER: Amber8 compilation in Dec-Alpha
- AMBER: Amber8 compilation in IBM-AIX
- AMBER: amber8 compilation on AIX (regatta)
- AMBER: Amber8 compilation problems on AIX
- AMBER: amber8 compile on Lemieux
- AMBER: AMBER8 compiling error under Itanium 2.
- AMBER: amber8 installation
- AMBER: Amber8 on Digital UNIX
- AMBER: Amber8 on Tru64 UNIX on Alpha systems
- AMBER: amber8 parallel installation with mpich
- AMBER: AMBER8 parallel job
- AMBER: amber8 parallel jobs
- AMBER: amber8 performance on linux cluster
- AMBER: amber8 performance problem on Itanium II's
- AMBER: amber8 tests
- AMBER: amber8 tutorial
- AMBER: Amber8: ifort 8.0.046 Woo hoo!
- AMBER: Amber8: Vlimit problem again
- AMBER: amber98 with amberffc+INSIGHT II
- AMBER: Amber: Anal program format
- AMBER: Amber: BOMB
- AMBER: Amber: Equilibrated DMSO solvent box
- AMBER: Amber: what different?
- AMBER: Amber: xleap crash
- AMBER: Amber:how to increase the memory allocation?
- AMBER: AMBPDB command requires libcxa.so.5
- AMBER: ambpdb in AMBER7
- AMBER: ambpdb segmentation fault
- AMBER: Ammonia
- AMBER: amparm
- AMBER: An question about PTRAJ
- AMBER: anal error
- AMBER: ANAL memory problem.
- AMBER: Anal module on PDBs
- AMBER: ANAL problem.
- AMBER: ANAL: how can i buld the anal.in file?
- AMBER: Analysis mm_pbsa result
- AMBER: angle bending
- AMBER: Angle parameters in phosphate groups
- AMBER: Angle Restraining
- AMBER: Angle restraint during MD
- AMBER: Angle restraint during MD and namelist problem in amber8
- AMBER: animation?
- AMBER: anisotropic scaling
- AMBER: announcing normal mode analysis web server ElNemo
- AMBER: another cpinutil.pl error
- AMBER: antechamber
- AMBER: Antechamber & Ptraj/Rdparm
- AMBER: antechamber + FAILED TO ACHIEVE SCF
- AMBER: antechamber + mopac + MAXIMUM NUMBER OF ATOMIC ORBITALS EXCEEDED
- AMBER: antechamber + mopac +scf failed
- AMBER: antechamber + mopac error
- AMBER: antechamber - improper torsions
- AMBER: antechamber - missing improper torsions
- AMBER: Antechamber and dummy atoms
- AMBER: antechamber and mopac5010mn
- AMBER: antechamber bcctype.c typo
- AMBER: Antechamber compilation error
- AMBER: Antechamber compilation: leap error
- AMBER: antechamber download files should now be available
- AMBER: antechamber error
- AMBER: antechamber error in test / differences in prmtop files
- AMBER: Antechamber Failure
- AMBER: antechamber gives GDP 0 charge
- AMBER: Antechamber license ?
- AMBER: Antechamber MOPAC
- AMBER: Antechamber on cluster with queue?
- AMBER: antechamber prepin
- AMBER: Antechamber problems
- AMBER: antechamber test
- AMBER: antechamber, mopac RESTART
- AMBER: antechamber/mopac question
- AMBER: antechamber/Mopac: strange GTP charges
- AMBER: antechamber/parmchk ATTN: needs revision
- AMBER: antechamber: atomtype assignment of cc/cd etc pairs in GAFF / creating atom type definition file
- AMBER: antechamber: frcmod parameter need revision
- AMBER: Antechamber: problems with bcc correction
- AMBER: any program or tool
- AMBER: Assignment of parameters, missing parameters
- AMBER: Atom distance
- AMBER: Atom Labels
- AMBER: atom out of bounds
- AMBER: atom out of bounds (fwd)
- AMBER: Atom type
- AMBER: atom type CM
- AMBER: atom type for GBSA
- AMBER: Atom type with/without POL
- AMBER: Atomic Charge in Residue
- AMBER: Atomic charges in Lactose
- AMBER: atomic positional fluctuation
- AMBER: atomicfluct in ptraj
- AMBER: atoms not in residue templates
- AMBER: atoms out of bounds
- AMBER: average structure from traj
- AMBER: average structure using ptraj
- AMBER: average using ptraj
- AMBER: averaged structure with unknown elements
- AMBER: B factors --- one more explanation
- AMBER: B factors from simulation and from cryst
- AMBER: Babel
- AMBER: back interpret
- AMBER: Bad atom symbol, K+ and IB in vacuum
- AMBER: Bad contacts
- AMBER: bad crd file
- AMBER: basis set
- AMBER: bending
- AMBER: best PC laptop system to run Amber 8
- AMBER: binary files
- AMBER: Binding free energy from separate/single trajectory
- AMBER: Biotin/streptavidin tutorial.
- AMBER: bond between two polypeptides
- AMBER: bond constraints in nmode
- AMBER: BOND energy during minimisation
- AMBER: Bond type in leap
- AMBER: Bondi radii for BR and F in mm_pbsa calculation
- AMBER: Born radii
- AMBER: born radius and screening parameter for Br
- AMBER: Box information from Amber
- AMBER: Box of mixed solvant
- AMBER: Box range in vacuum when restart MD
- AMBER: Bug and Patch in ANAL
- AMBER: Bug in babel conversion
- AMBER: Bug in babel conversion (while following the RED manual in pp.15)
- AMBER: bug in leap?
- AMBER: bug of leap?
- AMBER: Bug: ptraj adds spurious box information
- AMBER: bugfix.17
- AMBER: bugfix.all
- AMBER: build a cyclic peptide
- AMBER: Build a H+ ion in Leap?
- AMBER: building a small molecule
- AMBER: building parameters with Amber
- AMBER: Building the parallel version in AMBER 8 and GIBBS
- AMBER: Cadmium
- AMBER: Calcium and GB
- AMBER: calcium van der Waals parameters
- AMBER: calculate ligand's rmsd
- AMBER: Calculating H-Bond networks using ptraj
- AMBER: calculation of pKa values
- AMBER: Can anybody help me with CHARMM
- AMBER: can MM-PBSA be applied to Charmm format trajectory file?
- AMBER: Can parallel simulation have a nonperiodic boundary condition?
- AMBER: Can xleap handle homology model altogether with X-ray structure?
- AMBER: Can xleap to handle homology model altogether X-ray structure?
