 | |||||||||||||||
 |
 |
 |
|
 |
|
 |
|
 |
|
 |
|
 |
|
 |
 |
AMBER Archive (2005) - By Subject
3972 messages sorted by: [ author ] [ date ] [ thread ]About this archive
Starting: Sat Jan 01 2005 - 08:25:14 CST
Ending: Sat Dec 31 2005 - 12:51:27 CST
- 75% Off for All New Softs Now! haberman
- [pgannett@hsc.wvu.edu: AMBER: compiler error, SGI Octane]
- A new rollax repliccas is in the mark. attitudinal
- about run time in GB and PB
- Amber 8 dual-Xeon compile problem
- amber 8 problem
- Amber 8 with lam compilation problem
- AMBER :LINMIN problem
- Amber installation
- AMBER Test Error (Follow Up)
- AMBER:
- AMBER: "ERROR TERMINATION DUE TO SHAKE OR TORCON" in Gibbs
- AMBER: "personality" of Amber force field
- AMBER: "The system has extended beyond" error
- AMBER: &dipoles in sander
- AMBER: (no subject)
- AMBER: *** Proper torsion parameters missing ***
- AMBER: .dat and frcmod files
- AMBER: 1-4 scaling factors
- AMBER: 10-12 potential and create atom type
- AMBER: 6-thioguanine
- AMBER: [FWD] water minimalization problems
- AMBER: [OT] A nab programming question
- AMBER: a bimolecular reaction
- AMBER: A few question about RDF input preparation
- AMBER: a nomenclature question
- AMBER: A problem about Gaussian
- AMBER: A problem about removing waters and counterions by ptraj
- AMBER: a problem encountered when trying to equalibrate alanine dipeptide in explicit water
- AMBER: A problem in TI approach - test case: meth2eth and eth2meth
- AMBER: a problem with mm_pbsa
- AMBER: a question about varying positions of dihedral restraints with step number
- AMBER: A question on connecting residues in xleap
- AMBER: a quistion about compile
- AMBER: a trivial question
- AMBER: about antechamber(amber8)
- AMBER: about equilibration dynamics
- AMBER: About Gaussian Key Words
- AMBER: About Gaussian Key Words (fwd)
- AMBER: about install amber8 on windows
- AMBER: About NAB
- AMBER: about radius of Br in MMPBSA calculation
- AMBER: about resp
- AMBER: about run time in GB and PB
- AMBER: about salt bridges
- AMBER: About Salt concentration
- AMBER: about the %occupied of hydrogen bond
- AMBER: About WHAM program
- AMBER: acceptor and donor in hbond calculation
- AMBER: across-correlation in ptraj
- AMBER: Add constraints over time
- AMBER: add waters to a system + leap problem with solvateOct command
- AMBER: Adding residues to a DNA sequence
- AMBER: Adding/recognizing calcium atoms
- AMBER: addition to the last mail (lahey F95) !
- AMBER: addles question
- AMBER: adenine test for LMOD in amber8
- AMBER: advice needed for minimization and dynamic protocol
- AMBER: again: F, Cl, Br, I in MMPBSA
- AMBER: AIX problem
- AMBER: align snapshots to a reference
- AMBER: Alignment tensor and Interia tensor
- AMBER: All the tests passed except prmtop and prepin...
- AMBER: AMBBER: ptraj question
- AMBER: Amber 7 Compiler Error
- AMBER: Amber 8 : installation problems : undefined reference to `mpi_allreduce_'
- AMBER: AMBER 8 : Water cap problem
- AMBER: Amber 8 and LAM compilation problem
- AMBER: Amber 8 and PATH buffer overflow
- AMBER: amber 8 benchmarks dec alpha
- AMBER: AMBER 8 compilation with lahey F95 !
- AMBER: amber 8 installation
- AMBER: AMBER 8 installation problem -- undefined reference to `EXIT'
- AMBER: amber 8 leap topology file dihedral term problem
- AMBER: Amber 8 on cygwin install problem
- AMBER: amber 8 problem
- AMBER: amber 8 REM possible test problem
- AMBER: amber 8 system requirements
- AMBER: Amber 8 with lam compilation problem
- AMBER: AMBER 8.0 problems with impose (tleap) on linux
- AMBER: Amber 8: all_nucleic94.lib nucleotide geometry
- AMBER: Amber 8: create topology for solvent - PBC box size problem
- AMBER: AMBER 8: Freeze AND restrain questions
- AMBER: Amber 8: heterogeneous multiple copy LES method
- AMBER: Amber 8: questions about free energy perturbation
- AMBER: AMBER antechamber; dimenion size
- AMBER: amber code
- AMBER: AMBER compilation - RH Enterprise 4, Xeon EM64T
- AMBER: AMBER compilation error
- AMBER: Amber compilation on opteron with PGI compiler
- AMBER: amber compilation on SGI ALTIX 350 (TEST FAILD)
- AMBER: Amber compilation problem
- AMBER: AMBER compilation with -DREM
- AMBER: Amber crashes at simulation in the NVT ensemble with the periodic box equiilbrated in the NPT ensemble.
- AMBER: amber file formats.
- AMBER: AMBER frcmod+off input vs. prep input
- AMBER: AMBER goes in a Loop
- AMBER: Amber Installation
- AMBER: AMBER on g5 10.4 w/g95 or gfortran
- AMBER: AMBER on Mac OS X
- AMBER: amber on sgi
- AMBER: Amber parameters for ADP
- AMBER: Amber PBMD:Energy fluctuation
- AMBER: Amber Performance in Parallel on Itanium
- AMBER: Amber Poisson-Boltzmann MD :Equilibration Problem
- AMBER: amber question about leap
- AMBER: AMBER related employment
- AMBER: AMBER Test
- AMBER: AMBER Test Error
- AMBER: AMBER tests (x86-64, PGI / Intel)
- AMBER: AMBER topology file format
- AMBER: AMBER tutorial ambpdb question
- AMBER: AMBER under MOSIX?
- AMBER: AMBER vs QM: base pairing and stacking
- AMBER: amber with mpich-G2
- AMBER: AMBER-process_mdout.perl
- AMBER: Amber7 nmropt
- AMBER: AMBER7 xleap problem
- AMBER: amber7.0: F,Br,radius in MMPBSA
- AMBER: amber8 and moil-view
- AMBER: AMBER8 Build on Linux x64 running Opterons
- AMBER: Amber8 compilation error
- AMBER: AMBER8 Compile Error on Dual Opteron
- AMBER: AMBER8 crashes machine(nodes) under IBM compiler, Suse Linux, amd IBM loadleveler
- AMBER: amber8 in IBM-SP4
- AMBER: Amber8 installation on IBM (power4) with SUSE 9.1 Linux (IBM XLF compiler)
- AMBER: amber8 installation problems
- AMBER: Amber8 installation problems on Sparc/Solaris9
- AMBER: Amber8 installation test possible failures
- AMBER: AMBER8 limitation of memory in QM/MM calculation
- AMBER: Amber8 Parallel installation troubles
- AMBER: amber8 parallel sander
- AMBER: Amber8 Solaris installation failure
- AMBER: amber8 test error
- AMBER: amber8/antechamber installation problem
- AMBER: AMBER8: compiling under cygwin using lahey fortran
- AMBER: amber8installation
- AMBER: Amber: sander error segmentation fault.
- AMBER: ambpdb core dump
- AMBER: ambpdb radii
- AMBER: ambpdb TER problems
- AMBER: An atom name with 4 characters is not compatible with Leap ?
- AMBER: An error during minimization using RED
- AMBER: Anal - problems with energy analysis
- AMBER: anal and periodic boundary conditions
- AMBER: ANAL module/AMBER8
- AMBER: ANAL problem
- AMBER: Analysing my simulation data..
- AMBER: Andersen thermostat: target T?
