Amber Archive Jul 2013 by subject
- [AMBER-Developers] Amber Workshop in Brazil
- [AMBER] "Incomplete Improper Torsion line" error
- [AMBER] &ewald skinnb=2.0d0 /
- [AMBER] 'undefined reference to MPI::...' error messages when compiling Amber 12 on CentOS 6 for "-mpi -cuda"
- [AMBER] 2013 Symposium on Theoretical Chemistry in Erlangen, Germany, September 22nd to 26th
- [AMBER] 4x Asus Titan boards :) GB/nucleosome passed
- [AMBER] A General Question with regards to the NVT & NPT ensembles in MD Simulations
- [AMBER] Abnormal simulation in the sulfonic acid group.
- [AMBER] about adding counter ions
- [AMBER] About cntrl error...please help..
- [AMBER] about run REMD(replica exchange molecular dynamic)
- [AMBER] Active site focusing in using "pbsa"
- [AMBER] Amber 12 installation on OSX
- [AMBER] Amber 12 on OSX 10.8.4
- [AMBER] AMBER atom types in parm10.dat don't match antechamber
- [AMBER] AMBER COMPATIBILITIES
- [AMBER] Amber force field for Benzene sulfonamide.
- [AMBER] AMBER GPU Job Write Fails
- [AMBER] amber on-line server
- [AMBER] Amber11 AmberTools1.5 installation problem
- [AMBER] Amber11 bugfixes 19, 20 and 22 failed
- [AMBER] Amber12 installation on SGI cluster
- [AMBER] amber12's performance on AMD
- [AMBER] Ambertools compilation without Netcdf
- [AMBER] ambertools update 10 problem
- [AMBER] aMD tutorial
- [AMBER] ANN: mdtraj 0.3 released
- [AMBER] Anomalous peak of RDF of water when using ptraj of AmberTools12
- [AMBER] antechamber
- [AMBER] Antechamber atom types and all_nuc94.in atom descriptions
- [AMBER] antechamber issues
- [AMBER] Antechamber problem with sqm
- [AMBER] Asking suggestion
- [AMBER] Assigning protonation o residues for parallel tempering
- [AMBER] atom type for N bond to conjugated chain using antechamber
- [AMBER] bad atom type: cl MMPBSA.py
- [AMBER] bond command
- [AMBER] Bridging waters
- [AMBER] Calculating diffusion Constant D
- [AMBER] can thermodynamics integration be used for calculating binding free energy of peptides and proteins?
- [AMBER] Checking Sander energy values
- [AMBER] compilation error: /usr/bin/ld: cannot find -lStatistics
- [AMBER] compilation of amber12 on cray system
- [AMBER] constant pressure simulation
- [AMBER] constructing single nucleotides in leap
- [AMBER] Copper parametrization for a laccase center
- [AMBER] cpptraj hbond bridgeout problems with V13.0
- [AMBER] Creating a new Solvatebox
- [AMBER] Crystallization of K+ Cl- ions during the protein+lipid bilayer simulation
- [AMBER] CUDA MPI compilation issue
- [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure
- [AMBER] Custom Heme Parameters
- [AMBER] cyclic-di-nucleotid
- [AMBER] differences between amber ff10 and ff12SB
- [AMBER] different results by sander and sander.MPI
- [AMBER] DihedralSearch.cpp:53: error: unknown escape sequence '\*'
- [AMBER] Distance based mask for qmmask
- [AMBER] DNA Phosphate error
- [AMBER] Entropy calculation error
- [AMBER] error in running MMPBSA.MPI , mmpbsa_py_energy could not be found
- [AMBER] Error while umbrella sampling with distance restraint
- [AMBER] Error: Atom type amber99_42 (residue HOH) not found in atomtype database
- [AMBER] espgen and G09
- [AMBER] Estimate error for TI calculations
- [AMBER] Exclude H-atom from bfactor calculation
- [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
- [AMBER] Explicit vs Implicit solvent for REMD
- [AMBER] extraction of specific region of the trajectory file using ptraj
- [AMBER] FATAL: Atom XXX does not have a type
- [AMBER] First to Second Frame Position Jump
- [AMBER] fix_traj_parm.py problems
- [AMBER] Fixing pdb files prepared in VMD, minor errors
- [AMBER] Force Field for DNA-Protein complex
- [AMBER] GTX-770
- [AMBER] GTX780
- [AMBER] GTX780 News
- [AMBER] GTX780 Update
- [AMBER] GTX780s
- [AMBER] hbond analysis - bridgeout
- [AMBER] How to add metal ions?
- [AMBER] how to add the pseudopotential via the Amber-Gaussian interface
- [AMBER] How to assign initial velocities (directly not by increasing temeperature) to water molecules
- [AMBER] How to define NO SHAKE
- [AMBER] How to define reaction coordinate in Umbrella sampeling
- [AMBER] How to modify the formula for non-bonded interactions
- [AMBER] How to run aMD with amber?
- [AMBER] igb8 SURFTEN SURFOFF
- [AMBER] improper dihedral with gaff
- [AMBER] instablity of ligand during minimization
- [AMBER] installing Amber 11 and Amber tools 1.5
- [AMBER] Interaction energy-based residue-residue correlation matrix
- [AMBER] Is it possible to do constant pH simulations by titrating the basic residues as well?
- [AMBER] Is it possible to merge static PDB files of the same PDB ID to become a mdcrd file?
- [AMBER] Is it possible to run accelerated MD with amber10?
