Amber Archive Mar 2020 by subject
- [AMBER] "Error of reading the .dat file" in MCPB.py step 2
- [AMBER] ** NFE-Error ** : Cannot read &colvar namelist!
- [AMBER] 2DRMS before clustering
- [AMBER] A problem of "Could not import Amber Python modules"
- [AMBER] Abasic Site and Leap Polymerization
- [AMBER] About the D form amino amber force field
- [AMBER] about TREE_CHAIN_CLASSIFICATION
- [AMBER] adding Na, K and Cl ions matching intracellular conc
- [AMBER] AMBER 18 compilation error with CUDA 10.2
- [AMBER] AMBER Digest, Vol 2934, Issue 1
- [AMBER] Amber parameters for heme b / d coordinated with deprotonated tyrosine
- [AMBER] Amber restart simulation
- [AMBER] AMBER19: error in reading namelist cntrl
- [AMBER] AmberTools on Ubuntu 19.04: compilation
- [AMBER] AmberTools19 install error
- [AMBER] AmberTools19 serial installation test errors
- [AMBER] AmberTools19 update.8 fails to install
- [AMBER] Ambmask Error in group input::atommask.f::pop_evalstack stack underflow
- [AMBER] Are the 6-character atom types of CGenFF compatible with parmed-chamber
- [AMBER] Boron compunds with "pdb" file with novel frcmod file
- [AMBER] checkstructure with cpptraj
- [AMBER] Citing DNA OL15 forcefield
- [AMBER] Clustering analysis
- [AMBER] Clustering query
- [AMBER] cross angle analysis
- [AMBER] CUDA single gpu usage issue
- [AMBER] CUDA version for AMBER 16 and 20?
- [AMBER] DBscan gives me errors in clustering
- [AMBER] Differences in Lennard-Jones interactions in CPU vs GPU pmemd?
- [AMBER] dvdl.dat file details AMBER18 TI
- [AMBER] error job.sh
- [AMBER] Error while amber installation
- [AMBER] Error: Could not find angle parameter
- [AMBER] EXTRACTING A PARTICULAR FRAME
- [AMBER] FATAL Error: Atom does not have a type (Cation)
- [AMBER] ff19SB + BSC1 + OPC + which ions ?
- [AMBER] Found an invalid periodicity in the prmtop file: ... CalcError: bin/mmpbsa_py_energy failed with prmtop .prmtop!
- [AMBER] g09 genecp in QM/MM MD in amber
- [AMBER] GAFF/AMBER peptide bond
- [AMBER] GPU support information
- [AMBER] heme B parameter by mcpb
- [AMBER] How to setup a QM/MM calculation in Amber
- [AMBER] how to turned off C N terminal amino in tleap
- [AMBER] If a non-standard force field is used for proteins, how would you approach parameterization of lipids and ligands?
- [AMBER] Inconsistency in energy values between out files and cpptraj
- [AMBER] Incosistency in energy values from out files and cpptraj energy tools
- [AMBER] information regarding space filling visualization
- [AMBER] Installation problem for a parallel version of Amber18/AmberTools19
- [AMBER] Issue in drug parameter
- [AMBER] issue while installing AMBER tools on windows10 Linux subsystem
- [AMBER] KeyError: 'MG'
- [AMBER] linear interaction energy tool in AMBER
- [AMBER] Lone Pairs in AMBER FF
- [AMBER] MM-PB(GB)/SA error message
- [AMBER] mmpbsa_py_energy failed with prmtop dim_gas.prmtop
- [AMBER] Modified AA residue without NH2 end.
- [AMBER] Modified force fields
- [AMBER] MPI+threads in Amber
- [AMBER] nastruct and modified base pairs
- [AMBER] Not recognising output file for N_OF_BONDS reaction coordinate
- [AMBER] NPT equilibration is crashing
- [AMBER] parameterization with crystal water
- [AMBER] parameters for Si3N4
- [AMBER] PDB Modification
- [AMBER] problem adding MG.off file
- [AMBER] problem in MCPB.py
- [AMBER] problems implementing tiMerge for base pair mutation
- [AMBER] Problems with Nvidia Drivers
- [AMBER] QM/MM Convergence questions
- [AMBER] Query regarding 3DRISM in Amber with CHARMM force field
- [AMBER] Question about MMPBSA calculation
- [AMBER] Question of units
- [AMBER] questions about paramfit and frcmod file
- [AMBER] Questions on force field
- [AMBER] Reg: MMGBSA for NAMD trajectory
- [AMBER] REMD hybrid solvent model
- [AMBER] replica exchange with GPU
- [AMBER] residue library for na_link AmberTools19
- [AMBER] RTX 2020 Super GPU Random Memorry Errors
- [AMBER] RTX 2020 Super GPU Random Memory Errors
- [AMBER] setting pdb file
- [AMBER] sieve keyword in cpptraj clustering
- [AMBER] SImulation prepared using CHARMM GUI terminates with no error at the NTP step
- [AMBER] simulations of proteins with 2 domains connected by a linker
- [AMBER] Simulations Without Network
- [AMBER] sum of charges from parm file
- [AMBER] tar-MD with custom J-coupling relation
- [AMBER] Texas red force field
- [AMBER] TI production error in nstep =1
- [AMBER] TI runs on GPU
- [AMBER] tleap for Mg2+ data type
- [AMBER] tleap/xleap performance enhancement
- [AMBER] Unavailability of the file related to -cprestrt flag in equilibration (NPT) step of constant pH MD in Amber14 with AmberTools15
- [AMBER] units of the calculated diffusion coefficient
- [AMBER] unusual planarity change during md.
- [AMBER] Weird error with antechamber for metal ion / MCPB tutorial
- [AMBER] What is the default pH when loading a protein in Amber environment
- [AMBER] What's the least biased way to stop a molecule from crossing a periodic boundary?
- [AMBER] When I use fitted parameters as initial parameters in paramfit, I am getting different results?
- [AMBER] Writing Trajectories as netcdf files
- Last message date: Tue Mar 31 2020 - 16:00:02 PDT
- Archived on: Mon Dec 09 2024 - 05:55:52 PST