- AMBER: aniso and iso
- AMBER: Announcing the LMOD website
- AMBER: Announcment: Nucleic Acid Builder (NAB) version 5 is released
- AMBER: Another question about surface area calculation
- AMBER: antechamber
- AMBER: ANTECHAMBER & DIVCON
- AMBER: antechamber + mopac failure
- AMBER: antechamber -- missing improper torsions
- AMBER: Antechamber -reorders atom sequence
- AMBER: antechamber and multiplicity
- AMBER: antechamber availability
- AMBER: antechamber charge methods
- AMBER: antechamber dimesion size, again
- AMBER: Antechamber error
- AMBER: Antechamber error "Cannot successfully assign bond type for this molecule"
- AMBER: antechamber error message
- AMBER: antechamber for cyano group
- AMBER: Antechamber help needed
- AMBER: antechamber not working .. for thio residue..
- AMBER: antechamber problem
- AMBER: antechamber problem using RESP
- AMBER: antechamber problems
- AMBER: Antechamber RESP failed for large organic molecule
- AMBER: antechamber, reference?
- AMBER: Antechamber/Divcon assigned charges
- AMBER: Antechamber/formatting question
- AMBER: Antechamber/Leap, problem with Improper angles
- AMBER: Any way to get different charge on same type atom
- AMBER: Apologies - LMOD website down
- AMBER: archive
- AMBER: Are the constant pH simulations with explicit water possible?
- AMBER: Argon Box
- AMBER: Ask for helpf to get examples for MM-PBSA with AMBER8
- AMBER: Asking how to creat alanine "dipeptide" in amber8
- AMBER: atmtypenumbers
- AMBER: ATOM TYPE
- AMBER: Atom type :Si
- AMBER: atom type designation
- AMBER: atom type for -CH=CH-
- AMBER: Atom type problem
- AMBER: atom type question
- AMBER: atommask error
- AMBER: atommask question
- AMBER: Atoms restrain
- AMBER: ATTN REVISION
- AMBER: average struct without solvent
- AMBER: average structure
- AMBER: average structure after MD
- AMBER: average structure-ptraj
- AMBER: bad atom type: H
- AMBER: big fluctuation in MM-PBSA/GA
- AMBER: Bio-Image summer school in Paris this year
- AMBER: blows up
- AMBER: Bond angle restraints setting files
- AMBER: bond breaking/ energetic ion
- AMBER: bond connectivity among dummy atoms
- AMBER: bond parameters
- AMBER: bond type for a virtual bond in a biomolecular transition state
- AMBER: Boron and Amber
- AMBER: box size in explicit water
- AMBER: breaking symmetry in minimization
- AMBER: broblem of replica exchange MD with polarizable force field
- AMBER: Bromelain PDF xleap load error
- AMBER: Bromelain PDF xleap load error (Proton Problems?)
- AMBER: bug report
- AMBER: bugfix 49
- AMBER: Build an acetone Box
- AMBER: Build for single precision
- AMBER: Build of AMBER for YDL ?
- AMBER: building amino acid based surfactants?
- AMBER: building helix bundle
- AMBER: building monosaccharides with glycam force field
- AMBER: building nucleic acids
- AMBER: Bus error - ambpdb
- AMBER: Calculate vdw parameters for alkaline earth metal ions
- AMBER: calculating electrostatic potential
- AMBER: calculating end-end distance
- AMBER: calculating hydrogen bonds
- AMBER: Calculating of radius of gyration in Carnal
- AMBER: calculating time correlation functions with ptraj
- AMBER: calculating torsion angles
- AMBER: Can constant pH be used for minimization?
- AMBER: Can GB and MS work correctly together in mmpbsa?
- AMBER: Can I add iodide anione?
- AMBER: Can I get each corresponding sanpshots' delta delta energy term from mm_pbsa
- AMBER: can I setup a simulation with restrain the COM of a group to a reference structure?
- AMBER: Can I trust ANAL result?
- AMBER: Can REM be used as multiple normal sander jobs on parallel machine
- AMBER: Can someone recommend a tutorial?
- AMBER: Can we load prmtop and inpcrd files into xleap?
- AMBER: cap and ptraj
- AMBER: cap simulations questions
- AMBER: capping
- AMBER: capping?
- AMBER: Carbonane
- AMBER: carnal - water-mediated HBond
- AMBER: Carnal in Amber8
- AMBER: carnal problem
- AMBER: cavity volume
- AMBER: CD spectrum
- AMBER: center-of-mass distance restraints
- AMBER: change of prmtop file
- AMBER: charges
- AMBER: charges difference of atom in xleap and prmtop
- AMBER: check in leap
- AMBER: checkoverlap
- AMBER: Citing Generalized Born Implicit solvent Model (igb=5)
- AMBER: Citing the PBSA module of AMBER8
- AMBER: classes
- AMBER: Cluster - input files
- AMBER: cluster analysis
- AMBER: Cluster analysis by MMTSB or ptraj
- AMBER: clustering
- AMBER: Clustering - MMTSB Toolkit kclust
- AMBER: clusters
- AMBER: collision frequency in GBSA dynamics
- AMBER: combine mdcrd using ptraj
- AMBER: Comparing EELEC from amber and that calculated in the trivial fashion.
- AMBER: comparing md trajectories
- AMBER: Comparison of AMBER against DL-POLY
- AMBER: compilation problem (Mac OS X.4)
- AMBER: Compilation problem at dual processor linux !
- AMBER: compile amber8 on RHEL4
- AMBER: Compile Error on Running Amber on AMD opterons in the Linux-based clusters
- AMBER: Compile Problems of Parallel Amber8 on Mac G5
- AMBER: Compile question??
- AMBER: compiler
- AMBER: compiler error, SGI Octane
- AMBER: compiler for amber8 on opteron
- AMBER: Compiling AMBER 8 for Mac OSX (Parallel)
- AMBER: compiling amber with pgi 5.2.4
- AMBER: Compiling Amber7 wint Intel Fortran v8 Compiler
- AMBER: Compiling just sander
- AMBER: compiling leap with Xeon EM64 (suse linux 9.2)
- AMBER: Compiling on dual-opteron with pathscale 2.1 on RHEL 4 AS
- AMBER: compiling pmemd on dual xeon
- AMBER: Compiling/Runing on BSD - emulation and/or gfortran (Linux and BSD)
- AMBER: Conformational energy (QM) for parameterization
- AMBER: conformational sampling of a peptide
- AMBER: Connecting two molecules
- AMBER: constant pressure vs. constant volume heating
- AMBER: constrains
- AMBER: Controlling number of water residues...
- AMBER: Convert .prmtop (AMBER7/8) to old format (AMBER6)
- AMBER: convert one functional group to another with TI
- AMBER: Convert to Pdb
- AMBER: convert_trajectory
- AMBER: Converting prmtop and inpcrd files
- AMBER: Coordinate Superimposition in PTRAJ
- AMBER: coordinated water molecules deleted when addions
- AMBER: coordinates translation
- AMBER: Copper library?
- AMBER: Copyright for PBSA
- AMBER: correlation
- AMBER: correlation along PCA modes
- AMBER: Could not open file (Melb.mdcrd) with mode (r)
- AMBER: Could not open file (trajin) with mode (r)
- AMBER: crashing xleap
- AMBER: crashing xleap; bugfix.44
- AMBER: Create new Unit
- AMBER: creating a new residue
- AMBER: creating a resp input file without Gaussian.
- AMBER: creating a respgen file without Gaussian.
- AMBER: Creating an Ester with Antechamber/Gaff
- AMBER: Creating an input file for GRASP using AMBER 8
- AMBER: creating pdb file....
- AMBER: Creating protonated cytidine residue
- AMBER: creating residues - charge assign problems
- AMBER: Critical PMEMD 8 Bugfix
- AMBER: cross-correlation
- AMBER: Cu++ and RED
- AMBER: Cut pdb files
- AMBER: cut-offs in non-periodic simulations
- AMBER: Cutoff for anal
- AMBER: cutoff in ANAL
- AMBER: Cyclic peptide
- AMBER: Cyclohexane solvent Box
- AMBER: D-amino acid prep-files(simple method)
- AMBER: D-enantiomers
- AMBER: delphi and surface in MMPBSA
- AMBER: Density of Cyclohexane box
- AMBER: density problem
- AMBER: density profiles in ptraj or carnal
- AMBER: desc NEWRES and blank unit type
- AMBER: details of new aminoacid
- AMBER: determining solvent/ion densities
- AMBER: dielectric constant
- AMBER: difference of energy in sander and nmode in amber 7
- AMBER: dihedral driver?
