Amber Archive May 2018 by subject
- [AMBER] .rst and .mdcrd file outputted in ascii
- [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1"
- [AMBER] 1x PCI-E Riser card for MD/TI?
- [AMBER] [cpptraj] Angle between atom and two centroids
- [AMBER] ABMD with multiple walkers
- [AMBER] adding NME and ACE terminals
- [AMBER] Advice on SMD QM/MM for Cyanogenic Glucoside
- [AMBER] Amber 18 manual shows TI as not supported in pmemd.cuda
- [AMBER] Amber 18 Thermodynamic integration question
- [AMBER] AMBER Digest, Vol 2280, Issue 1
- [AMBER] AMBER NFE SMD calculation with new collective variable
- [AMBER] AMBER TI more examples
- [AMBER] Amber16 pmemd.cuda.MPI simulation can drop a frame with an inopportune node crash
- [AMBER] amber18 pmemd.MPI compile fails with Fatal Error: Can't delete temporary module file 'memory_module.mod0': No such file or directory
- [AMBER] AMBER: trouble while running constant pH simulation
- [AMBER] AMBER: trouble while running constant pH simulation > (Cruzeiro, Vinicius Wilian D)
- [AMBER] Angle calculation between three amino acids
- [AMBER] autoimage problem
- [AMBER] Automatic patching failed!
- [AMBER] Boost not linking when compiling on Mac
- [AMBER] calculation of cavity water
- [AMBER] change the charge of the chlorine ion
- [AMBER] combining trajectories with different parameter files
- [AMBER] Computing interaction energies from trajectory
- [AMBER] Conda Installation error
- [AMBER] Configure CUDA issues
- [AMBER] CPPTRAJ Ensemble Keyword: "Too Many Open Files"
- [AMBER] Creating a Gold surface library file
- [AMBER] Cremer Pucker values using Pytraj
- [AMBER] CUDA v9.0 with AMBER16 Question
- [AMBER] DEADLINE EXTENDED: Call for Papers, GCC 2018, 14th German Conference on Chemoinformatics
- [AMBER] DFT method for calculating amino acids partial charges in AMBER99
- [AMBER] Different outputs of external electric field
- [AMBER] Dimension Box visualization
- [AMBER] eCheminfo Milano July 16-29, Training and Innovation Course in Drug Design 2018, bursary and early-bird deadline ending soon
- [AMBER] eCheminfo Oxford, UK Training and Innovation Course in Drug Design 2018, first announcement
- [AMBER] Electrostatic potential calculation
- [AMBER] error in rst file during Minimization
- [AMBER] Error in using pdb4amber command
- [AMBER] Error: No data sets selected - Problem or not?
- [AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters. with pmemd.cuda
- [AMBER] Extracting infromation from topology file
- [AMBER] Facing problem to generate ala10_chir.dat in REMD tutorial
- [AMBER] GBNSR6 with MMPBSA.py
- [AMBER] GPU benchmark - Amber18
- [AMBER] GPU questions
- [AMBER] GUI for TI setup
- [AMBER] How to evaluate the impact of PH on protein structures by Amber
- [AMBER] How to extract frames with particular hydrogen bonds only
- [AMBER] How to prepare prmtop and inpcrd files from a PDB file?
- [AMBER] Hydrogen Bond Occupancy
- [AMBER] I: help please
- [AMBER] info grafic about MD
- [AMBER] Initial configuration of ADP and ion simulation using AMBER.
- [AMBER] input files from AmberTools 16/17 run on Amber14 pmemd.cuda engine problem
- [AMBER] lipid 14 MSD with OPC water
- [AMBER] lipid MSD values for lipid 14 FF
- [AMBER] MD stops due to the distortion of a molecule
- [AMBER] MMPBSA energy decomposition
- [AMBER] MMPBSA.py - PrmtopError: Inconsistent charge definition for atom
- [AMBER] MMPBSA.py execution error
- [AMBER] MMPBSA.py.MPI and matching topology files a problem
- [AMBER] MMPBSA.py.MPI: questions about output warnings and discrepancies
- [AMBER] Multiple temperature groups
- [AMBER] nativecontacts command in CPPTRAJ
- [AMBER] need QMMM interface for TURBOMOLE
- [AMBER] NetCDF error: NetCDF: Not a valid ID
- [AMBER] Novice Question: MD Visualisation in VMD
- [AMBER] optimization of QM zone in QM/MM-GBSA calculations.
- [AMBER] Parametrization of Small Molecules
- [AMBER] Parametrization: consistency with gaff force field
- [AMBER] parmed/chamber verify including CMAP corrections
- [AMBER] PC modes per residue from existing evecs file?
- [AMBER] PhD/Junior position, AMBER sims DNA/RNA
- [AMBER] Plotting phi-psi plots with free energy scale
- [AMBER] pmemd.MPI compatible for REMD simulation IN AMBER package
- [AMBER] pmemd.MPI won't work in Amber 18
- [AMBER] Poly amino acid helix form topology files
- [AMBER] Possible memory leak with LMOD
- [AMBER] Problem in distance restraint
- [AMBER] Problem with g++ compiler with boost (AmberTools18)
- [AMBER] problems with MCPY.py step 2
- [AMBER] QM/MM issue with boron containing compound (AMBER16)
- [AMBER] QM/MM minimization issue using sander (AMBER 18)
- [AMBER] QMMM surface scan
- [AMBER] Query related to the Umbrella sampling method
- [AMBER] Reg. AMBER ff14SB force filed / GAFF (recent version).
- [AMBER] Reg. generating empty frcmod file for ligand molecule
- [AMBER] Request of help on Leap PDB preparation error "atom does not have a type"
- [AMBER] Reservoir REMD using GPUs
- [AMBER] Restart From Check point File
- [AMBER] S-S bond
- [AMBER] sander failed with prmtop complex.top!
- [AMBER] Scabilility of the code in cpus
- [AMBER] Setting initial velocities
- [AMBER] SGLD
- [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3 water model
- [AMBER] Simulation does not restart from restart file written in previous step.
- [AMBER] TI for side chain mutation in dimer protein
- [AMBER] TiMergeError: Cannot have dihedral cross through softcore region
- [AMBER] tleap error 'FATAL: Atom .R<NMET 1>.A<CAY 20> does not have a type'
- [AMBER] TMD : Doubts regarding TGTMDFRC
- [AMBER] Total Energy Decomposition
- [AMBER] Troubleshooting SHAKE problems in minimization
- [AMBER] Ubuntu 18
- [AMBER] update ambertools
- [AMBER] update_amber URL time out problem
- [AMBER] Use of Amber12 and 14 on the same simulation
- [AMBER] Using infe = 1, &pmd, and pmemd.cuda (AMBER16)
- [AMBER] Using multiple CPU threads
- [AMBER] VMD window
- [AMBER] what are the benefits of cuda9 vs. 8 with amber 18?
- SHAKEH: Extra bond between hydrogen atoms of TIP3 water model
- Last message date: Thu May 31 2018 - 13:00:03 PDT
- Archived on: Mon Dec 02 2024 - 05:55:40 PST