- [AMBER] isothermal compressibility
- [AMBER] Ligand show error in Dock complex
- [AMBER] Line minimizer aborted: step at lower bound
- [AMBER] MCPB
- [AMBER] MD simulation parameters: urgent please
- [AMBER] mdread
- [AMBER] mdread MMPBSA
- [AMBER] Message to AMBER GeForce GPU Users
- [AMBER] Methods for RESP charge generation
- [AMBER] Methylated histidine lib and frcomd files
- [AMBER] minimization codes
- [AMBER] MM-GBSA igb=2 or igb=5? [Ref: Exploring Protein Native States and Large-Scale Conformational Changes With a Modified Generalized Born Model]
- [AMBER] MMPBSA
- [AMBER] MMPBSA Alanine scan terminal residues
- [AMBER] mmpbsa input parameters
- [AMBER] mmpbsa nonpolar contribution using stability calculations
- [AMBER] MMPBSA.MPI:IndexError: list index out of range
- [AMBER] MMPBSA.py
- [AMBER] MMPBSA.py decomp, -deo, PB only problem
- [AMBER] MMPBSA.py decomposition CSV output -- proposal for improvement
- [AMBER] MMPBSA.py problem
- [AMBER] MMPBSA.py problem on G gas
- [AMBER] MMPBSA.py.MPI run issues
- [AMBER] mmPBSA.py: mmGBSA and solute dielectric constant
- [AMBER] Modified Nucleic Acid
- [AMBER] Multiple Trajectory MMPBSA
- [AMBER] NAB atom manipulation
- [AMBER] Negative Pressure During Equilibrium
- [AMBER] NVE Energy/Temperature Drift Issue
- [AMBER] online server of amber
- [AMBER] Parmed.py deletedihedral
- [AMBER] PCA Contributions
- [AMBER] plane-plane angle restraint
- [AMBER] pmemd.cuda Energy Minimization Slow
- [AMBER] pmemd.cuda.MPI NPT Issues
- [AMBER] problem (re)compiling pmemd.cuda_SPFP: Reading module netcdf at line 23 column 34: Expected integer
- [AMBER] Problem in running antechamber.Unable to achieve self consistency to the tolerances specified
- [AMBER] problem on heating with restraints on the solute
- [AMBER] Problem regarding the cuda installation using NetCFD.
- [AMBER] Problem related to the umbrella sampling
- [AMBER] Problem related to the WHAM analysis
- [AMBER] Problem with increasing values in limits.h for resp
- [AMBER] Problem with visualization in VMD after using AUTOIMAGE
- [AMBER] Problems running NAB scripts in the manual
- [AMBER] Problems with generating histograms in AMBER tutorial 18
- [AMBER] Problems with NAB
- [AMBER] Processing of output files using process_mdout.perl
- [AMBER] Ptraj B Factor PDB
- [AMBER] ptraj, outprefix not giving a stripped prmtop
- [AMBER] QM/MM using Gaussian03 as External
- [AMBER] quality membrane protein
- [AMBER] question about hydroxyproline and new atom type'OO'
- [AMBER] question of Radius of Gyration
- [AMBER] re
- [AMBER] Re-Imaging Trajectories
- [AMBER] read trajectory using ambertools
- [AMBER] Reference for TI derivation
- [AMBER] repeat amber run on cuda
- [AMBER] Request Force Fields References
- [AMBER] Residue chirality
- [AMBER] residue selection
- [AMBER] Resp charges for large number of atoms in an ONIOM calculation
- [AMBER] Resp fiiting method and theory
- [AMBER] SA Bomb in sa_arc()3 error
- [AMBER] sander option "-radii"
- [AMBER] Segmentation Error
- [AMBER] setting up non-standard amino acid residues for MD simulation
- [AMBER] simulating complexes
- [AMBER] simulating Modified residue of Cysteine attached to mercury
- [AMBER] solvent accessible surface area (SASA)
- [AMBER] speed of amber12
- [AMBER] stopping simulation in between
- [AMBER] TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
- [AMBER] the question about the atom type of my molecule
- [AMBER] The recommended way to create periodic box around lipid bilayer system ?
- [AMBER] TI solvated ligand simulation "vlimit exceeded for step"
- [AMBER] TI with ifsc==2
- [AMBER] TIME(ps) value
- [AMBER] timecorr
- [AMBER] Troubles with making a movie in VMD,
- [AMBER] Units of summary files produced by process_mdout.perl
- [AMBER] unsubscribe
- [AMBER] unsupported GNU version! gcc 4.7 and up are not supported
- [AMBER] Update 12 for AmberTools 13: CPPTRAJ
- [AMBER] update Ambertools 12 to 13 fails
- [AMBER] using acpype with AMBER13 Error: /bin/sh: 1: -i: not found
- [AMBER] validation of MMPBSA results
- [AMBER] viewing PREPIN/PREPC files
- [AMBER] VMD prepared errors (precise error messages)
- [AMBER] What's the difference between NetCDF files and .crd files?
- [AMBER] Wrong results in GTX TITAN, correct results on GTX580
- [AMBER] xleap, unit connectivity and atom name
- [AMBER] xlf Command not found
- [AMBER] 答复: timecorr
- [AMBER] 答复: 答复: timecorr
- [AMBER] 答复: 答复: 答复: timecorr
- [AMBER] 答复: 答复: 答复: 答复: timecorr
- [AMBER] 答复: 答复: 答复: 答复: 答复: timecorr
- Copper parametrization for a laccase center
- DihedralSearch.cpp:53: error: unknown escape sequence) '\*'
- FATAL: Atom XXX does not have a type
- MMPBSA problem
- Last message date: Wed Jul 31 2013 - 20:30:04 PDT
- Archived on: Mon Dec 02 2024 - 05:54:49 PST