- AMBER: Dihedral Energy calculation
- AMBER: dihedral term in prmtop file
- AMBER: Dipolar coupling refinement
- AMBER: dissolving micelle structure in water.. amber7
- AMBER: distance between images
- AMBER: distance restraint and file fort.35
- AMBER: distance restraint simulation
- AMBER: distance restraints
- AMBER: distance restraints between two centers of mass
- AMBER: Disulfide bond
- AMBER: disulfide bonds by "bond" or "edit -> draw" ?
- AMBER: DIVCON optimization
- AMBER: Division by zero in sander
- AMBER: DNA base-flipping: TI vs PMF
- AMBER: DNA melting free energy calculation
- AMBER: DNA simulations
- AMBER: DNA strands separate
- AMBER: DNA Tutorial
- AMBER: doble C and N terminal
- AMBER: Does anybody know the experimental solvation free energies of Efavirenz and some other DPC drugs
- AMBER: Does delta.charge mean "final charge" for a dummy atom?
- AMBER: does the result of H bond is consistent with the ?Eele of MM_PBSA?
- AMBER: does the result of H bond is consistent with the ∆Eele of MM_PBSA?
- AMBER: doesn't work in pmemd, and no output in parallel simulations
- AMBER: double counting of potentials
- AMBER: doubt on the value of Pressure on MD run
- AMBER: doubts with a new aminoacid
- AMBER: dppsv returns error code: 29
- AMBER: Dr. Cornell's calculation of Sulfur vdw epsilon value in parm94.dat?
- AMBER: Dual Xeon EM64T Intel Fortran Compile Problem
- AMBER: Dual Xeon EM64T Intel Fortran Compiler
- AMBER: Dummy Atom Types on both states
- AMBER: Dummy atoms: Changing the source code
- AMBER: Dummy Atoms: How to create them?
- AMBER: dynamics
- AMBER: Dynamics error
- AMBER: E of amber calculations
- AMBER: eedmeth=5
- AMBER: EEL and EAMBER values
- AMBER: eelnb
- AMBER: eigenvalues in vector of ptraj
- AMBER: Energy Comparisons
- AMBER: Energy decomposition parameters
- AMBER: Energy fluctuations
- AMBER: Energy output problem!
- AMBER: energy plot in minimization
- AMBER: enhanced sampling methods
- AMBER: Equilibration MD
- AMBER: Equillibration run
- AMBER: error - compiling antechamber
- AMBER: error about using ambmask
- AMBER: Error check COM velocity!!
- AMBER: error during MD run
- AMBER: Error in "restrt" output file
- AMBER: error in chirality.c?
- AMBER: Error in MD
- AMBER: Error in MD run!
- AMBER: Error in minimization
- AMBER: error in parallel
- AMBER: error in pbsa calculation
- AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN
- AMBER: ERROR in readParm: ...failed to find BONDS_WITHOUT_HYDROGEN
- AMBER: error in safe
- AMBER: Error in sander: stack trace terminated abnormally.
- AMBER: Error limits of TI and MM_PBSA methods
- AMBER: Error message
- AMBER: Error on restrained MD equilibration (AMBER 7)
- AMBER: Error while running resp.
- AMBER: Error with antechamber
- AMBER: error with compiling amber8 with lam on intel pc clusters
- AMBER: error with ptraj
- AMBER: Error: vlimit exceeded for step
- AMBER: ESP exceeds the MAXESP(20000),
- AMBER: essential dynamics
- AMBER: estimation of interface size
- AMBER: ew_bspline.h error
- AMBER: ew_legal.h
- AMBER: EWALD and belly not strictly correct
- AMBER: example script for hbond calculation
- AMBER: expected error in mean (Amber 8 TI tutorial)
- AMBER: Extended bonds-MD
- AMBER: External Electric Field
- AMBER: External Field in AMBER?
- AMBER: F,Cl,Br,I in MMPBSA
- AMBER: fail of minimization in sander
- AMBER: Fail to load the trajectory file.
- AMBER: Fail to run parallel
- AMBER: Failed sander runs for large systems
- AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on"
- AMBER: false bond created upon coordinate retrieval
- AMBER: fast 1/r methods
- AMBER: Fatal Error on loading a pdb in xLeap
- AMBER: FATAL error with ATP and MG2 - fixed
- AMBER: FATAL error with ATP, MG2 residue
- AMBER: fedora installation problem
- AMBER: ff02EP + pol3 (2)
- AMBER: fit
- AMBER: fixing protein for minimisation of solvent
- AMBER: Floating Exception and installation on Digital Unix.
- AMBER: Floating Exception in sander
- AMBER: floating point exception
- AMBER: Fluorine in MM-PBSA (AMBER8)
- AMBER: For calculating the energy rised from deviation of equalibrium values of bond angles does amber use degree or radians
- AMBER: For further question about Targeted MD
- AMBER: force constant Unit used in TMD
- AMBER: Force field modification problem
- AMBER: Format of atom specifiication after FIND
- AMBER: Formatting a restraint file
- AMBER: Formatting Questions
- AMBER: frcmod info for Nickel
- AMBER: frcmod.mod_phipsi.2
- AMBER: Free energy
- AMBER: Free energy calculation for protein-protein complex using MM_PBSA
- AMBER: Free energy calculation for protein-protein complex usingMM_PBSA
- AMBER: Free Energy Calculation torsion missing
- AMBER: Free energy extimate for the same structure but different conformers
- AMBER: Free energy for L and D amino acids
- AMBER: Free energy pertubation (thermodynamic intergration)
- AMBER: freee energy calculation without minimised structure
- AMBER: GAFF angle parameters
- AMBER: gaff atom types
- AMBER: gaff frcmod file for TI calculation
- AMBER: gaff sugar residue instability
- AMBER: gaff.dat typo
- AMBER: gaff: ca-ca-c -o torsion parameter
- AMBER: GAFF: H type on carbon bearing a cyano group
- AMBER: gaussian output file
- AMBER: GB - igb=1 versus dielc=?
- AMBER: GB and mm_pbsa.pl
- AMBER: GB differences between AMBER7 and AMBER8
- AMBER: GB dynamics
- AMBER: GB refinement of CYANA structures
- AMBER: GB solvation and "boxed" environment simulation
- AMBER: GB with dipoles !
- AMBER: GB with Langevin dynamics - solution
- AMBER: GB with Langevin dynamics problem
- AMBER: GB with Langevin dynamics problem 2
- AMBER: GB/SA/LD parallel sander
- AMBER: GBSA and thermodynamic ensemble
- AMBER: GBSA calculation
- AMBER: GBSA simulation problem
- AMBER: GCC for AMBER on 64 bit machine
- AMBER: General Question about AMBER's Free Energy Perturbation Method
- AMBER: generate charmm paramater file from amber parm file
- AMBER: generating over 16 bps of DNA in nucgen
- AMBER: generation of conformations for multi-conf. RESP fitting
- AMBER: Geometrical distortion because of charge?
- AMBER: Gibbs compilation problem
- AMBER: Gibbs perturb DNA strands separate
- AMBER: global pH variation in AMBER.
- AMBER: Glycam-parameters and antechamber
- AMBER: glycan
- AMBER: GNU Autotool integration for Amber8!
- AMBER: gold atoms
- AMBER: GRID program used to add ions and solvate AMBER minimized structures
- AMBER: group-based cutoff
- AMBER: guanidinium chloride
- AMBER: gyration radius
- AMBER: H-atom types attached to a carbon atom next to carbonyl group
- AMBER: H-bond energy
- AMBER: Have the parameters for dUMP been calculated by somebody?
- AMBER: Hbond analysis
- AMBER: hbond analysis in ptaj/carnal
- AMBER: hbond detailed analysis over time?
- AMBER: Hbonds restraints OK but Dihedral restraints not applied
- AMBER: heating
- AMBER: helical parameters obtaining
- AMBER: hi
- AMBER: Hi..I am new to AMBER.(compilation with MPICH-G2 libraries)...
- AMBER: highly fluctuating reaction field energies in MM/PBSA
- AMBER: Holes in water
- AMBER: how can I constitute T-phosphotyrosine group ?
