AMBER Archive (2009) - Sep 2009 By Subject475 messages sorted by:
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Starting: Tue Sep 01 2009 - 00:02:08 CDT
Ending: Wed Sep 30 2009 - 13:40:58 CDT
- [AMBER] "nan" in gaussian input files generated by antechamber
- [AMBER] (no subject)
- [AMBER] about the number of residues after MD
- [AMBER] About the PMEMD compiling for CUDA
- [AMBER] ACE and NME patch: VMD ???
- [AMBER] ACS COMP division awards- Oct 19th deadline
- [AMBER] Active site - Ion - Search engine
- [AMBER] AmberTools 1.3 / CHAMBER
- [AMBER] ambertools and Snow Leopard 64 bits kernel
- [AMBER] amoeba.prm problem?
- [AMBER] antechamber bug: output of incorrect bond character
- [AMBER] antechamber error
- [AMBER] Antechamber generate a prep file in a wrong order...
- [AMBER] Any tutorial on the proper way to merge a ligand and protein?
- [AMBER] apbs-amber
- [AMBER] ATP and GTP parameters
- [AMBER] ATP/GTP parameters
- [AMBER] Attaching a ligand to a protein residue.
- [AMBER] can antechamber convert a prep file from cartesian to internal coordinates?
- [AMBER] Carbon Nanotube Library file (CNT)
- [AMBER] CH3Hg+ parameters
- [AMBER] Changing pH of the system
- [AMBER] charge consideration
- [AMBER] combining MD runs for post-MD analysis
- [AMBER] Compiling Amber with gfortran-4.5.0 on a mac
- [AMBER] Compiling Amber10
- [AMBER] cpin error
- [AMBER] Creating new counterions
- [AMBER] Cygwin Home Directory
- [AMBER] database
- [AMBER] dihedral force calculation
- [AMBER] Discrepancy between AMBER and VMD calculation
- [AMBER] DMF solvent box
- [AMBER] Dummy atoms and MM-PBSA
- [AMBER] Enquiry about MM/GBSA output file.
- [AMBER] Error in minimal
- [AMBER] error xleap: XaLeap_wcl is empty
- [AMBER] Ewald error estimated
- [AMBER] fatal "does not have a type" error in tleap for a protein-ligand complex
- [AMBER] Force Field Fitting
- [AMBER] gaff.dat questions
- [AMBER] Gap in rst file
- [AMBER] general query: implicit solvation
- [AMBER] generate prmtop file from CHARMM psf file
- [AMBER] group distance restraint
- [AMBER] Hbond analysis: Direction of the hydrogen
- [AMBER] Heme + Fe(II) + O2 + histidine parameter
- [AMBER] how to calculate correct RMSF?
- [AMBER] How to consider the off centre charges
- [AMBER] how to deal with aromatic nitro group with antechamber
- [AMBER] How to denature DNA
- [AMBER] How to derive charges from the output
- [AMBER] How to find a protein's energy
- [AMBER] How to find water-mediated hydrogen bond?
- [AMBER] how to give force values in TMD
- [AMBER] how to make 50% aqueous TFE box?
- [AMBER] How to obtain amber top and crd from pdb file with POPE lipids?
- [AMBER] how to ouput the electrostatic potential at a single atomic position?
- [AMBER] How to prepare the coordinate and toplogy files in leap ?
- [AMBER] how to pull a dna
- [AMBER] How to remove Hydrogen using ptraj
- [AMBER] How to use AMBER 10 for PCA analysis.
- [AMBER] input file
- [AMBER] input file / skinnb
- [AMBER] install ambertools
- [AMBER] Installation issue
- [AMBER] Installing AmberTools and Amber10 in Ubuntu - Instructions.
