Amber Archive Jul 2016 by subject
- [AMBER] a question about resp restraints strength
- [AMBER] A question on SMD simulations
- [AMBER] addAtomType problem
- [AMBER] adding missing ligand records to $AMBERHOME/dat/reduce_wwPDB_het_dict.txt
- [AMBER] adding non-standard residue to RNA strand
- [AMBER] Amber 16 Installation
- [AMBER] AMBER Digest, Vol 1646, Issue 1
- [AMBER] Amber with Amoeba force field
- [AMBER] Amber12 or lated on POWER8 platform
- [AMBER] Amber16 Parallel CUDA Tests
- [AMBER] Amber16 tutorials
- [AMBER] Ambertool16 - MCPB.py angle cut off and Error with Pdbsearcher.py
- [AMBER] aMD with chloroform
- [AMBER] An attempt for TI with QM/MM Hamiltonian
- [AMBER] Applying different restraints to different sets of atoms
- [AMBER] average pdb distorted
- [AMBER] bad atom type decomp
- [AMBER] Binding deltaG in ligand pose selction
- [AMBER] Born Mayer Potential
- [AMBER] Calculating lipid diffusion using stfcdiffusion
- [AMBER] Calculating Salt bridge interactions- Protein and RNA
- [AMBER] can amber14 be run with gtx1060
- [AMBER] can MCPB build non amino-acid containing complex?
- [AMBER] carbon nanotube
- [AMBER] charmmlipid2amber not found
- [AMBER] Compute SASA through molsurf
- [AMBER] convert amber topology and coordinates files into gromacs topology
- [AMBER] CPPTRAJ
- [AMBER] Cpptraj - Stat bug?
- [AMBER] cpptraj grid command multiple trajectories
- [AMBER] cpptraj.hbond: water in the complex
- [AMBER] Create x.out and x.rst from x.mdcrd
- [AMBER] Creating topology file in MMPBSA
- [AMBER] Decomposition in minimization step
- [AMBER] Defining reaction coordinate for US
- [AMBER] Dielectric asymptotic parameter of mixtures for DRISM in rism1d
- [AMBER] Difference of two trajectories
- [AMBER] Discrepancy between mdcrd and output files for MD run
- [AMBER] DPPC simulation temperature
- [AMBER] dssp xlabel conversion.
- [AMBER] EEL become ****** in minimization
- [AMBER] Energy overflow in MD with distance restraint under PBC (aMD problem?)
- [AMBER] Error cuda
- [AMBER] Error during amber 12 installation
- [AMBER] Error MCPB when send the input
- [AMBER] Exposed hydrophobic surface area
- [AMBER] Failed to solvate the molecule during the TUTORIAL A8
- [AMBER] ff14SB compatible with Glycam_06j-1?
- [AMBER] ff99SB*-ildn again
- [AMBER] figure legend problem in the tutorial?
- [AMBER] Gaussian error with MCPB ion modeling calculation
- [AMBER] Generating a HETATM database to use with reduce
- [AMBER] GLYCAM naming
- [AMBER] Gunning GIST in parallel
- [AMBER] Help with SMD
- [AMBER] Help with Umbrella Sampling
- [AMBER] Help: make test fails during parallel amber installation
- [AMBER] Hii
- [AMBER] HMR 4fs failure?
- [AMBER] how to fix COM of a group of atoms?
- [AMBER] How to modify forcefield to use TIP4P-D water model
- [AMBER] hydrogen bond occupancy plot cpptraj
- [AMBER] ibelly to fix protein.
- [AMBER] Implicit solvent with Glycam force field
- [AMBER] InVacuoWithDielc
- [AMBER] Is the surf or the molsurf calculate the protein surface?
- [AMBER] iwrap=0
- [AMBER] Library errors while using NAB on Amber16
- [AMBER] ligand bond distortion during MD run.
- [AMBER] Ligand RMSD
- [AMBER] Lipid14 with ntr=1
- [AMBER] make test.cuda failed
- [AMBER] MCPB
- [AMBER] MCPB.py
- [AMBER] MCPB.py - coordinate sphere FE
- [AMBER] MCPB.py cannot recognize Cl
- [AMBER] MD of an elongated active site protein.
- [AMBER] MD simulation can not proceed normally
- [AMBER] MDCRD
- [AMBER] MDGX tutorial?