- AMBER: how can I deal with the puzzle?
- AMBER: How can I read parm99.dat file?
- AMBER: How can i use AMBER with CHARMM forcefield parameter?
- AMBER: How does Amber8 implemnet ntf=4?
- AMBER: How does leap choose params ?
- AMBER: How is the origin of the grid defined?(PBSA question)
- AMBER: how is truncated octahedron box calculated
- AMBER: how the phosphated threonine to be recognized in leap
- AMBER: How to add water to calculate MMPBSA
- AMBER: How to add water to calculate MMPBSA. .
- AMBER: how to average the structure along md trajectory
- AMBER: How to build a crystal structure from a unit cell pdb?
- AMBER: How to build dynamics input for guanine with tleap ?
- AMBER: How to calculate binding free energy of ligand bound to complex with two active-site water molecules?
- AMBER: How to calculate hydrogen bond involved with water molecules quickly?
- AMBER: How to calculate RESTRAINT value
- AMBER: how to cap regions
- AMBER: How to check for water mediated hydrogen bonds?
- AMBER: how to constitute T-phosphotyrosine group?
- AMBER: How to construct a lipid bilayer
- AMBER: How to converts a binary mdcrd file
- AMBER: how to creat leaprc.gaff
- AMBER: How to create a parallel job for amber 8?
- AMBER: How to deal with the Non-standard residue
- AMBER: How to deal with the problem that a molecule go out the virtual box in vaccum
- AMBER: how to excite a single residue ?
- AMBER: how to extract the residues of first solvation shell from the simulated system after the production?
- AMBER: How to fix certain bond angles
- AMBER: How to fix the atom in NPT case?
- AMBER: How to fix the torsion angles during energy minimization
- AMBER: How to generate a RMSd-residue number graph using AMBER8 ptraj?
- AMBER: how to generate frcmod file for using prepin file..
- AMBER: How to get PDB structures optimized for RED-II
- AMBER: how to get the parameters for modified amino acid residue?
- AMBER: How to insert a protein in lipid bilayer
- AMBER: how to make a nonsymmetric box around the solute
- AMBER: how to make cluster files?
- AMBER: How to make PDB file by myself
- AMBER: how to make the prepin file for dimer and clusters of organic molecule in Amber7
- AMBER: How to modify force constants and equalibrium values for standard residues
- AMBER: how to pull out frames
- AMBER: How to read unformatted restart file in PTRAJ ?
- AMBER: how to reduce box size and delete excess solvent
- AMBER: How to restart MM_PBSA or doing the statistics only
- AMBER: How to run amber more efficiently?
- AMBER: how to see the box lines
- AMBER: How to set AMBER parameter files for lipid?
- AMBER: How to set constraint
- AMBER: How to set the virtual box size for a calculation run in vacuum
- AMBER: How to set up dihedral constraints in amber
- AMBER: How to simulate a crystal structure?
- AMBER: how to solvate in TIP5P box
- AMBER: How to split LES trajectory using TRAJ
- AMBER: How to turn off pme when using periodic box
- AMBER: How to use XLEAP to link one atom in a monomer to another atom in ano
- AMBER: How to use XLEAP to link one atom in a monomer to another atom in another monomer? (where both the 2 monomers are in a same pdb file)
- AMBER: How to wrap a truncated octahedron water box into the primary box?
- AMBER: huge bond distances in new residue
- AMBER: Hydrogen bonding question
- AMBER: I am looking forward to hearing from you.
- AMBER: ibelly and free energy calculations
- AMBER: ibelly in nmode
- AMBER: ibelly not working
- AMBER: ico(i)=-1?
- AMBER: Identifying water molecules with ptraj
- AMBER: IDIEL in sander
- AMBER: if setting ntf=4, will it cause someproblem?
- AMBER: ifort compiling problem
- AMBER: IGB parameter
- AMBER: igb10 vlimit exceeded
- AMBER: igb=10 some vdW terms disappear?
- AMBER: implementing AMBER in NAMD
- AMBER: improper torsion parameters
- AMBER: Improper Torsional Parameters
- AMBER: in vacuo parameters
- AMBER: in vacuo?
- AMBER: inconsistent ordering in an improper dihedral of TRP
- AMBER: Incorrect imaging when using Periodic Boundary Conditions in NAMD with AMBER parameters
- AMBER: increase the limit of restraintmask
- AMBER: Increase the runtime of Amber benchmarks
- AMBER: Increasing Volume with ntb=1
- AMBER: Induced dipole in AMBER8
- AMBER: infinite DNA
- AMBER: inpcrd file
- AMBER: input for mm_pbsa
- AMBER: Installation error - icc: command not found
- AMBER: installation of amber 8 on windows
- AMBER: Installation of AMBER8 on a PC with a Pentium EE type CPU
- AMBER: installation on a dual core
- AMBER: Installation problem
- AMBER: Installation problem - wrong address
- AMBER: Installation problem. .
- AMBER: installing amber7 on 64bit cluster
- AMBER: interaction between residues
- AMBER: Interpreting Amber8 Benchmark Results
- AMBER: INTRA molecular hbonds
- AMBER: intramolecular nonbonded interactions in AMBER force field
- AMBER: Invalid Digit "*"
- AMBER: ipol=1 & use_pme= ??
- AMBER: Is Amber able to constrain(not restrain) certain angles at certain values?
- AMBER: Is AMBER package suitable for simulating multiple molecule in solvent?
- AMBER: is calculated B-factors always smaller than experimental ones?
- AMBER: Is droplet boundary condition option possible ?
- AMBER: Is MM-PBSA doable for transition metals ?
- AMBER: Is the MD simulation normal
- AMBER: istart2
- AMBER: iwork array for nmr
- AMBER: Joining residues/units
- AMBER: just one more try:) xleap, opteron, pgi and segmentation fault. (fwd)
- AMBER: keeping two domains closed together during a simulation
- AMBER: langevin, GB and simulated annealing - 2
- AMBER: langevin, GB and simulated annealing - 3
- AMBER: langevin, GB and simulated annealing - 4
- AMBER: langevin, GB and simulated annealing - 5
- AMBER: langevin, GB and simulated annealing?
- AMBER: large std error in entropy estimation
- AMBER: last call for early registrations for "Horizons2005"
- AMBER: lastrst
- AMBER: layer
- AMBER: LCPO SASA parameters for other elements when using gbsa=1 option
- AMBER: LEAP
- AMBER: leap bond angle building
- AMBER: leap bond error
- AMBER: Leap compilation issues
- AMBER: Leap compilation with pgf77 under 64bit platform
- AMBER: Leap error: Could not find atom type: CE
- AMBER: Leap handling crystallographic waters
- AMBER: leap issues on a powerbook
- AMBER: Leap problem
- AMBER: leap problem: savepdb
- AMBER: leap question
- AMBER: leap saveamberparm chain types response
- AMBER: leap segmentation fault-bugfix1 didn't work
- AMBER: Leap set head/tail question
- AMBER: leap single precision
- AMBER: Leap task
- AMBER: leap warnings
- AMBER: least square fit of snapshots in md trajectory to a reference frame
- AMBER: Lennard-Jones coeff...
- AMBER: lib file for nonstandard residue
- AMBER: lib-4324 : UNRECOVERABLE library error
- AMBER: Ligand problem
- AMBER: Linear Interaction Energy
- AMBER: linit in mm-pbsa
- AMBER: Linux Enterprise
- AMBER: lipid bilayer membrane force field parameter
- AMBER: Lipid bilayer parameters
- AMBER: Lipid bilayer parameters and charmm force field parameters
- AMBER: lipid parameter file
- AMBER: Lipid parameters
- AMBER: lmanal input file problem
- AMBER: Loading a macmodel file complex
- AMBER: loading DNA-RNA hybrid in xleap
- AMBER: loading pdb
- AMBER: loading pdb in leap to create parmeter files
- AMBER: Loading pdb-residue (re)numbering in leap
- AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list
- AMBER: local dielectric constant
- AMBER: Mainchain example needed
- AMBER: Make Distance restraints for non-standard residues
- AMBER: Make test error
- AMBER: make test.lmod error
- AMBER: makeDIST_RST ERROR
- AMBER: Making movie from AMBER trajectory
- AMBER: Making movie from AMBER trajectory using UCSF Chimera
- AMBER: Making prep file of sugar derivative
- AMBER: Making prepin file for individual residues of huge molecule.