- AMBER: Can you write me how can I add the ACE and NMe groups in the Xleap?
- AMBER: cannot load frcmod file properly
- AMBER: Cannot read in sander
- AMBER: Cannot read in sander-again
- AMBER: CAP PROTOCOL SIMULATION
- AMBER: cap waters always flexible?
- AMBER: carnal
- AMBER: Carnal & Radius of gyration
- AMBER: Carnal in Amber7
- AMBER: Carnal question
- AMBER: CARNAL RMS
- AMBER: CARNAL- movement of an axis
- AMBER: Cartitian Restraint Error
- AMBER: cell dimensions
- AMBER: center of mass in CARNAL
- AMBER: CG maxitn exceeded
- AMBER: changepot
- AMBER: changepot & mol2 file
- AMBER: Changing MAXPR in Amber 8?
- AMBER: charge not zero
- AMBER: charge perturbation - xleap question
- AMBER: charge problem in minimization
- AMBER: Charges and atom type
- AMBER: CHARMM PSF to PRMTOP
- AMBER: check unit + saveamberparm
- AMBER: Checking Results?
- AMBER: choosing 3 atoms for reorientaion in R.E.D
- AMBER: Clean in RESP
- AMBER: Close contact warnings
- AMBER: cluster analysis
- AMBER: cluster analysis with ptraj in amber 8.0
- AMBER: cluster MD conformations from sander
- AMBER: Clustering in PTRAJ
- AMBER: Co-ordination error while running tleap
- AMBER: cobalt parameters
- AMBER: combination rules
- AMBER: combine crd files
- AMBER: Comparison of simulation results on amber7 and amber 8
- AMBER: Compilation Problem in Amber 7
- AMBER: Compilation problem in SUN OS 5.7!
- AMBER: compilation under fedora core 1
- AMBER: compile amber8 in linux with ifort
- AMBER: Compile xleap (amber8) in linux Red Hat 8.0
- AMBER: compiling Amber 8
- AMBER: Compiling AMBER MPI program using GCC/G77 compiler and MPICH on AMD OPTERON 64
- AMBER: Compiling AMBER MPI program using GCC/G77 compiler andMPICH on AMD OPTERON 64
- AMBER: Compiling AMBER8
- AMBER: Compiling Amber8 on Mac OS X
- AMBER: Compiling Antechamber/Amber8 with ia64_ifort
- AMBER: compiling on SGI
- AMBER: Compiling question
- AMBER: compiling software(RESP)
- AMBER: compiling software(RESP) on MAC G5
- AMBER: Compiling using pgf90
- AMBER: compiling xleap on MAC OS X.3
- AMBER: compressed files
- AMBER: Computing psec/day using Amber 8
- AMBER: Config file for installing Amber 8 on PC with Windows XP
- AMBER: confusion about epsilon=4r for nmode calclation of nucleic acid
- AMBER: const-P MD at high T
- AMBER: constant pH simulations reference
- AMBER: Constant Pressure Problem of MD
- AMBER: constraints on atoms
- AMBER: constructing a small colecule
- AMBER: continue for No radius for F atom in MM_PBSA
- AMBER: Continued:No skew or curtosis when zero variance in moment
- AMBER: contributed parameters
- AMBER: contributed parameters (modified base - PSU)
- AMBER: conversion of Amber 7 .pdb file to .bgf file
- AMBER: conversion of amber trajectories to gromos /(xtc)
- AMBER: convert .pdb to .mol2
- AMBER: convert restart to mdcrd?
- AMBER: converting from NAMD trajectory format
- AMBER: Converting ORAC's topology file to AMBER's prepi file
- AMBER: Core Dump ERROR When Using TIP4P
- AMBER: Correl in Amber8: Diagonal elements not 1?
- AMBER: correlation in Amber 8
- AMBER: Could not assign parameters
- AMBER: cpinutil.pl error
- AMBER: Creating Parmtop files for NAMD
- AMBER: crosslink a residue with a small molecule
- AMBER: crystal lattice determination
- AMBER: Cubic Ice
- AMBER: Curves 5.3
- AMBER: cut offs in amber?
- AMBER: cut-off & MD
- AMBER: cys protecting group parameters
- AMBER: cys protecting groups parameters
- AMBER: CYS, CYX and CYM
- AMBER: DEBUG and GB
- AMBER: Decomposition in MMPBSA
- AMBER: Deeper problem with the energetics of the system
- AMBER: Defining residues
- AMBER: density calculation in AMBER output
- AMBER: DENSITY in constant pressure MD
- AMBER: description of toplogy file format?
- AMBER: details for Namelist problem
- AMBER: Diastereoisomers of ATP
- AMBER: DIELC
- AMBER: Dielectric Constant
- AMBER: difference in GBSOL in amber7 and amber8
- AMBER: Differences in RESP charges for G in RG and DG residues
- AMBER: different cooling schedules for simulated annealing
- AMBER: diffusion coefficient with external applied electric field
- AMBER: dihedral
- AMBER: dihedral driver
- AMBER: Dipole moment changes during MD
- AMBER: dipole moment in ptraj
- AMBER: distance between images
- AMBER: distance dependent dielectric
- AMBER: distance measurement in carnal and ptraj
- AMBER: Distance Restraints
- AMBER: distance-aromatic ring
- AMBER: Disulfide bond command
- AMBER: disulfide bonds
- AMBER: disulfide bonds/ Engineered
- AMBER: DMF box
- AMBER: DNA
- AMBER: Do I need to repeat MD simulation?
- AMBER: Do we have to optimize the structure in order to do MEP Calculations?
- AMBER: Does this warning matter? (about improper torsion parameters)
- AMBER: downloading antechamber
- AMBER: Dr. Herman Von Grafenstein
- AMBER: dummy atom other than H
- AMBER: Dummy Atoms: How to create them?
- AMBER: Dummy torsion paramters for thermodynamic integration
- AMBER: eedmeth
- AMBER: Electrolyte concentrations in MD
- AMBER: Electrostatic potential from the trajectory !
- AMBER: end point contribution in MCTI
- AMBER: Energy change for isomerization reaction of cyclic peptide
- AMBER: energy conservation with GB !!
- AMBER: energy criteria.
