Amber Archive Oct 2015 by subject
- [AMBER-Developers] [AMBER] problem with randomizing velocities
- [AMBER] "Vlimit exceeded for step..." error
- [AMBER] &rst + distance + coordinate restraint
- [AMBER] (too) high absolute values for charges using resp and gaussian
- [AMBER] /share/apps/amber/amber14/bin/sander.MPI: error while loading shared libraries: libmpi_cxx.so.1: cannot open shared object file: No such file or directory
- [AMBER] 1-4 nonbonded interactions does not cancel in MMPBSA calculation
- [AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II)
- [AMBER] [AMEBR] Amino acid side-chain carbonyl C=O(ASP, GLU) and side-cahin -HN (LYS, ARG) close proximity
- [AMBER] [cpptraj] Changes in RMSF functionality?
- [AMBER] [SPAM] AMBER Digest, Vol 1365, Issue 1
- [AMBER] ^.^. as a new atom type when running DFTB with sander from Ambertools 15
- [AMBER] A question about MMPBSA calculation
- [AMBER] AIB parameter
- [AMBER] ALA but must be GLY MM-PBSA
- [AMBER] AMBER Digest, Vol 1361, Issue 1
- [AMBER] AMBER Digest, Vol 1364, Issue 1
- [AMBER] AMBER14 testing error
- [AMBER] AmberTools 15, Mac El Captain and Fink
- [AMBER] AmberTools14 configuration problem
- [AMBER] aMD: Bad data for namelist object ethreshp
- [AMBER] ante-MMPBSA question
- [AMBER] applying restraints using tinker
- [AMBER] Atom 1512 was assigned a lower molecule # than previous atom
- [AMBER] Atom match error in MMPBSA calculation
- [AMBER] atomiccorr
- [AMBER] Best suitable 'igb' value for MMPBSA.py calculation
- [AMBER] Building a structure of levansucrase (1PT2) with a fructosyl residue attached to Asp86
- [AMBER] Can't install AMBER14: MissingProgram...Install patch from your package manager
- [AMBER] Charmm to Amber (where’s chamber?)
- [AMBER] compare two trajectories
- [AMBER] compatibility of targeted MD with GPU amber vs. sander
- [AMBER] Constant pH MD
- [AMBER] Controlling size of the box
- [AMBER] coordination number
- [AMBER] Correctly deriving force constants for Amber
- [AMBER] CpHMD for non protein residues
- [AMBER] cpin file
- [AMBER] CPPTRAJ
- [AMBER] cpptraj - bridging water
- [AMBER] CPPTRAJ : different RMSD calculation in a single run
- [AMBER] cpptraj density
- [AMBER] cpptraj uses huge memory space while doing molsurf calculation
- [AMBER] cutoff problem with a periodic crystal box
- [AMBER] Cytochrome P450 with heme simulation
- [AMBER] Differences on MMPBSA calculation results
- [AMBER] Different Parameters for Nonbonded Interactions
- [AMBER] difficulties in generate .prmtop and .inpcrd file
- [AMBER] difficulties in generate .prmtop and .inpcrd file for complex using Guassian calculated ligand charges
- [AMBER] Dihedral/improper coefficient in AMBER + rmin vs sigma for lennard jones
- [AMBER] Documentation on Prepin File Format
- [AMBER] donor and acceptor masks
- [AMBER] Elementary VMD Problem with Amber Trajectory
- [AMBER] error with line 165 of cpinutil.py
- [AMBER] Error: ptraj is needed for MMPBSA
- [AMBER] EVB related query
- [AMBER] ff12SB vs ff14SB for protein-ligand MD simulations?
- [AMBER] Fwd: donor and acceptor masks
- [AMBER] Fwd: EVB related query
- [AMBER] Glycam force field parameters for derivatives?
- [AMBER] gromacs to amber file format
- [AMBER] Guanine base pair planarity in G-guadruplex
- [AMBER] h-bond calculation - tokenise error
- [AMBER] Halogen bond force field in AMBER
- [AMBER] Help
- [AMBER] Help - buy the Amber software
- [AMBER] Ho Atom Inclusion in PDB from Leap
- [AMBER] How can amber differentiate between terminal Oxygens
- [AMBER] How do you place two molecules in one water box?
- [AMBER] how to convert mdcrd to NetCDF trajectory file?
- [AMBER] How to do a QMMM calculation with a dynamic QM region
- [AMBER] how to generate a model beta-sheet structure
- [AMBER] How to prevent the water molecules entering into the binding pocket during the MD simulation ?
- [AMBER] http://q4md-forcefieldtools.org/ unavailable
- [AMBER] hydrogen bond cpptraj
- [AMBER] If it's possible to add restraint on the steered MD ?