- AMBER: Making topology files of big moleucles in antechamber
- AMBER: Manganese ion parameter
- AMBER: Manuals need update: protonate -b and -c options gone in Amber 7 and 8
- AMBER: masks in ptraj - Hbond analysis
- AMBER: maxgrp error
- AMBER: maximum number of processors
- AMBER: MD on surface
- AMBER: MD problems (SHAKE)
- AMBER: MD problems/shake
- AMBER: MD problems/shake-many thanks
- AMBER: MD simulation on a protein solvated by a combination of some water mod
- AMBER: MD simulation on a protein solvated by a combination of some water models ?
- AMBER: MD without a thermostat
- AMBER: MD: Water network analysis + visualization
- AMBER: mean structure calculation
- AMBER: Meaning of induced dipole moments for atom pairs?
- AMBER: meaningful tax for sander question
- AMBER: memory_mm_pbsa
- AMBER: Merry Xmas
- AMBER: Message in .out file
- AMBER: mesure dihedral angle during MD
- AMBER: Metals with Amber
- AMBER: Methionine with both C-ter and N-ter
- AMBER: Mg2+ issues of using MM-PB/GBSA
- AMBER: Mg2+ issues of using MM-PB/GBSA. .
- AMBER: Mg2+ radius in my_parse_delphi.siz
- AMBER: min problem
- AMBER: minimization
- AMBER: Minimization failure
- AMBER: Minimization in sander and nmode
- AMBER: Minimization of avg structure-SANDER Bomb
- AMBER: minimization stuck problem
- AMBER: minimization.out
- AMBER: minimize a ptraj average pdb structure
- AMBER: Minimized structure
- AMBER: minimizing structures before MM-PBSA?
- AMBER: missing residue
- AMBER: mixture solvent model
- AMBER: MM-GBSA
- AMBER: MM-PBSA and 1-4 nonbonded interactions
- AMBER: MM-PBSA calculation
- AMBER: MM-PBSA error
- AMBER: MM-PBSA in protein-Zn-ligand system
- AMBER: mm-pbsa with multiple-processors
- AMBER: MM-PBSA-big energies
- AMBER: MM-PBSA: plot the "Ggas+Gsol" vs time
- AMBER: MM/PBSA basic questions
- AMBER: mm/pbsa error
- AMBER: MM_PB/GBSA
- AMBER: mm_pbsa
- AMBER: MM_PBSA !
- AMBER: MM_PBSA arguments for MM calculations
- AMBER: mm_pbsa energy decomposition error
- AMBER: MM_PBSA error
- AMBER: mm_pbsa example doesn't run
- AMBER: mm_pbsa example number 3
- AMBER: MM_PBSA fillratio error
- AMBER: MM_PBSA for NMR restrained structures
- AMBER: MM_PBSA help, please
- AMBER: MM_PBSA parameters
- AMBER: MM_PBSA problem
- AMBER: MM_PBSA problem---Illegal division by zero at ...
- AMBER: MM_PBSA question
- AMBER: mm_pbsa script !
- AMBER: MM_PBSA stopped at some snapshot
- AMBER: mm_pbsa: problems with dielec constant when using
- AMBER: MM_PBSA_parameter
- AMBER: MMGBSA and dielectric constant with AMBER8 - dielc and intdiel
- AMBER: MMPBSA calculations on Highly charged systems
- AMBER: mmpbsa test problem
- AMBER: Modeling of a radical
- AMBER: modeller
- AMBER: Modified RNA Bases
- AMBER: Moil view trajectory clusters
- AMBER: moil-view
- AMBER: Moil-view and Quicktime movie
- AMBER: Mol2 to prepin file conversion
- AMBER: molecular dynamics
- AMBER: molecular dynamics course
- AMBER: molecular dynamics simulation of protein containing Mg2+ cation
- AMBER: molecule blowing apart during equilibration
- AMBER: molsurf error
- AMBER: molsurf error in MM/PBSA calculation
- AMBER: molsurf: problem with calculate surface area
- AMBER: more data points on the parmchk problem
- AMBER: MPI for sander8
- AMBER: mpirun sander8 problem
- AMBER: Multiple dihedral restraints
- AMBER: Multiple dihedral restraints (follow up)
- AMBER: my frcmod file created using parmchk
- AMBER: My last posting
- AMBER: My model loses its motion in MD
- AMBER: my prepin file in lowe-case
- AMBER: N Metyl amino acids
- AMBER: NAN errors
- AMBER: NaNQ
- AMBER: NCOPY definition
- AMBER: need clarification on EWALD BOMB error
- AMBER: Need help in charge fitting through RESP
- AMBER: Neutral C-terminal residue
- AMBER: new aminoacid
- AMBER: New information about AmberFFC
- AMBER: New parametrs
- AMBER: New pmemd build utility; pathscale vs. pgi vs. ifort em64 opteron benchmarks
- AMBER: New problem of parallel sander
- AMBER: new residue
- AMBER: new tutorial available
- AMBER: nmode
- AMBER: nmode calculation
- AMBER: Nmode calculations
- AMBER: nmode entropy calculations in MMPBSA
- AMBER: nmode error: GNORM is greater than the requested maximum
- AMBER: nmode in mmpbsa
- AMBER: nmode minimization and normal mode calculation
- AMBER: nmode with ibelly
- AMBER: Nmode with residues excluded
- AMBER: NMR refinement
- AMBER: nmropt =1 AND ntr=1 in pmemd
- AMBER: no corrected reaction field energy in *.out files after running mm_pbsa
- AMBER: No exchange among replicas in REMD!
- AMBER: No skew or curtosis when zero variance in moment
- AMBER: no statistics part
- AMBER: no thermostat versus very weak thermostat
- AMBER: No vdW parameters for HO..
- AMBER: No. of Snapshots in MM/GB/SA
- AMBER: NOE constraints
- AMBER: non bond over flow
- AMBER: Non-Bonded Cutoff vs PME
- AMBER: non-periodic condition
- AMBER: nonbond_list question .
- AMBER: nonbonded interaction
- AMBER: nonbonded interactions
- AMBER: normal mode mm/pbsa interupted
- AMBER: Nose-Hoover thermostat
- AMBER: NRESPA
- AMBER: nscm
- AMBER: NTWPRY problem
- AMBER: nucgen and nukit
- AMBER: nucgen bdna types
- AMBER: nucgen error (U not generated)
- AMBER: nucgen H5T H3T
- AMBER: nucgen problem
- AMBER: number of processors
- AMBER: Odd Antechamber Behavior
- AMBER: OH- dynamics
- AMBER: On the role of neutralizing ions in GB-MD and GBSA
- AMBER: Opinion needed-Solvents
- AMBER: output of force field info
- AMBER: oxidised methionine residue
- AMBER: oxo-heme
- AMBER: P4 EM64T Intel Fortran Compile Problem
- AMBER: pairwise energy decomposition using MM-PBSA
- AMBER: parallel AMBER on cluster
- AMBER: parallel AMBER/pmemd installation problem on Opteron
- AMBER: parallel amber8 with mpi through qsnet
- AMBER: parallel error
- AMBER: parallel run
- AMBER: Parameter files for general lipids
- AMBER: Parameter for alpha-lactose
- AMBER: parameter for sulfur in thio-glucoside residue
- AMBER: parameter for sulfur in thio-octyl-glucopyranoside
- AMBER: parameter meaning
- AMBER: Parameters and topology for Diacylglycerol (DAG)
- AMBER: parameters for fluorine atom
- AMBER: Parameters for phosphorylated amino acids
- AMBER: parameters for pyridoxal phosphate
- AMBER: Parameters for S-substituted nucleic acids
- AMBER: parameters in gaff.dat
- AMBER: parametrization problem
- AMBER: params for cofactors
- AMBER: PARM-99
- AMBER: parm99.dat non-bonded parameters
- AMBER: parmchk bug fix
- AMBER: parmchk bug fix, with attachment
- AMBER: parmchk error : Cannot open CONNECT.TPL, exit
- AMBER: parmchk segfaulting
- AMBER: PARMSCAN program
- AMBER: parralel test
- AMBER: PB Bomb in circle(): Stored surface points over limit
- AMBER: PB dynamics
- AMBER: pb_pgb test fail
- AMBER: PBCAL=0. Problems in MM/PBSA
- AMBER: PBSA error: PB bomb in pd_aaradi
- AMBER: pbsa problem
- AMBER: PBSA residual and pairwise decompostion
- AMBER: PCA
- AMBER: pca with ptraj
- AMBER: PDB conversion to gzmat using antechamber
- AMBER: pdb file and xleap
- AMBER: pdb files from traj file
- AMBER: peptide side chain modification with LEAP
- AMBER: periodic boundaries and repeating structure
- AMBER: Periodic box imaging using ptraj
- AMBER: periodicity problem
- AMBER: pH=1 MD simulation
- AMBER: Phi-Psi-Energy plot
- AMBER: phosphorylated DNA not recognized
- AMBER: plane definition in ptraj
- AMBER: platinum atom in Xleap
- AMBER: please help us on partial charge calculation of PT complex using RESP
- AMBER: PLease remove my post
- AMBER: pmemd + pgi 5.1 + ntr = 1
- AMBER: pmemd - bug report
- AMBER: pmemd and distance restraint
- AMBER: pmemd and restraints
- AMBER: PMEMD limitation on NFFT
- AMBER: PMEMD on Opterons; building/benchmarks/recommendations
- AMBER: PMEMD with big systems
- AMBER: PMF calculations with TI using the sander
- AMBER: Poisson Boltzmann dynamics error
- AMBER: Polarization & energy analysis
- AMBER: porblem in ptraj
- AMBER: position of protonation info from constant pH run
- AMBER: Position restraints and Models
- AMBER: Position Restraints!