- [AMBER] Ki and G
- [AMBER] Kinetics
- [AMBER] Leap warning
- [AMBER] LINMIN failure notice
- [AMBER] LJ-partial charges and force field parameters for ethylene glycol and glycerol
- [AMBER] load .crd & .top in xleap
- [AMBER] loading a following attached protein in amber 10
- [AMBER] loading PDB of a RNA sequence
- [AMBER] loading RNA sequence in xleap
- [AMBER] loadpdb
- [AMBER] logdvdl does not work
- [AMBER] makeDIST_RST: no map function
- [AMBER] MM-GBAS decomp error
- [AMBER] MM_PBSA
- [AMBER] MM_PBSA decomp problem
- [AMBER] momentum in MD simulation
- [AMBER] NAB syntax
- [AMBER] nmropt option
- [AMBER] No restrt file
- [AMBER] No sp2 improper torsion term for NB-CA-CB-CB
- [AMBER] parameter for manganese
- [AMBER] Parameter Problem
- [AMBER] parameterization of protein-ligand complex
- [AMBER] partial charges in Amber force field
- [AMBER] PBSA for gp41 binding free energy
- [AMBER] Pentane UA model
- [AMBER] periodic boundary condition for implicit solvent simulation and SHORT command
- [AMBER] PES QM and MM
- [AMBER] pH calculations
- [AMBER] PK zero for specific dihedral and parmchk
- [AMBER] pmemd and internal dielectric
- [AMBER] prep file
- [AMBER] Problem about adding a small residue to DNA
- [AMBER] problem building sander.apbs
- [AMBER] Problem in compiling AMBER9 in parallel !
- [AMBER] problem in QM/MM input file
- [AMBER] Problem in test run
- [AMBER] problem of PBCAL/GB
- [AMBER] Problem on PMEMD
- [AMBER] Problem regarding Hbond analysis
- [AMBER] problem running pmemd gbrna tests
- [AMBER] problem when doing mm/pbsa: bad atom type Br
- [AMBER] problem with 4-Hydroxyl-Proline tutorial
- [AMBER] PROBLEM WITH CHCL3BOX pdb
- [AMBER] Problem with GROUP input
- [AMBER] Problem with loading PDB into tleap
- [AMBER] Provisional Support for AMBER 10 PMEMD on NVIDIA GPUs
- [AMBER] QM/MM minimization
- [AMBER] QM/MM simulation
- [AMBER] QMMM NEB with PM3-PDDG fails with ASSERTion 'ierr.eq.0' pimd_init.f line 320
- [AMBER] question about ptraj
- [AMBER] Question about the debug forces
- [AMBER] Question on ECAVITY term of MM_PBSA
- [AMBER] Question regarding PCA analysis.
- [AMBER] question with hbond
- [AMBER] question with radial distribution function
- [AMBER] R.E.D. : Gaussian Error
- [AMBER] radial distribution function in amber
- [AMBER] RDC analysis: "No restraint defined"
- [AMBER] Reg. snapshot_statistics.out.snap
- [AMBER] Regarding united atom force field
- [AMBER] RESP RED
- [AMBER] RMSDf of heavy atoms
- [AMBER] Simulation short peptide and protein interaction
- [AMBER] Solvate in an alkaline solution
- [AMBER] solvent accessible surface area
- [AMBER] symbol lookup error
- [AMBER] Teragrid
- [AMBER] TI in Amber9/10
- [AMBER] too many missing parameters in frcmod for the prep of my ligand
- [AMBER] trouble using iAPBS
- [AMBER] unit of force constant
- [AMBER] variable header for ABMD
- [AMBER] warning in dispatchToken
- [AMBER] What is dual topology
- [AMBER] What is the Optimum Ph for solvating a protein
- [AMBER] What is the unit of RMSF?
- [AMBER] What should be the standard input file when imin=5
- [AMBER] why should one restrain the position of the counterions?
- [AMBER] xleap problem !
- [AMBER] Your help about ptraj in AmberTools!]]
- [AMBER] Zinc
- charge consideration
- charge interaction
- Problem with GROUP input
- ظ [AMBER] Problem about adding a small residue to DNA
- 回复: [AMBER] Problem about adding a small residue to DNA
Last message date: Thu Dec 31 2009 - 22:57:46 CST
Archived on: Thu Dec 31 2009 - 22:58:33 CST
475 messages sorted by:
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