- [AMBER] Minimization of a small molecule in gas phase
- [AMBER] MMPBSA
- Thakur, Abhishek (Mon Jul 11 2016 - 14:33:41 PDT)
- Hai Nguyen (Mon Jul 11 2016 - 13:57:53 PDT)
- Thakur, Abhishek (Mon Jul 11 2016 - 13:53:27 PDT)
- Hai Nguyen (Mon Jul 11 2016 - 13:49:37 PDT)
- Thakur, Abhishek (Mon Jul 11 2016 - 13:46:54 PDT)
- Hai Nguyen (Mon Jul 11 2016 - 13:41:40 PDT)
- Thakur, Abhishek (Mon Jul 11 2016 - 13:31:32 PDT)
- Thakur, Abhishek (Fri Jul 08 2016 - 14:14:08 PDT)
- Daniel Roe (Fri Jul 08 2016 - 13:09:46 PDT)
- Thakur, Abhishek (Fri Jul 08 2016 - 11:42:13 PDT)
- Thakur, Abhishek (Fri Jul 08 2016 - 11:38:34 PDT)
- Thakur, Abhishek (Fri Jul 08 2016 - 11:20:25 PDT)
- Hai Nguyen (Fri Jul 08 2016 - 11:07:46 PDT)
- Thakur, Abhishek (Fri Jul 08 2016 - 11:02:45 PDT)
- Nhai (Fri Jul 08 2016 - 10:03:40 PDT)
- Thakur, Abhishek (Fri Jul 08 2016 - 09:57:16 PDT)
- [AMBER] MMPBSA (inp=1 or inp=2)??
- [AMBER] MMPBSA (MD or aMD)
- [AMBER] MMPBSA -O: command not found
- [AMBER] MMPBSA.py for complex or receptor or ligand only
- [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein.
- [AMBER] modified potentials
- [AMBER] Multiple Replicas on a Single GPU
- [AMBER] Multiplicity in antechamber
- [AMBER] NAB
- [AMBER] NEW parameters with AMBER
- [AMBER] NMode binding entropy Error -- Line minimizer aborted
- [AMBER] NMR restraint
- [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda)
- [AMBER] ntr vs ibelly.
- [AMBER] paramfit
- [AMBER] ParmEd
- [AMBER] parmed chamber
- [AMBER] Patching Plumed 1.3 with Amber12
- [AMBER] phosphorylated residues
- [AMBER] Potential on each atom
- [AMBER] predicting RDCs for un-restrained bonds
- [AMBER] Problem setting AMBERHOME as environment variable Ambertools 16 Linux
- [AMBER] Problem to extending Simulation
- [AMBER] Problem with Gaussian09 with B97D/def2TZVPPD basis set from EMSL
- [AMBER] Problem with Gaussian09 with B97D/def2TZVPPD basis set fromEMSL
- [AMBER] Proton wanders away from tryptophan and histadine sidechain carbon
- [AMBER] Proton wanders away from tryptophan and histidine sidechain carbon
- [AMBER] QM/MM issue
- [AMBER] QM/MM problems with Amber/Gaussian
- [AMBER] QM/MM simulations with Amber/deMon2k
- [AMBER] Query on SMD
- [AMBER] Question about Charge derivation for GLYCAM force field
- [AMBER] Question about QM/MM
- [AMBER] Question on SMD
- [AMBER] RDF
- [AMBER] re-imaging bilayer
- [AMBER] Regarding GIST calculation
- [AMBER] Regarding ho parameter in gaff
- [AMBER] Regarding Parameter file not saved
- [AMBER] REMD Reg
- [AMBER] Remove rotation in postoprocess
- [AMBER] Restrain COM of a group of atoms
- [AMBER] restraintmask: select residues around the coordinates of a point
- [AMBER] rism1d convergence for solvent mixtures
- [AMBER] rmsd calculations on multiple trajectories
- [AMBER] rmsd plot error
- [AMBER] RMSD plot query
- [AMBER] Sander bomb: how to create a larger box
- [AMBER] sander QM/MM MD
- [AMBER] Save individual PDBs from MD trajectory
- [AMBER] selecting frames with distribution
- [AMBER] Slow performance of Amber12 on cluster
- [AMBER] SMD and free energy value
- [AMBER] SMD at constant force
- [AMBER] SMD simulation protocols
- [AMBER] Steered Molecular Dynamics
- [AMBER] strategies to speed up MM/GBSA screening
- [AMBER] Structural refinement of the protein complexed with metalo-ions
- [AMBER] Stuck somewhere using antechamber
- [AMBER] Umbrella Sampling
- [AMBER] VMD
- [AMBER] WHAM-2D analysis
- [AMBER] where is amber.jupyter?
- [AMBER] Wierd line in amber-TI output Files
- MD simulation can not proceed normally
- Last message date: Sun Jul 31 2016 - 07:00:03 PDT
- Archived on: Wed Dec 25 2024 - 05:55:24 PST