- AMBER: potential of mean force calculation along reaction coordinates
- AMBER: power supply crash==>boot problems
- AMBER: precision switch from 64 to 32 bit (double from single precision)
- AMBER: prepi format and question about it
- AMBER: pressure output
- AMBER: Problem during Production
- AMBER: Problem during production!!
- AMBER: Problem finding transition state using NMODE
- AMBER: problem in minimization
- AMBER: Problem in ptraj
- AMBER: Problem in running AMBER 7 in solaris !
- AMBER: problem in writing
- AMBER: problem of calculate the charge
- AMBER: problem of calculate the charge2
- AMBER: problem runing parallel (REM) on tru64
- AMBER: Problem saving file in xleap
- AMBER: Problem when converting AMBER trajectories to CHARMM format
- AMBER: Problem with "Thermodynamic integration calculations" tutorial ,unsuspected error
- AMBER: problem with addIons
- AMBER: problem with belly calculation restart
- AMBER: Problem with building AMBER7 on SUSE Linux 9.2
- AMBER: Problem with computing Resp charges using RED
- AMBER: problem with gb md
- AMBER: problem with improper torsions in parmchk
- AMBER: problem with input files when using ff02EP + pol3
- AMBER: Problem with installation AMBER8 on Solaris 8 using original SUN compilers
- AMBER: problem with MD simulation
- AMBER: problem with nmode using ntrun=5
- AMBER: problem with nmode using ntrun=5 (2)
- AMBER: problem with position restraints (refc file)
- AMBER: problem with pressure equilibration
- AMBER: problem with protein ligand complex
- AMBER: problem with protein minimization
- AMBER: problem with ptraj and randomizeions
- AMBER: Problem with restart file
- AMBER: problem with running AMBER with lam-mpi though PBS script
- AMBER: Problem with sander test suites in solaris !
- AMBER: problem with solvateBox
- AMBER: problem with ssh and xleap
- AMBER: problem with temperature weights
- AMBER: Problem with the QMMM example in AMBER 2004 tutorial
- AMBER: problem with xleap
- AMBER: Problems Binding Protein to DNA
- AMBER: problems installing amber 7 on a RH Linux 8 machine
- AMBER: problems with "protonate"
- AMBER: problems with bonds in sander
- AMBER: Problems with Iodine
- AMBER: Problems with parameter lib and prep püarameter files
- AMBER: Problems with protonate on Linux
- AMBER: problems with running sander in parallel on linux
- AMBER: Problems with xLEaP
- AMBER: program to visualize crystal symmetries
- AMBER: Protein dynamics.
- AMBER: Protein ions?
- AMBER: Protein residue numbering
- AMBER: Protein With Structural Ions
- AMBER: Protein-surface interaction
- AMBER: protonate
- AMBER: protonate and input conversion error
- AMBER: Protonate state of ARG and LYS.
- AMBER: protonated aspartic acid
- AMBER: PSC Summer Workshop: Modeling Proteins and Nucleic Acids with AMBER, VMD and the MMTSB Toolkit
- AMBER: ptraj
- AMBER: PTRAJ $ Antechamber
- AMBER: ptraj - hbond detailed analysis over time?
- AMBER: ptraj analysis
- AMBER: Ptraj and order of operations
- AMBER: ptraj command inputs
- AMBER: ptraj correlation facility
- AMBER: ptraj crash error
- AMBER: ptraj distance mask
- AMBER: ptraj efficiency
- AMBER: ptraj error and min problems
- AMBER: ptraj for RDF calculations
- AMBER: ptraj Hbond analysis
- AMBER: ptraj help, how to enable disabled ptraj routine?
- AMBER: ptraj output missing
- AMBER: ptraj problem
- AMBER: ptraj, hbond problem
- AMBER: ptraj-acceptor mask format
- AMBER: ptraj8: trajectory windows
- AMBER: ptraj: determining solvent/ion densities
- AMBER: PTRAJ:"hbond" analysis
- AMBER: PTRAJ:"hbond" doubts
- AMBER: pucker: deatails about pucker calculation
- AMBER: puzzling gaff parameter
- AMBER: Pyranose pucker parameters
- AMBER: QM/MM
- AMBER: QM/MM with pmemd
- AMBER: QMMM for copper complexes!
- AMBER: QMMM question
- AMBER: quadrupole in resp
- AMBER: Quantifying DNA perterbation
- AMBER: Query: Problem during Production
- AMBER: Question about "nmanal"
- AMBER: Question about "quasih"
- AMBER: question about amber parameter file format etc.
- AMBER: question about Carnal
- AMBER: Question about GAFF atom types
- AMBER: question about grid in ptraj
- AMBER: question about initial conditions for amber
- AMBER: question about leaprc.gaff and xxx.top
- AMBER: Question about Lennard-Jones Parameters in Topology file
- AMBER: question about loadiing pdb file of a molecule complex
- AMBER: question about mm_gbsa output file
- AMBER: question about mmpbsa
- AMBER: Question about NVE simulation.