- AMBER: energy unit
- AMBER: Enthalpy of solvent-solute vanderWaals
- AMBER: entropy implementation in ptraj
- Amber: Equilibrated DMSO solvent box
- AMBER: equilibration does not start with SHAKE
- AMBER: erreo in sander
- AMBER: erroe in installing amber8
- AMBER: error estimates in AMBER
- AMBER: error for performing MD
- AMBER: error in antechamber
- AMBER: Error in building a molecule
- AMBER: error in installing amber8
- AMBER: error in minimization
- AMBER: error in mm_pbsa
- AMBER: error in using AM1-BCC charge by antechamber
- AMBER: error message about the input file of sander
- AMBER: Error message in antechamber
- AMBER: Error message while testing
- AMBER: error of performing simulation
- AMBER: error while loading shared libraries: libcxa.so.5
- AMBER: Error while protonating a PDB file
- AMBER: Errors in MM-PBSA???
- AMBER: errors in SGI
- AMBER: Errors when running tleap
- AMBER: ESP fitting from Gaussian03 cube files
- AMBER: esp or resp for all_amino94.lib
- AMBER: ESPGEN problems to read G03 output files
- AMBER: Euclidean distances
- AMBER: Ewald
- AMBER: EWALD BOMB?
- AMBER: Ewald calculation using PME for charged system
- AMBER: Ewald parameter range
- AMBER: exclusion list
- AMBER: execution time
- AMBER: extra points
- AMBER: extracting energy from trajector?
- AMBER: Extracting torsional angles for specific conformation
- AMBER: F90 compiler for linux ppc64
- AMBER: factor used in b-factor calculation
- AMBER: FAD cofactor.
- AMBER: Fe parameter
- AMBER: FEP - GIBBS of charged sidechains using IELPER
- AMBER: FEP along a reaction coordinate in sander
- AMBER: FEP and charges
- AMBER: FEP error/early termination - why?
- AMBER: Fifth European Workshop in Drug Design
- AMBER: file corruption with ptraj
- AMBER: File format generated by respgen
- AMBER: fit a 3D line to points
- AMBER: fix two groups
- AMBER: flexible water potential
- AMBER: Fluctuation in temperature
- AMBER: fluorine in mmpbsa
- AMBER: Force Compiling AMBER8 for an SGI O2
- AMBER: force field
- AMBER: found unknown atflg PB
- AMBER: frcmod_dmso
- AMBER: Free energies using Sander in Amber8
- AMBER: free energy
- AMBER: Free energy in Amber8
- AMBER: free energy perturbation
- AMBER: free energy perturbation questions
- AMBER: Free Energy Perturbation using Sander (TI Method)
- AMBER: free energy profile calculation
- AMBER: freezing atoms in impliciti solvent
- AMBER: From Andrew Box: Invitation and new email address
- AMBER: from gaussian to antechamber
- AMBER: Fwd: NVE & polarizable force field]
- AMBER: gaff "ha" atom type
- AMBER: gaff parameter ambiguities
- AMBER: gaff: hydrogen atom types
- AMBER: Gaussian 98 Installation
- AMBER: gaussian command line
- AMBER: Gaussian in RED
- AMBER: Gaussian Interface ?
- AMBER: gaussian03 output in antechamber
- AMBER: GB and Atom Type
- AMBER: GB and langevin dynamics
- AMBER: GB parameters for Calcium
- AMBER: GB+LES
- AMBER: GBSA frequency update
- AMBER: General Question about AMBER's Free Energy Perturbation Method
- AMBER: general questions
- AMBER: generalized Born parameters
- AMBER: generating parmfile containing topology and parameter information
- AMBER: getting new box info
- AMBER: GIBBS + vlimit exceeded
- AMBER: GIbbs : failure to start
- AMBER: Gibbs and solvent caps
- AMBER: gibbs calculation
- AMBER: gibbs compilation error
- AMBER: gibbs dynamic memory error
- AMBER: gibbs error
- AMBER: gibbs in amber8
- AMBER: gibbs termination
- AMBER: GIBBS: FEP and TI
- AMBER: Gigabit Ethernet Switch/Opteron 246
- AMBER: glibc version
- AMBER: GLYCAM web site
- AMBER: Glycam-04 Parameters in Amber 7
- AMBER: Glycam04
- AMBER: Glycam_04.prep
- AMBER: GO lie Amber simulation
- AMBER: Great help:Analysis mm_pbsa result
- AMBER: Group in sander
- AMBER: h bond
- AMBER: H bond calculation of CHARMM trajactory using PTRAJ
- AMBER: H Bonds
- AMBER: H-bonded waters selection
- AMBER: hbond analysis in ptraj(%occupied>1)
- AMBER: HBOND calculation
- AMBER: hbond in ptraj
- AMBER: Heme parameters
- AMBER: High B-factor!!
- AMBER: HIS protonation
- AMBER: histidine and its various forms
- AMBER: HIV-RT Nevirapin
- AMBER: Hot solvent/cold solute reference
- AMBER: How does LEaP place Na+ ions?
- AMBER: How is optimization done during energy minimization of the force field?
- AMBER: How many ions?
- AMBER: How to add ACE and NME groups?
- AMBER: how to add force field parameters
- AMBER: How to add H+ ion in leap?
- AMBER: How to apply OPLS force field?
- AMBER: how to calculate E-pot from restart file?
- AMBER: how to check metal ion bonding ?
- AMBER: How to choose force constant?
- AMBER: How to compile antechamber?
- AMBER: How to compile the downloadable RESP in UNIX
- AMBER: How to convert charmm parameters to amber
- AMBER: how to correct the charge of oligosaccharides
- AMBER: how to correctly change frcmod?
- AMBER: How to covalently bind a ligand to a residue?
- AMBER: how to deal with the initial structure?
- AMBER: How to make leap recognise inosine?
- AMBER: How to make leap recognise Zn2+?
- AMBER: How to neutralize system?
- AMBER: how to neutralize the peptide
- AMBER: how to prepare Zn.lib
- AMBER: how to read in CHARMM or AMBER binary trajectories
- AMBER: How to remove Cl- ions
- AMBER: how to set up more than 3 groups constrain
- AMBER: How to solve these warnings?
- AMBER: How to test the used parameters.
- AMBER: how to use mm_pbsa_statistics.pl independently
- AMBER: how to use prep file
- AMBER: How to use these parameters?
