AMBER Archive (2009) - Dec 2009 By Subject427 messages sorted by:
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Starting: Tue Dec 01 2009 - 02:30:07 CST
Ending: Thu Dec 31 2009 - 22:56:50 CST
- [AMBER] (No reply) Compatibility of ONIOM and Amber
- [AMBER] .rst file error
- [AMBER] a problem in building oligosaccharides using LEaP
- [AMBER] a question about ptraj
- [AMBER] About APBS radiopt
- [AMBER] Adding single distance restraint
- [AMBER] addles - neb error
- [AMBER] Amber 10 installation: /bin/sh: ./Makelist: not found
- [AMBER] amber10 pmemd fail
- [AMBER] AMBER: segmentation fault when running parmchk
- [AMBER] amber@ambermd.org
- [AMBER] ambertools and Snow Leopard 64 bits kernel
- [AMBER] AmberTools modifications for Ubuntu 9.10
- [AMBER] AmberTools-1.3 not compiling on MacOsX
- [AMBER] ambpdb water removal for rst files
- [AMBER] antechamber bond type error
- [AMBER] antechamber error
- [AMBER] aromatic ring getting distorted
- [AMBER] atom type
- [AMBER] ATP/GTP parameters
- [AMBER] binding energy of multiple ligand-receptor complex
- [AMBER] branched aminoacids
- [AMBER] C1, C2 & C3 carbon types in generalized Born implementation igb=5
- [AMBER] can I install amber11 on a windowsPC under cygwin?
- [AMBER] CHARMM psf file to Amber prmtop file
- [AMBER] chemical shifts: nter and cter
- [AMBER] clarification DNA forcefield
- [AMBER] coarse grained
- [AMBER] comparing coordinates from restart file and ptraj outputs
- [AMBER] Comparison of the CHARMM and AMBER parameters for alkane
- [AMBER] Compatibility of ONIOM and Amber
- [AMBER] COOH group troubling
- [AMBER] Custom RNA modeling
- [AMBER] Different simulation times for similar systems
- [AMBER] distance-dependent dielectric constant minimization
- [AMBER] ERROR: Could not read coords from {filename}
- [AMBER] exchange attempt in REMD
- [AMBER] force field parameters
- [AMBER] Gaff compatible with ff899.SB
- [AMBER] hbond analysis
- [AMBER] heating system in NEB
- [AMBER] help with TIP4P and mpi pmemd
- [AMBER] hi
- [AMBER] how can i include ANP residue
- [AMBER] how to add desired number of water
- [AMBER] how to add desired numberof water
- [AMBER] how to add desirednumberof water
- [AMBER] How to get total energy of a system from QM/MM
- [AMBER] HOW TO OPTIMISE INDI-DIELC_MM VALUE for MM_PBSA calculation ?
- [AMBER] How to put another 10 ligands into the simulation system?
- [AMBER] how to restart the stopped MM-GBSA job
- [AMBER] How to run LEaP in a shell file?
- [AMBER] implicit solvent MD with fixed residues
- [AMBER] Inorganic Phosphate Parameters
- [AMBER] Inorganic Phosphate Parameters. .
- [AMBER] Installation on MacOSX
- [AMBER] iron in prepi file generation for heme
- [AMBER] look at Amber's slides, email
- [AMBER] looking for parameters for DHFR substrates and inhibitors... [one more try]
- [AMBER] MM PBSA stats
- [AMBER] MM_PBSA Problem (no radius for ion)
- [AMBER] mm_pbsa- Decomposition: bad atom type
- [AMBER] MMGBSA
- [AMBER] MMGBSA error
- [AMBER] MMPBSA on a selected region
- [AMBER] mpirun error
- [AMBER] myristate to palmitate transformation
- [AMBER] NAB example scripts in AmberTools (Amber 10)
- [AMBER] nab installation
- [AMBER] NAMD dcd files in ptraj
- [AMBER] neb error while heating
- [AMBER] NEB-error
- [AMBER] NEB-NAN error
- [AMBER] Nmode "not running properly" problem in MM_PBSA
- [AMBER] non standard residue and bond command
- [AMBER] Non-Standard Atoms
- [AMBER] note on Antechamber error
- [AMBER] Number of Cycles
- [AMBER] OE and CG types
- [AMBER] Output Does Not Match in Tutorial B1
- [AMBER] parameter file for the sulphate ion
- [AMBER] Parameters for HYP and CGU
- [AMBER] Parametrizing charges for modified DNA bases
- [AMBER] phosphorus to carbon on minimization
- [AMBER] PIMD test stalling
- [AMBER] PQR file - HELP PLEASE
- [AMBER] PQR files
- [AMBER] preparation of small molecule libraries with most probable conformations using Amber
- [AMBER] pressure tensor components
- [AMBER] problem in installing amber tools on Mac OSX 10.6
- [AMBER] Problem of MM-PBSA
- [AMBER] problem with antechamber
- [AMBER] problem with FAD in tleap
- [AMBER] ptraj image
- [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial
- [AMBER] ptraj utility
- [AMBER] pupil and amber
- [AMBER] QM/MM input file error
- [AMBER] QM/MM minimization
- [AMBER] question about failures
- [AMBER] reg.changing velocity
- [AMBER] Regarding rigid bond
- [AMBER] Release of AmberTools, version 1.3
- [AMBER] Sander crash, corrupt rst file...
- [AMBER] Scripting tleap
- [AMBER] Segmentation fault
- [AMBER] Segmentation fault in antechamber
- [AMBER] semiempirical copper
- [AMBER] SGLD in pmemd??
- [AMBER] sleap in AmberTools 1.3 is not working anymore for me
- [AMBER] sodium ions before or after solvation makes a difference
- [AMBER] SQM and AMBER
- [AMBER] SQM and AMBER :again
- [AMBER] sqm x mopac in AmberTools 1.3
- [AMBER] Tests to check for proper MMPBSA.py installation
- [AMBER] Topology Reorder for EVB
- [AMBER] trajout problem
- [AMBER] trouble with antechamber
- [AMBER] typo in AmberTools.pdf (release 1.3)
- [AMBER] using sqm from AmberTools 1.3
- [AMBER] Van der Waals and electrostatic Forces
- [AMBER] what the value of "Br" bondi radii, and how to modify "fillratio" error message.
- [AMBER] why is the ff03 force field in Amber8 and Amber10 different for Ala2 dipeptide
- [AMBER] XLEaP Error on Closing Edit
- [AMBER] Zinc parameters?
- Amber question
- ATP/GTP parameters
- COOH group trouble
- COOH troubling
- EEL = *************
- how to change velocities
- looking for parameters for DHFR substrates and inhibitors... [one more try]
- nab normal mode analysis has imaginary frequencies
- PIMD test stalling
- 答复: [AMBER] MMGBSA error
Last message date: Thu Dec 31 2009 - 22:57:46 CST
Archived on: Thu Dec 31 2009 - 22:58:33 CST
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