- AMBER: Question about partial charge for ligand molecules
- AMBER: Question about PB bomb
- AMBER: Question about PDB format
- AMBER: question about periodicity of torsion parameter
- AMBER: question about placing a substrate in a protein pocket
- AMBER: Question about Prep file
- AMBER: Question about radial command in ptraj
- AMBER: question about sander minimization error
- AMBER: question about spline in sander -- array size of eed_cub
- AMBER: question about surface area to GBsurf calculation
- AMBER: question about TGMD: vlimit exceeded for step
- AMBER: Question about TI integral method
- AMBER: question about tleap load pdb file
- AMBER: Question about tutorial-9
- AMBER: Question about using MM_PBSA
- AMBER: question about xwin load pdb file
- AMBER: question convert crd files to pdb files
- AMBER: Question of PB bomb
- AMBER: Question on makeing up of missing atoms
- AMBER: question replica exchange acceptance ratio
- AMBER: question temperature coupling tautp value for RNA
- AMBER: question whem using leap
- AMBER: questions about MG ions
- AMBER: Questions about MM-PBSA in Amber8
- AMBER: questions about RNA
- AMBER: Questions about sander.QMMM
- AMBER: questions about topology file
- AMBER: Quick question about xLeap
- AMBER: R factors in NMR intensity refinement
- AMBER: R.E.D
- AMBER: radial distribution function
- AMBER: Radial Distribution functions by ptraj
- AMBER: radii "leap" from which file
- AMBER: RADIOPT=1
- AMBER: radius parameter for F atom
- AMBER: radius parameter for Mg2+ in mm_pbsa calculation
- AMBER: random-coil polymer
- AMBER: rborn(i) in egb.f
- AMBER: rdc multiple tensors
- AMBER: RDF input preparation problem
- AMBER: rdparm
- AMBER: rdparm bug
- AMBER: rdparm: a parameter array overflowed
- AMBER: re Updating Tutorials
- AMBER: read pdb back to xleap after solvation of chloroform
- AMBER: reading frcmod torsional parameters
- AMBER: recent Chimera MD enhancements
- AMBER: recompiling problem on IBM aix
- AMBER: RED and EP from GAMESS
- AMBER: RED and Multi-Orientation
- AMBER: RED II and Gaussian
- AMBER: RED question
- AMBER: RED&GAMESS: sorry ... my mistake
- AMBER: RED-II failure to recognize GAMESS output
- AMBER: RED: extra variable definition
- AMBER: Redhat Enterprise Linux
- AMBER: Reference (?) for normal-mode analysis in nmode
- AMBER: reference of Targeted MD
- AMBER: regarding ambpdb
- AMBER: Relative stability with MMPBSA
- AMBER: Relax in tLEaP ?
- AMBER: Release of R.E.D-II
- AMBER: REM difficulties
- AMBER: REM error
- AMBER: REM mdinfo file
- AMBER: REMD error!!!
- AMBER: REMD trajectory error!!!
- AMBER: reordering atoms after antechamber
- AMBER: Rep Exch. suggestion
- AMBER: Replica exchange
- AMBER: Replica Exchange crashing
- AMBER: replica exchange trouble with unit 6
- AMBER: Replica-Exchange MD from AMBER8!
- AMBER: Representation of cations in MD
- AMBER: Request for calculating free energy using AMBER6
- AMBER: Request for g98 (IOP...)
- AMBER: residence time of electrons/holes in DNA
- AMBER: Residual Dipolar Refinement
- AMBER: RESP charge fitting for N-methylguanine cation
- AMBER: RESP charges - multiple conformations
- AMBER: RESP charges of RNA nucleotides with 3' and 5' ends
- AMBER: RESP charges with Gaussian03 and Amber
- AMBER: Resp install problem
- AMBER: Resp install problem, again
- AMBER: RESP of negatively charged molecule
- AMBER: RESP problem RESP
- AMBER: RESP: Question
- AMBER: restart coordinate file
- AMBER: restart file
- AMBER: restart file and crd file
- AMBER: Restart Problem
- AMBER: RESTARTED DUE TO LINMIN FAILURE
- AMBER: Restrained-MD
- AMBER: Restraint of atoms during minimization
- AMBER: restraint only for Z cartegian coordinate?
- AMBER: restraintmask dimension
- AMBER: Restraints
- AMBER: reverse TI charge perturbation
- AMBER: rms
- AMBER: RMS fluctuations along modes obtained from PCA
- AMBER: rmsd
- AMBER: RMSD Calculations
- AMBER: roar question
- AMBER: rotameric populations?
- AMBER: rotating and repositioning molecules in xleap
- AMBER: rotational motion in periodic simulation
- AMBER: rounding in xleap when using saveoff command...
- AMBER: rst file problems
- AMBER: running shell scripts in tleap?
- AMBER: runtime error in sander?
- AMBER: Sample more conformational space
- AMBER: Sander and NMODE energy minimization
- AMBER: Sander bomb - atom out of bounds
- AMBER: SANDER BOMB: volume of ucell too big
- AMBER: sander error
- AMBER: sander errors with atom restraints on ia64
- AMBER: sander failure
- AMBER: sander free energy calculation
- AMBER: Sander is changing directories
- AMBER: Sander minimization & dynamic question
- AMBER: sander prob
- AMBER: sander problem
- AMBER: Sander questions on dual-processor Sun with MPICH
- AMBER: Sander Replica Exchange exits with unit 6 error
- AMBER: Sander Replica Exchange exits with unit 6 error]
- AMBER: Sander Restart Problem
- AMBER: sander run
- AMBER: sander segmentation fault
- AMBER: Sander.LES questions
- AMBER: sander.QMMM and fcap
- AMBER: Sander/Mpich2 error with mpd_singinit
- AMBER: Sander: idecomp
- AMBER: Saturated DNA bases
- AMBER: scaleCharges with polarisable force fields
- AMBER: Scaling factor of NMR restraint
- AMBER: Scaling of charges in a polarizable simulation !
- AMBER: script for calculating hydrogen bond
- AMBER: Searching for NAD parameter files / Problems with parameter file creation
- AMBER: seg fault error in resp
- AMBER: segmentation fault in radial ptraj
- AMBER: segmentation fault in sander
- AMBER: segmentation problem
- AMBER: separate solvent-solvent and solvent-solute interaction
- AMBER: Separating solvent and solute energy in the microcanonical mode
- AMBER: serial and parallel
- AMBER: setBox buffer in leap
- AMBER: Setting Amber force field parameters
- AMBER: setting up Parallel processing
- AMBER: setting up restraint with ntr option
- AMBER: shake
- AMBER: SHAKE error
- AMBER: SHAKE in md with partial solvation
- AMBER: Silicon related parameters
- AMBER: Simple 3D Molecule Visualization
- AMBER: Simulating transition metals in amber
- AMBER: simulation with explicit water molecules
- AMBER: simulation with Mg2+ ions and counter ions
- AMBER: single-stranded poly(rC) simulation
- AMBER: size of solventbox
- AMBER: skip snapshots with ptraj in amber 8.0
- AMBER: small target pressure in constant pressure dynamics
- AMBER: SO4 prep file
- AMBER: soft-cores and Amber
- AMBER: software for real polymer MD simulation
- AMBER: SollvateBox with ethanol
- AMBER: Solute-solvent boundary in pbsa
- AMBER: Solution for those who have mpich problem while building the parallel version of AMBER 8
- AMBER: solutions of amber installation problems
- AMBER: Solvate question?
- AMBER: solvate water box
- AMBER: Solvate with mixture of ethanol and water(Newbie question)
- AMBER: solvatebox problem in the antechamber tutorial
- AMBER: solvateOct method
- AMBER: solvateoct mymolecule CHCL3BOX 10 PROBLEM!!!
- AMBER: solvation energy
- AMBER: Solvation in trifluoroethanol
- AMBER: solvent accessible surface area
- AMBER: solvent problem
- AMBER: Solvents
- AMBER: Some explanations of MM_PBSA @DECOMP OUTPUT file?
- AMBER: some problems with Antechamber
- AMBER: some question about MM-PBSA
- AMBER: some questions about nmode
- AMBER: some questions when using ATP
- AMBER: SOURCE3 in gaff.dat
- AMBER: sp0 console message after using addAtomTypes
- AMBER: sp2 carbon atom parametrization
- AMBER: spherical boundary condition
- AMBER: stack terminated abnormally
- AMBER: Stacking energy
- AMBER: STARTING WHERE I LEFT OFF
- AMBER: Steered Molecular Dynamics with AMBER?
- AMBER: stereo
- AMBER: STOP 0
- AMBER: strange case
- AMBER: Strange difference in speed between Altix (Itanium2) and Tezro (MIPS) SGI for small GB/SA run
- AMBER: strange minimalization output
- AMBER: strange mm_pbsa.pl bug
- AMBER: strange VDWAALS and EEL energies calculated by pbsa
- AMBER: stripwater
- AMBER: structures extracted from mmpbsa
- AMBER: substitute missing residues?
- AMBER: substrate exit from protein in Amber 8.0 TI vdw simulation
- AMBER: sugar pucker with Carnal and ptraj
- AMBER: surface area
- AMBER: surfen and surfoff
- AMBER: Suspended (tty input)
- AMBER: system size limit
- AMBER: Target MD and nmode test hang
- AMBER: Targeted MD
- AMBER: Temperature equilibration
- AMBER: temperature keep increasing in high temp.