- AMBER: How to use tleap convert *.pdb file to *.crd and *.top files
- AMBER: how to visualize modes from PCA
- AMBER: Hydrogen Bond-statistics
- AMBER: hydrogen bonds
- AMBER: IBELLY
- AMBER: Ibelly and Ewald error message when ewald should be off
- AMBER: icc 8.0 built antechamber
- AMBER: Ideal bonds and angles
- AMBER: idecomp
- AMBER: IFC COMPILER
- AMBER: ifort -parallel
- AMBER: ifort 8.0
- AMBER: ifort installation
- AMBER: IGR1/grnam1 problem
- AMBER: image and restart problems
- AMBER: image in ptraj
- AMBER: Imaging problem
- AMBER: imin=5 in sander
- AMBER: Implicit 4r md
- AMBER: Implicit MD problem
- AMBER: Implicit MD simulation
- AMBER: Implicit Solvent Models
- AMBER: Implicit solvents
- AMBER: impose: Illegal angle internal definition
- AMBER: Improper dihedral
- AMBER: Improper Torsional Parameters
- AMBER: Improving PMEMD Performance on gigabit ethernet - CORRECTION
- AMBER: Improving PMEMD performance on gigabit ethernet Linux clusters
- AMBER: Increase lastrst in the &cntrl namelist
- AMBER: Increasing MAXATOM in antechamber
- AMBER: increasing the maximum value of NPHB parameter
- AMBER: information PROTON_INFO
- AMBER: input conversion error [Amber8]
- AMBER: instalation of amber7 on SUN
- AMBER: instalation of RES
- AMBER: Install Amber8 under cygwin
- AMBER: install problem
- AMBER: install RESP
- AMBER: Installation AMber 8: "cannot find -lU77"
- AMBER: Installation of AMBER8 on AMD cluster using pgf90
- AMBER: installation test question (antechamber, ash)
- AMBER: installing amber 8 on 64 bit amd opteron
- AMBER: Installing Amber on IBM AIX cluster
- AMBER: Installing AMBER on SGI Octane 2-CPU - erfcfun.c compile prob.
- AMBER: installing amber8
- AMBER: installing amber8 on a dual processor single box
- AMBER: installing RESP
- AMBER: INtel Fortran 90 compiler
- AMBER: Intel Fortran Compiler 8.0 / pmemd 3.1 warning
- AMBER: Intel fortran compiler and -static switch in older pmemd releases
- AMBER: Intel Fortran Compiler Problem
- AMBER: Intel Fortran Compiler, 7.1 status
- AMBER: intense and spectrum
- AMBER: intramolecular energies
- AMBER: intrinsic born radius of Br
- AMBER: ions in mm_pbsa
- AMBER: ions94.lib file
- AMBER: IOUTFM and binary/unformatted files error
- AMBER: Is AME equal to NME?
- AMBER: is it a bug in mmpbsa
- AMBER: Is it a bug?(in prep file opls_unict.in)
- AMBER: jump in temperature + problem in trajectory files
- AMBER: just sander not run
- AMBER: Kinetics energy
- AMBER: klambdas and Weights for Gaussian Quadrature
- AMBER: langevin dynamic in sander
- AMBER: langevin dynamics
- AMBER: Lattice structures in xleap
- AMBER: LCPO parameters in gbsa
- AMBER: Leap
- AMBER: Leap & x86_64 / PGI (was: xleap solvatebox/oct problem)
- AMBER: LEAP - Error loading units
- AMBER: leap - orientation of sequenced residues
- AMBER: Leap atom removal bug?
- AMBER: LEaP compilation error on Solaris 9
- AMBER: leap compiling problem on a 64-bit machine
- AMBER: Leap could not find atom type CK
- AMBER: leap problem in AMBER7 (residue insertion)
- AMBER: LEaP- Error reading frcmod parameters.
- AMBER: leap.log warnings
- AMBER: leap: impose
- AMBER: Lennard-Jones particle simulation
- AMBER: LES
- AMBER: LES error
- AMBER: LES methodology question
- AMBER: LES question
- AMBER: LES Simulations
- AMBER: lib file
- AMBER: Ligand from CCDC.
- AMBER: ligand minimization
- AMBER: LINMIN failure
- AMBER: literature question/residue charges
- AMBER: loading frcmod.mod_phipsi.1
- AMBER: Loading mol2 Files in XLEaP
- AMBER: loading PDB problem in leap
- AMBER: long minimization in sander
- AMBER: Low frequency in quasi-harmonic analysis!!
- AMBER: M7G parameters
- AMBER: MAC Based Beowulf Cluster
- AMBER: Mac OSX xleap compilation
- AMBER: make install error
- AMBER: make sure of the Magnesium parameters
- AMBER: MAXATOM failure in ANTECHAMBER
- AMBER: MAXMASK problem
- AMBER: MAXRING Antechamber problem
- AMBER: MAXRMSPT error in MOIL-view
- AMBER: MCSS
- AMBER: MD & folding
- AMBER: MD & net charge
- AMBER: MD & running time
- AMBER: MD after partially solvated
- AMBER: MD at different pH !!
- AMBER: MD for protein-carbohydrate complex
- AMBER: md problem
- AMBER: MD problem (very long parhabs endless runtime)
- AMBER: MD problem.
- AMBER: MD run: frozen
- AMBER: MD simulation : problem
- AMBER: MD simulation : problem :THANK YOU
- AMBER: MD simulation at pH=1
- AMBER: MD simulation of a DNA decamer
- AMBER: MD simulations on heparin and heparin sulfate
- AMBER: MD simulations with 2 molecules
- AMBER: MD with NTR + NMROPT
- AMBER: md's
- AMBER: md.out & plot
- AMBER: MD: Water network analysis + visualization
- AMBER: mdinfo on amber6
- AMBER: Membrane protein simulation
- AMBER: Memory for AMBER 6 simulation
- AMBER: memory problem in NMODE
- AMBER: memory prolem of the nmode calculation
- AMBER: metal atoms in Xleap
- AMBER: methane box
- AMBER: Minimiation (AMBER5/AMBER7) does not reach the tageted rmsd
- AMBER: minimizating complex-protein with AMBER
- AMBER: Minimization error
- AMBER: minimization of GLH
- AMBER: minimization output
- AMBER: minimization output file format
- AMBER: minimization problem
- AMBER: Minimum imaging
- AMBER: missing XaLeap_wcl file
- AMBER: MM binding energy with ANAL
- AMBER: mm-gbsa
- AMBER: mm-pbsa problem
- AMBER: MM-PBSA: molecular charges and active site water
- AMBER: mm-pbsa:- atom charges and radii ?
- AMBER: MM-PBSA:??Decomposition of receptor energies??