- [AMBER] Info: Bond types are assigned for valence state 5 with penalty of 1
- [AMBER] ions cannot be viewed in gaussview
- [AMBER] Is it possible to simulate a periodic crystal ?
- [AMBER] Leap : problem with copying and combining DNA items
- [AMBER] Leap PDB Input Error
- [AMBER] Lennard-Jones parameter for Sp, Sp2 and Sp3 Nitrogen
- [AMBER] Making Parameter and Topology Files for Protein-Ligand Complex
- [AMBER] many atoms, same name
- [AMBER] Measuring distance between protein and graphene surface
- [AMBER] Measuring minimum distance between protein and graphene surface
- [AMBER] Membrane protein imagining problems
- [AMBER] Metal Ion Model
- [AMBER] Minimization
- [AMBER] missingdisulfide
- [AMBER] mixing rules for various water models in AMBER
- [AMBER] MMPBSA for multiple mutants
- [AMBER] MMPBSA for peptides interaction
- [AMBER] MMPBSA tutorial A3.2
- [AMBER] mmpbsa.py error
- [AMBER] MMPBSA: multiple trajectory approach usage
- [AMBER] N- and C- terminals constant PH simulation
- [AMBER] No Internet Access
- [AMBER] non-standard residue (DNA-protein crosslink)
- [AMBER] Not atom type for Bromine atom in amber GAFF
- [AMBER] Not atom type for Bromine atom in amber GAFF force field?
- [AMBER] Oxygen parameters for AMBER99SB-ILDN
- [AMBER] Pairwise energy decomposition
- [AMBER] parameters for Boron
- [AMBER] Parameters for trigonal bi-pyramid and square bi-pyramid Fe(II)
- [AMBER] paramfit multiple dihedral commbination
- [AMBER] paramfit multiple dihedrals combination
- [AMBER] pmemd.cuda.MPI on Comet- MPI dying
- [AMBER] Polardecomp in 3D-RISM fails
- [AMBER] Prepgen difficulty
- [AMBER] Problem configuring amber14
- [AMBER] problem with randomizing velocities
- [AMBER] Problem with VDW energy
- [AMBER] Problems with the installation of ambertools15.
- [AMBER] QM/MM performance
- [AMBER] QM/MM Umbrella
- [AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE in AMBER 12 using the new set 3ob-3-1
- [AMBER] QMMM with inorganic molecules
- [AMBER] Query about adding hydrogens
- [AMBER] query about Bromide ion forcefield parameter
- [AMBER] Question about mask in cpptraj
- [AMBER] R.E.D. server down or out?
- [AMBER] Random Number Generator Flag Ig
- [AMBER] Real-time hydrogen bond formation using VMD
- [AMBER] RED-tools
- [AMBER] Replica exchange temperature distribution
- [AMBER] RESP charge calculation
- [AMBER] RESP charge fitting
- [AMBER] resp input format 16I5
- [AMBER] Restraints
- [AMBER] Resulting cutoff is too small for your lower limit
- [AMBER] sander missing from AmberTools15?
- [AMBER] SC15 Call for abstracts - "Producing High-Performance and Sustainable Software for Molecular Simulation"
- [AMBER] SGLDg
- [AMBER] SIGSEGV: Segmentation Fault
- [AMBER] small energy jump when restoring a simulation production
- [AMBER] Steps after: AMBER annealing with restraints in vacuum.? towards improving the quality of structure with out RDC, Dihedrals
- [AMBER] Steps after: AMBER annealing with restriaints in vocuum.? towards improving the quality of structure with out RDC, Dihedrals
- [AMBER] Stopping sander in production phase. Why?
- [AMBER] System gets unwrap while iwrap=1 in ti
- [AMBER] Temperature fluctuations in stage heating
- [AMBER] The formulas of per-residue and pairwise-residue free energy decomposition in mm_pbsa
- [AMBER] The magnitude and the direction of the electric field
- [AMBER] Time correlation function of an atom
- [AMBER] tinker_to_amber does not work
- [AMBER] TIP3 water not recognized
- [AMBER] Tutorial 22 - aMD - how long should it last on Titan Black?
- [AMBER] Tutorial 3 section 1
- [AMBER] Units of the dipole moment?
- [AMBER] unusual structure_after equilibration
- [AMBER] Updates for PBSA energy calculations
- [AMBER] What is the formula for calculating EPtot?
- [AMBER] Why is water box getting bigger?
- [AMBER] Why PBSA decomposition takes so long time?
- System gets unwrap while iwrap=1 in ti
- Last message date: Sat Oct 31 2015 - 17:00:02 PDT
- Archived on: Fri Sep 06 2024 - 05:55:14 PDT