- AMBER: Temperature regulation
- AMBER: Temperature varible in MMPBSA script
- AMBER: temprature and restraint in constant volumm MD
- AMBER: test suite possible failures
- AMBER: Thanks
- AMBER: the averaged structure VS the specific snapshot
- AMBER: The default of HIS in leaprc : HID or HIE ?
- AMBER: the DNA conformation after engery minimization using NMODE
- AMBER: The effect appling paches
- AMBER: The error during calculating PB with pbsa
- AMBER: the out put I get... parameter for sulfur in thio-glucoside residue
- AMBER: The pressure
- AMBER: the restart of replica exchange method (REM) simulations in AMBER8
- AMBER: the restarting error
- AMBER: the restraint MD fail with amber8,but success with amber7
- AMBER: The “crystallographic” waters should be retained or deleted?
- AMBER: Thermodynamic Integration for conformational changes?
- AMBER: TI - frcmod file
- AMBER: TI calculation using sander
- AMBER: TI in Amber8
- AMBER: TI tutorial in Amber 8
- AMBER: TI with electrostatic decoupling at sander
- AMBER: TI-FEP for ALA --> GLY
- AMBER: TI-FEP for VAL --> ALA
- AMBER: time and lifetime in hbond analysis (ptraj)
- AMBER: Time Correlation Functions with Amber
- AMBER: tkbc2
- AMBER: tleap and water
- AMBER: tleap load pdb file
- AMBER: tleap,xleap bond order for triple bonds
- AMBER: TMD force constant
- AMBER: To post or mail to the list (subscribers only)
- AMBER: too much vacuum in the box created by Leap
- AMBER: Topology Format Amber 8
- AMBER: total energy leaps
- AMBER: total energy of solvation
- AMBER: trajectory alignment using ptraj
- AMBER: trajectory of minimization
- AMBER: Trajectory Problem
- AMBER: Trajectory problems
- AMBER: transfer data from Linux to windows
- AMBER: tRNA's modified bases in the Amber parameters database
- AMBER: trouble in calculating the distance between O atom of water molecule and atom of residue
- AMBER: Trouble with Amber8
- AMBER: Trouble with example tutorial
- AMBER: troubleshooting replica exchange
- AMBER: Tutoial 8 (Case Study)
- AMBER: Tutorial #1 ptraj/sander problem
- AMBER: Tutorial question and some more...
- AMBER: Tutorial Request
- AMBER: Two question about dielectric constant
- AMBER: Tyrosine CZ Parameterization Bug continues in Amber 8
- AMBER: tyrosyl charges
- AMBER: umbrella sampling output question
- AMBER: Unexpected stop of Sander run
- AMBER: Unformatted restart file cannot be read by sander when PME in use (AMBER8)
- AMBER: units
- AMBER: units describing projection onto modes
- AMBER: units of mwcovar matrix befor conversion
- AMBER: Unknown atomtypes in amber
- AMBER: unnatural ligand
- AMBER: unstable MD velocities
- AMBER: Use of ibelly with nmode analysis
- AMBER: Using AMBER for Carbon nanotubes
- AMBER: Using amber4 generated prep files in amber8?
- AMBER: using antechamber ... to get prepin file
- AMBER: Using Antechamber with Gamess and other molecular manipulations
- AMBER: using constraints with QM/MM
- AMBER: Using OPLS atom types
- AMBER: using periodic boundary conditions to create infinite double helix
- AMBER: using position restraints in target MD?
- AMBER: Using RED to calculate partial charges of new amino acid
- AMBER: using SALTCON for human cell cytoplasm
- AMBER: using xmgrace....
- AMBER: vacuum bubbles in system equilibration
- AMBER: value of SALTCON
- AMBER: van der Waals interactions (PTRAJ)
- AMBER: van der waals parameters
- AMBER: vdw for terminal phosphate
- AMBER: vdw of h atoms
- AMBER: vdw or center box dimensions, periodicity, and the jagged edge
- AMBER: Velocity Info
- AMBER: Vibrational spectrum?
- AMBER: Vibrational spectrum? [SOLUTION]
- AMBER: vlimit
- AMBER: vlimit exceeded and temperature blow up
- AMBER: vlimit exceeded in thermalization
- AMBER: vlimit heat
- AMBER: vlimit in heating
- AMBER: vlimit problem
- AMBER: warning in leap
- AMBER: warning in PBSA
- AMBER: Warning: Error opening "New" file from subroutine OPNMRG in pmemd
- AMBER: Warnings as a file
- AMBER: Water simulation
- AMBER: Watson-Crick restraints
- AMBER: Weighting of different restraint types?
- AMBER: What does a crash mean while running a md simulation?
- AMBER: What does this mean .. ?
- AMBER: what is wrong with my amber job or installation?
- AMBER: What PRESS is?
- AMBER: Which forcefield?
- AMBER: Which source file determine the initial value of IX XX arrray in AMBER8?
- AMBER: Why are some of the Lennard-Jones coeffs 0 ?
- AMBER: Why I couldnt used carnal for analyzed RMSD ?
- AMBER: why is snaupe.f is empty?
- AMBER: why not minimize snapshots before MM/PBSA calculations
- AMBER: why the dipeptide always moving out the virtual box
- AMBER: wierd behavior of addions
- AMBER: Will Amber 9 available?
- AMBER: with two water molecules in active site, how to calculate the free energy of ligand bound to complex?
- AMBER: Working with a nickel-organometallic compound
- AMBER: Workshop Tutorials Downtime this weekend.
- AMBER: write format of restart crd in sander/pmemd
- AMBER: writing MASKs
- AMBER: wtmol and resp
- AMBER: X Windows for LEaP on SGI
- AMBER: Xleap execution problems on Solaris
- AMBER: Xleap menu bar problems
- AMBER: xleap MOVE and .lib file
- AMBER: xleap with modified residue
- AMBER: xleap, lib file question
- AMBER: xleap, opteron, pgi and segmentation fault.
- AMBER: xleap: different distance results from "check" command in xleap
- AMBER: XMGR
- AMBER: XRED II error while initializing
- AMBER: Xserve and amber
- AMBER: Zn complex parametrization question
- AMBER: Zymeworks job posting
- AMBER: | ERROR: Could not read coords from *.rst
- AMBER: | ERROR: Could not read coords from rst file
- AMBER:Bond lengths aren't reasonable after minimisation.
- AMBER:FAD can't be minimized.
- AMBER:how to analyse trajectory files
- AMBER:how to deal with metal ion?
- AMBER:Hydroxy Proline
- AMBER:idecomp
- AMBER:Sander errors: Unit 6 Error on OPEN: mdout
- Antechamber
- antechamber not working .. for thio residue..
- ask for your help: parallel on mm_pbsa
- AW: AMBER: compiling amber with pgi 5.2.4
- Bank of the West Alert
- EBAY Update Information
- Fwd: AMBER: rdc multiple tensors
- gaff sugar residue instability
- Gibbs compilation problem
- Important Information About Your Sky Bank Account
- inconsistent ordering in an improper dihedral of TRP
- Installing PMEMD on IBM machine (CPU power4) running SUSE_9.1
- is calculated B-factors always smaller than experimental ones?
- leap compilation problems xeon EM64 processor
- Ligand problem
- Office XP - 60 dolars! coagulate
- pca with ptraj
- pmemd problems
- Problems with ptraj/rdparm
- Purchased a New Home
- R.E.D. question
- Re :AMBER: Holes in water
- restraints
- single-stranded poly(rC) simulation
- system comparison for amber
- The default of HIS in leaprc : HID or HIE ?
- The new ganaration of repliccas is here capella
- TI tutorial
- TI tutorial --> ALA --> GLY TI calculation
- tutorial 8
- Tutorial#1 ptraj/sander problem
- We can send you disccounted errection mads party
- You wont believe these pr1ces on name-brannd soft's! kerchief
Last message date: Sat Dec 31 2005 - 12:51:27 CST
Archived on: Sat Dec 31 2005 - 12:51:44 CST
3972 messages sorted by: [ author ] [ date ] [ thread ]
About this archive
|
VU Home |
VUMC Home |
People Finder |
University Calendar
webmaster- modified on January 30, 2009 |