- AMBER: mm_gbsa results for charged ligands
- AMBER: mm_pbsa
- AMBER: mm_pbsa + vertex atom mismatch
- AMBER: mm_pbsa +fillratio
- AMBER: mm_pbsa Abmer8 example
- AMBER: MM_PBSA calculation error
- AMBER: MM_PBSA calculations
- AMBER: mm_pbsa energy decomposition error
- AMBER: mm_pbsa examples; delphi in mm_pbsa
- AMBER: mm_pbsa for Delphi
- AMBER: MM_PBSA GB parameters
- AMBER: mm_pbsa nmode problem
- AMBER: mm_pbsa problem
- AMBER: mm_pbsa question
- AMBER: mm_pbsa question: MAXAT=10000 exceeded
- AMBER: MM_PBSA reproduction of literature values and accuracy
- AMBER: mm_pbsa test problem
- AMBER: mm_pbsa.pl in Amber8
- AMBER: mm_pbsa.pl nmode entropy estimating problem
- AMBER: mm_pbsa.pl question
- AMBER: mm_PBSA: problems calculating molecular surface for some snapshots
- AMBER: MMPBSA PB parameters - PARSE implementation in Amber
- AMBER: MMPBSA problem
- AMBER: mmpbsa question
- AMBER: mmpbsa qustion
- AMBER: mmpbsa: can not generate coordinates/snapshots
- AMBER: modeling GPCR in lipid environment
- AMBER: modes analysis in ptraj
- AMBER: Moil View on Linux
- AMBER: Moil-view & Amber trajectory
- AMBER: MOIL-View question
- AMBER: Moil-view, prmtop, inpcrd question
- AMBER: mol2 vs. prepin
- AMBER: Molecular dynamic
- AMBER: Molecular dynamic & Acknowledgement
- AMBER: Molecular Frame
- AMBER: Molecular modelling.
- AMBER: Monte Carlo simulation
- AMBER: MOPAC 7 - How to modift the mopac.sh file to run antechamber properly?
- AMBER: mopac.sh
- AMBER: More AMBER 8 compilation problems on OSF1 4.0F
- AMBER: More details about free energy
- AMBER: More installation problems on Solaris 8
- AMBER: more vlimit exceeded problems...
- AMBER: MPICH problem
- AMBER: multiple heat bath GB+LES
- AMBER: multiple messages on the amber reflector
- AMBER: mutation of atoms
- AMBER: mutation of Tyr to Leu with TI
- AMBER: My strange result of TI.
- AMBER: N-terminal Arg charges in ff99 not 1.00
- AMBER: name error
- AMBER: Namelist problem
- AMBER: namelist problem solved
- AMBER: nanotube parameters
- AMBER: NB pairs exceeds?
- AMBER: nbflag
- AMBER: NEC and Regatta
- AMBER: neutral Arg, charged Tyr ??
- AMBER: Neutral C and N termini.
- AMBER: neutral residues
- AMBER: neutrality of charge in AMBER 7
- AMBER: new atom and increase the number of bonds
- AMBER: new leap with old gibbs
- AMBER: New problem on our 64bit box: xleap Segmentation fault
- AMBER: new wed site for amber tutorials
- AMBER: newer OPLS/AA?
- AMBER: NHE problem
- AMBER: Nitrogen vdw type
- AMBER: nmanal - segmentation fault
- AMBER: nmanal problem
- AMBER: nmode
- AMBER: nmode & mm-pbsa
- AMBER: nmode analysis
- AMBER: NMODE COMPILATION
- AMBER: Nmode convergence
- AMBER: nmode error
- AMBER: NMODE for protein via MM-PBSA-cntd
- AMBER: nmode problem
- AMBER: NMODE via MM-PBSA
- AMBER: nmode with mm/pbsa
- AMBER: nmode:Number of atoms in -p and -c files do not agree!
- AMBER: NMR constraint problem
- AMBER: NMR refinement
- AMBER: NMR restraint in sander
- AMBER: NMR restraints-Floating point exception
- AMBER: no 'water.lib' in /amber8/dat/leap/
- AMBER: No radius for F atom in MM_PBSA
- AMBER: No radius found for 2412 Zn Zn
- AMBER: No skew or curtosis when zero variance in moment
- AMBER: non-isotropic pressure scaling
- AMBER: non-periodic simulation and box information !!
- AMBER: nonpalar energy contribution-DMSO
- AMBER: Nonplanar ring systems in nucleic acid
- AMBER: normal mode analysis after energy minimizaiton using sander
- AMBER: Normal Mode Analysis possibility
- AMBER: Normal mode calculation with periodic boundary condition
- AMBER: Normal modes of protein-ligand
- AMBER: Nose Hoover chain thermostat
- AMBER: Note to all concerning filtering of messages posted to the amber list.
- AMBER: nrespa=2
- AMBER: NSCM
- AMBER: NSNB parameter
- AMBER: NSPSOL in parm file
- AMBER: NTF
- AMBER: NTR force constant for restraint !!
- AMBER: ntt parameter
- AMBER: NTT=0 and TAUTP
- AMBER: NTT=4
- AMBER: ntwprt feature in AMBER7
- AMBER: Nucgen and PNA?
- AMBER: nucgen generated RNA duplex: leap problems
- AMBER: nucgen problem
- AMBER: nucleic acid bases nonplanar during LES sim
- AMBER: NVE&polarizable force field
- AMBER: Octahedron Box
- AMBER: octavalent metal
- AMBER: off-subject ROCKS/Qbank
- AMBER: old trajectory file (amber6) to new trajectory file ?
- AMBER: One more question about the tree structure of looping residues
- AMBER: one question about dielectric dependent model
- AMBER: opteron 64 bit workstation
- AMBER: Opteron PMEMD
- AMBER: Opteron-64bit work station
- AMBER: Optimizing a structure and the interpretation of it
- AMBER: order parameter
- AMBER: output of mm_pbsa.log
- AMBER: Output of sander
- AMBER: overlap between HE and OE in GLH
- AMBER: oxs g5 machine file
- AMBER: oxygen positions around a DNA
- AMBER: Pang Zn2+ model - correction
- AMBER: Pang-model of Zn2+
- AMBER: parallel installation problem
- AMBER: parallel of sander_classic
- AMBER: parallel Sander (amber8): run-time error under Irix
- AMBER: parameter
- AMBER: parameter development
- AMBER: parameter development for nucleotide analogues
- AMBER: parameter error for a ligand
- AMBER: Parameter for chlorophyll
- AMBER: Parameter generation from RESP charges
- AMBER: parameter set
- AMBER: Parameters for deuterium
- AMBER: Parameters for Inosine
- AMBER: Parameters for ions?
- AMBER: parameters for neutral Arg
- AMBER: Parameters for new residue?
