Amber Archive May 2019 by subject
- [AMBER] 3D-RISM options
- [AMBER] [mjldehoon.yahoo.com: Files for Tutorial 32 (Deriving bonded parameters with mdgx)]
- [AMBER] amber 16 installation on Ubuntu 18
- [AMBER] AMBER 16 vs 18 on different cuda
- [AMBER] AMBER Digest, Vol 2638, Issue 1
- [AMBER] amber inputs
- [AMBER] amber18 parallel cpu make test hanging at first test
- [AMBER] AmberTools hardcodes library names into binaries
- [AMBER] Ambertools2018/SQM installation
- [AMBER] Any help on how to implement it in cpptraj?
- [AMBER] anybody has any idea?
- [AMBER] Are R.E.D. tools still a thing?
- [AMBER] Atom type (C.2) is not in PARMCHK.DAT Segmentation fault (core dumped)
- [AMBER] Average structure vs Individual frames
- [AMBER] Boron QM/MM
- [AMBER] Bubbles during NPT and NVT simulations
- [AMBER] Building inpcrd and prmtop for a non-standard residue containing cyclic peptide
- [AMBER] Capping a dipeptide with Boc
- [AMBER] Catalysis mechanism of ATPase
- [AMBER] Center of mass velocity autocorrelation function
- [AMBER] Changes to AmberTools antechamber Makefile
- [AMBER] check version
- [AMBER] compiling Amber Tools 19
- [AMBER] continuous DNA
- [AMBER] CPPTRAJ average residue-wise contact map
- [AMBER] CPPTRAJ gnu extension not working
- [AMBER] CPPTRAJ OPENMP - MPI
- [AMBER] Crashed dynamics : connectivity
- [AMBER] cuda test failing after installation
- [AMBER] deselect residues for step1 model in MCPB.py
- [AMBER] different energy values from mdout and cpptraj
- [AMBER] Different potential energies between recomputed and original simulations from PMEMD?
- [AMBER] Distance calculation and distance matrix giving discrepant results
- [AMBER] distance restraint failed in minimization and MD
- [AMBER] DRMSD utility in cpptraj
- [AMBER] ELECTRIC_FIELD in md.out file does not match with md.in file
- [AMBER] empty cein file redox potential calculations
- [AMBER] Energy shifted energy term
- [AMBER] Entropy calculation for a protein homodimerization
- [AMBER] Error in step 3 of MCPB.py
- [AMBER] Error using mm_pbsa.pl binding energy calculations
- [AMBER] error with loading HEM parameters for constph redox calcuations
- [AMBER] Failed to generate parameters
- [AMBER] FEW not producing *.lib file for ligand
- [AMBER] FEW- an issue generating *.lib for ligand
- [AMBER] Files for Tutorial 32 (Deriving bonded parameters with mdgx)
- [AMBER] FLAG_POINTERS in prmtop file
- [AMBER] Force field for intrinsically disordered proteins
- [AMBER] Force field for nucleobases, nucleosides and nucleotides
- [AMBER] Fwd: August 5-8.SBU: 2019 Summer School Parallel Computing in Molecular Sciences
- [AMBER] Fwd: The unperturbed charge of the unit: 4.003000 is not zero
- [AMBER] GCC 2019, November 3-5 in Mainz, Deadline extendend to June 23, 2019
- [AMBER] GPU versions: pmemd.cuda*
- [AMBER] graph
- [AMBER] Guidance on WHAM
- [AMBER] hbond lifetime filesize issues
- [AMBER] Help compiling AMBER18 GPU Code- Cannot find compiler cl.exe in PATH
- [AMBER] How to generate boron atom force field parameters
- [AMBER] How to generate the correct force field parameter for a large molecule?
- [AMBER] Installation of AMBER 18 regarding
- [AMBER] issues with pmemd.cuda
- [AMBER] jobs getting cancelled on cuda7 gpus
- [AMBER] Lennard Jones parameters in frcmod
- [AMBER] Library for Phosphate ion
- [AMBER] make test fail
- [AMBER] matching energies betwen amber-md and gromacs using amber parameters in both
- [AMBER] MC barostat cause the system to stuck indefinitely
- [AMBER] Minimization input
- [AMBER] Missing file amber tutorial
- [AMBER] MMPBSA radiopt effect on EDISPER
- [AMBER] mol2 files for FEW
- [AMBER] NetCDF trajectory file does not contain information about time/timestep
- [AMBER] Novel Force Field Parameters for Aromatic Dihedrals
- [AMBER] NVidia backwards compatibility
- [AMBER] nvidia tesla-t4 and amber
- [AMBER] Open position for doctoral candidate in biomolecular simulations
- [AMBER] Optimization of geometry in xleap
- [AMBER] parameter file for dUTP
- [AMBER] PCA with a really giant trajectory
- [AMBER] phosphor tyrosine bound to C5' terminal DA5
- [AMBER] pmemd.cuda "cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered"
- [AMBER] Print Hessian matrix in (3,3) dimension
- [AMBER] Problem in simulating peptide with modified amino acid - vlimit exceeded
- [AMBER] problem of srun
- [AMBER] Problem with preparing parameters with antechamber for modified amino acid
- [AMBER] Protein-Lipid Bilayer PDB preparation Issue(s)
- [AMBER] Qm minimization,
- [AMBER] Question about sander running parallel
- [AMBER] Question regarding compatibility of Temperature replica exchange MD (TREMD) with constant pH MD
- [AMBER] Radgyr or distance averages
- [AMBER] Random segfaults (invalid memory reference) in sander
- [AMBER] reduce info.log
- [AMBER] Regarding building of parallel version of AMBER18 in centos 7
- [AMBER] Regarding GTX 1050 Ti
- [AMBER] Releasing SIRAH lipids! A complete coarse-grained force field running on AMBER
- [AMBER] Residence time around ions
- [AMBER] rmsd
- [AMBER] RMSF of combined trajectory
- [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword]
- [AMBER] running qsub files in a single standalone workstation
- [AMBER] Selecting number of waters in tleap
- [AMBER] set RA, RT and n_partition in adQM/MM run
- [AMBER] Simulating Water Exchange to Buried Binding Sites
- [AMBER] Simulation with Protein, cofactor and Ligand
- [AMBER] SIRAH force field goes quantum in AMBER
- [AMBER] SMD using contact number
- [AMBER] Solute free non-water solvent
- [AMBER] Some basic question
- [AMBER] SPAM bulk solvent free energy parameters
- [AMBER] Suggestion about proper ANTECHAMBER usage
- [AMBER] Temperature variation in QM/MM simulation with AMBER18/G09
- [AMBER] Thermostat question
- [AMBER] three letter code for unprotonated carboxyglutamates
- [AMBER] tleap split lipid when it shouldn't
- [AMBER] Treat alpha helix as a rigid body during umbrella sampling simulations in amber/2016
- [AMBER] umbrella sampling using pmemd in amber/2016
- [AMBER] Unequal distribution of water
- [AMBER] Using a box of organic solvent
- [AMBER] Velocity rescaling between different temperatures?
- [AMBER] Vina Zinc
- [AMBER] Volmap command in cpptraj followed by SPAM
- Last message date: Fri May 31 2019 - 13:00:02 PDT
- Archived on: Sun Nov 10 2024 - 05:55:44 PST