- AMBER: Parameters for nonpolar contribution to solvation
- AMBER: Parameters for phosphorylated aminoacids
- AMBER: parameters-DGnp
- AMBER: parametrizacion partial charges
- AMBER: parametrization problem
- AMBER: paramitrization problem
- AMBER: parm94
- AMBER: Parm98 Vs 02
- AMBER: parmcal problem
- AMBER: PARMSCAN
- AMBER: PARSE radius for P
- AMBER: Partial Charge on ligand for MD & MM/PBSA
- AMBER: partition error in shake
- AMBER: Pasrameters for MAI
- AMBER: PB Bomb in pb_reslist(): maxnbr too small
- AMBER: PB bomb in pb_saarc
- AMBER: PB in mm-pbsa
- AMBER: pb_bomb in setgrd()
- AMBER: PBC in sander
- AMBER: PBCAL in mm-pbsa calculation
- AMBER: PBCAL in MM/PBSA
- AMBER: PBCAL in mmpbsa
- AMBER: pbsa
- AMBER: pbsa calculation on part of the molecule
- AMBER: pbsa calculation on part of the molecule & nmode analysis
- AMBER: pbsa error in mm_pbsa amber 8
- AMBER: PBSA parameter question (Radii and Charges)
- AMBER: PCA prep file
- AMBER: PDB files
- AMBER: pdb in RED
- AMBER: peoblemwith RED II
- AMBER: peptide-DNA crosslink modeling
- AMBER: performance of amber7/xlf/macosX 10.3 with JAC on xserve g5@2.0GHz
- AMBER: performance of periodic vs. non-periodic simulation
- AMBER: Periodic boundary simulation
- AMBER: PERT.charge problem in xleap
- AMBER: perturb a water to a dummy water with shake
- AMBER: PF6- force field parameters
- AMBER: PGA
- AMBER: pH effect on protein folding
- AMBER: phosphorylated serin / histidin
- AMBER: Phosphoserine
- AMBER: phosphoserine library component
- AMBER: Phosphoserine parameters
- AMBER: phosphothreonine
- AMBER: PKA calculation
- AMBER: pka questions
- AMBER: Plot B-factor extracted from PDB file
- AMBER: pls forget my first question in my last email
- AMBER: PMEMD
- AMBER: PMEMD and ifort 8 update
- AMBER: pmemd and ifort 8.1
- AMBER: pmemd and mpich - myrinet
- AMBER: PMEMD and myrinet trouble
- AMBER: PMEMD and nmropt=1
- AMBER: PMEMD Built ? Wont run..
- AMBER: PMEMD COMPILATION REDHAT
- AMBER: pmemd config.h request for athlon
- AMBER: pmemd machinefiles
- AMBER: pmemd problems
- AMBER: PMEMD Problems...
- AMBER: PMEMD scaling
- AMBER: pmemd speedup and interactions
- AMBER: pmemd.
- AMBER: pmemd. - OOPS!!!
- AMBER: PMF
- AMBER: pmf calculation using gibbs
- AMBER: pmf calculation using gibbs.
- AMBER: PMF correction factor
- AMBER: POPE membrane, How to obtain prep and parm files?
- AMBER: positive binding free energy
- AMBER: positive VDWAALS
- AMBER: Possible amber8 antechamber PDB parsing bug
- AMBER: prep file
- AMBER: prep file for zinc finger
- AMBER: prep files for modified bases
- AMBER: Preparing complex in Xleap for Amber calculations
- AMBER: principal axis
- AMBER: Principal Component Analysis
- AMBER: Problem : antechamber produces no output
- AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler
- AMBER: Problem compiling amber7
- AMBER: problem for compiling amber7 by ifc8
- AMBER: problem in antechamber
- AMBER: Problem in loading a PDB file in Leap - Please help me
- AMBER: problem in quasih.f diagonalising matrix
- AMBER: problem loading mdcrd to VMD
- AMBER: problem loading molecule in leap
- AMBER: problem loading pdb in leap.
- AMBER: problem not with sander, but with mpich
- AMBER: Problem solved
- AMBER: problem solved: leap compiling problem on a 64-bit machine
- AMBER: Problem to converge minimization
- AMBER: Problem to update antechamber package.
- AMBER: Problem using GLYCAM with sander
- AMBER: Problem with a single aminoacid as inhibitor
- AMBER: Problem with AMBER/ANAL
- AMBER: problem with antechamber
- AMBER: Problem with carnal on linux
- AMBER: Problem with computing Resp charges using RED
- AMBER: Problem with converting AMBER PREP to MOL2
- AMBER: Problem with divcon - increasing MXATTS?
- AMBER: Problem with EDIT (AMBER 5)
- AMBER: problem with frcmod file
- AMBER: Problem with installing Amber8: Where are the MK libraries?
- AMBER: Problem with MacroMolecule to AMBER7
- AMBER: Problem with menu bar in LEAP
- AMBER: Problem with minimisation of an protein-inhibitor complex
- AMBER: problem with MM/PBSA
- AMBER: problem with protonate
- AMBER: Problem with sander - Error on Open
- AMBER: Problem with sander tutorial.
- AMBER: problem with tleap in Amber
- AMBER: Problem with Water solute during MD
- AMBER: Problem: Installing Amber8 on PC with Windows XP
- AMBER: Problems in Amber MPI version (64 bits machine)
- AMBER: problems in using glycam
- AMBER: problems to run ptraj
- AMBER: Problems using mm_pbsa.perl
- AMBER: Problems with amber8 and pgf90
- AMBER: Problems with Carnal coordinate average
- AMBER: Problems with CPU scaling on cluster
- AMBER: problems with dihedrals
- AMBER: problems with dihedrals - extended information
- AMBER: problems with extra points
- AMBER: problems with mdcrd
- AMBER: problems with mpich
- AMBER: Problems with processing SYBYL-Tripos pdb files in LEAP
- AMBER: Problems with X.R.E.D.
- AMBER: Problems with xleap
- AMBER: process_mdout.perl
- AMBER: process_mdout.perl: work now
- AMBER: production input file
- AMBER: program compatibility
- AMBER: Program error in testing of Amber8
- AMBER: protein - fractional native contacts
- AMBER: protein is out of the water box
- AMBER: Protein MD
- AMBER: Protein with maximum hydrogen bonds
- AMBER: protein-carbohydrate complex
- AMBER: protein-protein interaction
- AMBER: protonation
- AMBER: ptraj
- AMBER: ptraj & LES
- AMBER: ptraj -- velocities set to zero?
- AMBER: ptraj analyze matrix entropy
- AMBER: ptraj analyze modes question
- AMBER: ptraj and clustering
- AMBER: ptraj and dipoles
- AMBER: ptraj and dipoles....
- AMBER: ptraj and hbond
- AMBER: ptraj and LES
- AMBER: ptraj and PCA
- AMBER: ptraj bug?
- AMBER: Ptraj data
- AMBER: ptraj hbond memory allocation on opteron
- AMBER: ptraj parser
- AMBER: ptraj problem
- AMBER: ptraj projections help
- AMBER: ptraj questions
- AMBER: ptraj radial
- AMBER: ptraj read in matrix
- AMBER: ptraj-6.5
- AMBER: ptraj-closestwaters command
- AMBER: ptraj: load crd without hydrogen (i.e. missing parm file)
- AMBER: ptraj: radius of gyration
- AMBER: Pulling versus Distance Restraints
- AMBER: pure aromatic?
- AMBER: Question about Amino acid mutations
- AMBER: question about antechamber program
- AMBER: question about building initial structure
- AMBER: question about building prmtop and inpcrd files in xleap
- AMBER: question about compilation of AMBER8 on MANDRAKE9.2
- AMBER: Question about compiling PMEMD
- AMBER: question about covariance matrix from ptraj
- AMBER: question about delphi and UHBD
- AMBER: Question about dummy atoms
- AMBER: question about force field
- AMBER: question about image
- AMBER: question about image - truncated octahedron
- AMBER: question about J. Am. Chem. Soc. 2001, 123, 5221 paper
- AMBER: question about LES simulation
- AMBER: question about md's
- AMBER: question about MGB and PB
- AMBER: question about mm-pbsa
- AMBER: question about mm_pbsa and nmode
- AMBER: question about mmpbsa
- AMBER: question about molsurf
- AMBER: question about nmode
- AMBER: question about NMODE for RNA
- AMBER: Question about Parallel Compilation
- AMBER: question about parallel simulation
- AMBER: question about production runs
- AMBER: question about ptraj
- AMBER: question about Ptraj - AND OR
- AMBER: question about ptraj's Mask
- AMBER: question about replica exchange in amber8
- AMBER: Question about restart MD
- AMBER: Question about RMSD calculation
- AMBER: question about the average structure from ptraj
- AMBER: question about water molecule
- AMBER: Question about Xleap
- AMBER: Question Amber8 install errer with Windows
- AMBER: Question concerning ANAL total energy calculation
- AMBER: Question for PMEMD users
- AMBER: Question on Amber7...
- AMBER: Question on Clustering Analysis
- AMBER: question on minimization
- AMBER: question on mm-pbsa
- AMBER: question on NAB
- AMBER: question on NMR restrain
- AMBER: question on simulated annealing
- AMBER: Question on tleap of amber8
- AMBER: question!
- AMBER: Questions about MD sampling
- AMBER: questions about mmpbsa
- AMBER: questions about NMODE
- AMBER: Questions about pert.charge and atom type change.
- AMBER: questions for PNA parameters
- AMBER: questions on dummy atom types in FEP setup
- AMBER: questions on mm_pbsa
- AMBER: Questions on simulating dendrimer in AMBER.
- AMBER: questions parm94/99 ff secondary structure
- AMBER: questions regarding JTREE
- AMBER: R.E.D.
- AMBER: R.E.D. II to Vlad
- AMBER: radial distribution
- AMBER: radius of gyration
- AMBER: rdparm problem
- AMBER: rdparm/ptraj writeparm
- AMBER: rdparm/ptraj writeparm + leap problem
- AMBER: rdparm: a parameter array overflowed
- AMBER: Re. HSG Convention
- AMBER: recompiling amber8
- AMBER: recovering total force array
- AMBER: RED
- AMBER: RED BUG!!!
- AMBER: RED BUG!!!!...perhaps I fixed it
- AMBER: RED fails to read g94 output
- AMBER: Redhat install
- AMBER: reference with ptraj
- AMBER: references?
- AMBER: Regarding Dielectric Constant in AMBER8
- AMBER: regular ewald sum in Amber8
- AMBER: Release announcement for Amber 8
- AMBER: REM make test
- AMBER: Removal of rotation: Flying ice cube
- AMBER: remove rotational motion
- AMBER: reorientation in R.E.D
- AMBER: replica exchange with thermodynamic integration
- AMBER: Reproducing the energy during restart in MD!
- AMBER: reproduction of RESP charges for Gly
- AMBER: Resend: Problem with converting AMBER8 PREP to MOL2
- AMBER: residence time
- AMBER: Residue Charges
- AMBER: residue database
- AMBER: residue insertion
- AMBER: Residue Loading Problem
- AMBER: Residue question
- AMBER: Resizing sizes.h and recompiling problem!
- AMBER: RESP calculation with different multiplicities
- AMBER: resp charge calculation for Fe+3 heme
- AMBER: RESP charge derivation
- AMBER: RESP charges for protein fragment
- AMBER: RESP charges in Fe+3 heme system
- AMBER: resp demo files
- AMBER: resp error message
- AMBER: RESP partial charge calculation
- AMBER: RESP problem...
- AMBER: RESP vs. AM1-BCC charges for isoprene
- AMBER: respgen
- AMBER: REST
- AMBER: restart a MD after replacing molecules
- AMBER: restart calculation
- AMBER: RESTARTED DUE TO LINMIN FAILURE ...
- AMBER: restrain on the distance between two molecules.
- AMBER: restrain one tosion angle
- AMBER: Restrain or freeze molecule question?
- AMBER: Restrained minimization problem
- AMBER: restrained options
- AMBER: restraining internal coordinates
- AMBER: restraint
- AMBER: restrainted torsion
- AMBER: restraintmask and ambmask
- AMBER: restraintmask problem in ptraj
- AMBER: restraints error
- AMBER: Restraints in sander.QMMM
- AMBER: restrt
- AMBER: Rigid counteranion during MD !!
- AMBER: rms fluct and displacement in modes analysis
- AMBER: rms fluctuation units from ptraj
- AMBER: rms in ptraj
- AMBER: RMS of energy in Minimization using SANDER
- AMBER: RMSD calculations in ptraj and Carnal
- AMBER: RMSD of ligand
- AMBER: rmsd over residues using ptraj
- AMBER: RMSD result from GB model
- AMBER: RNA sequence with DNA backbone?
- AMBER: RSM & ptraj
- AMBER: RSM fluctuation & residues
- AMBER: RSM fluctuation by residues
- AMBER: rstdip
- AMBER: Run calculations for protein in Amber
- AMBER: Run calculations for protein in Amber-distance dependent dielectric function
- AMBER: running MD simulatons
- AMBER: running on Itanium machines
- AMBER: Running on MPI
- AMBER: salt bridge detection
- AMBER: salt concentration
- AMBER: Sander
- AMBER: Sander & fix atoms
- AMBER: sander + child process died
- AMBER: sander + ew_legal.h
- AMBER: sander + ewald bomb
- AMBER: sander + vlimit exceed...
- AMBER: SANDER - Abnormal high velocities
- AMBER: sander : constraints to conserve hydrogen bonds
- AMBER: Sander : Vrand flag
- AMBER: sander and mpich
- AMBER: sander and mpich (which compilers/mpich work)
- AMBER: SANDER BOMB in subroutine nonbond_list
- AMBER: sander error
- AMBER: SANDER general questions.
- AMBER: sander gets stuck
- AMBER: sander imin=5
- AMBER: sander in parallel, amber8
- AMBER: Sander klambda question
- AMBER: sander of AMBER 8 doesn't work
- AMBER: sander on multiprocessors
- AMBER: sander output
- AMBER: Sander problem with different CPU
- AMBER: Sander TI
- AMBER: Sander TI with NTR = 1.
- AMBER: sander tutorial
- AMBER: Sander went through
- AMBER: sander, MD problems
- AMBER: Sander-7 for Win32
- AMBER: sander.LES on IBM SP cluster
- AMBER: sander.QMMM on Mac
- AMBER: sander.QMMM: CHARGE keyword in divcon.in file
- AMBER: sander7 on quad opteron
- AMBER: sander8
- AMBER: sander8 compile: myrinet and mpigm
- AMBER: sander8 performance
- AMBER: sander_classic for cap simulations?
- AMBER: saveamberparm warning in leap?
- AMBER: savepdb vs ambpdb
- AMBER: saving trajectory parameters
- AMBER: scali amber8
- AMBER: scaling 1-4 NB interaction for rings
- AMBER: Scaling nb between groups
- AMBER: script on tutorial page
- AMBER: segmentation fault
- AMBER: Segmentation fault (core dumped) error of antechamber program
- AMBER: segmentation fault in leap
- AMBER: Segmentation fault in SaveAmberParm
- AMBER: segmentation fault of minimization
- AMBER: segmentation fault when convert pdb to mol2
- AMBER: segmentation fault when running parmchk
- AMBER: segmentation fault with sander
- AMBER: separate the longitudinal and transverse vibrations frequencies
- AMBER: Setting up thermodynamic integration
- AMBER: Settings about frozen atoms in sander
- AMBER: Setup for parallel computing
- AMBER: SHAKE in thermodynamic integration
- AMBER: shake option in sander
- AMBER: SHAKE probelm
- AMBER: SIGSEGV
- AMBER: simulated anealing ...vlimit exceed
- AMBER: Simulated anealling
- AMBER: simulated annealing
- AMBER: Simulated annealing ...vlimit problem
- AMBER: simulated annealing..
- AMBER: Simulation of lipid bilayers
- AMBER: single amino acid energy
- AMBER: single strand simulation
- AMBER: size.h error
- AMBER: Slowly releasing restraints
- AMBER: small molecule simulation
- AMBER: snapshots of MD trajectory
- AMBER: Software to visualize normal modes!
- AMBER: Solaris f77 Machine file for Amber7?
- AMBER: solute leaving PBC box
- AMBER: solvate proteins in xleap/amber8
- AMBER: solvateCap warning
- AMBER: solvation energy
- AMBER: solvation free energies using mmpbsa
- AMBER: solvation free energy
- AMBER: Solvation free energy of a charged molecule.
- AMBER: Solvent accessible surface area(LCPO) computation
- AMBER: solvent cap and eedmeth
- AMBER: Solvent exposure measurement
- AMBER: solvents reference.
- AMBER: some bugfixes
- AMBER: Some questions in building a new residue
- AMBER: some questions....
- AMBER: Sorry about that...
- AMBER: Spike in energy and RMS
- AMBER: Star like (branching) molecule
- AMBER: strange bond energies
- AMBER: strange output of MD
- AMBER: Suface area parameter for fluorine in MM/PBSA
- AMBER: Suggestions for newer pentium chips and hyperthreading with PMEMD
- AMBER: Surface E&S Potential Mapping
- AMBER: SUSE 9.1 and AMBER 8
- AMBER: Suse AMD64 cluster installation
- AMBER: target rmsd
- AMBER: Temp control
- AMBER: temperature control in coupled potential runs
- AMBER: temperature in DelPhi for MM-PBSA calculation
- AMBER: Temperature in Nmode
- AMBER: Temperature Regulation
- AMBER: temperature scaling with ntt=3(Langevin thermostat)
- AMBER: TER in amber
- AMBER: test
- AMBER: Test Calculation of atomic charges (RESP) for RNA bases
- AMBER: test output of amber8
- AMBER: Test run error in amber8 : IBM-AIX
- AMBER: Testing Delphi for mm_pbsa
- AMBER: TFE parameters
- AMBER: Thank you
- AMBER: The charge given by xleap from amber 5
- AMBER: The convergence of energy minimisation
- AMBER: the energy difference between sander and nmode
- AMBER: The first and second derivatives
- AMBER: The parallel problem for umbrella sampling in Amber 8
- AMBER: The question about SAS calculation in MM_PBSA
- AMBER: the uses for Amber FFs
- AMBER: thermal ellipsoid-DNA
- AMBER: thermodynamic integration of ring opening
- AMBER: Thermostat comparison ?
- AMBER: Ti of CH3 -> NH2
- AMBER: TI with electrostatic decoupling
- AMBER: TI with sander
- AMBER: TI, angle parameters for nitrogen, frcmod
- AMBER: Time to minimize the energy by NMODE
- AMBER: time-averaged restraints
- AMBER: TIP4P
- AMBER: TIP4P extended
- AMBER: Titratable amino acid termini
- AMBER: tleap - FATAL error
- AMBER: tleap error and warnings
- AMBER: tleap input file error
- AMBER: tleap: automatically identify and connect disulfide bonds?
- AMBER: tmd question
- AMBER: tmd questions
- AMBER: TOP file in AMBER7/8
- AMBER: torsion angles
- AMBER: torsion scan
- AMBER: torsion term
- AMBER: traj. analysis
- AMBER: trajectory
- AMBER: Trajectory corruption
- AMBER: Trajectory file
- AMBER: Trajectory file conversion between Amber & Charmm
- AMBER: trajectory file corruption
- AMBER: trajectory file question?
- AMBER: translational and rotational entropy
- AMBER: Treating atom type LP the same as EP
- AMBER: trival question about format of pev file and covariance matrix
- AMBER: Trouble running molecular dynamics with an increase in temp in Sander