Amber Archive Jun 2011 by subject
- [AMBER] About "Must have more residues than processors"
- [AMBER] About difference between Sander and Pmemd
- [AMBER] About the coordinates of input or output files
- [AMBER] Adding NH2 at the end of peptide
- [AMBER] alanine mutagenisis in amber
- [AMBER] Alanine scanning
- [AMBER] Alanine scanning with CYS
- [AMBER] algorithm for rms
- [AMBER] Amber
- [AMBER] Amber 10: Compilation error
- [AMBER] AMBER 11 and Ambertools 1.5 Installs failing tests for mmpbsa_py
- [AMBER] Amber 11 and AmberTools 1.5 on Debian 6
- [AMBER] Amber Compilation error
- [AMBER] AMBER Workshop in Shanghai, China, August 22-26, 2011
- [AMBER] amber10 output
- [AMBER] AMBER11 Installation on FEDORA 15
- [AMBER] AMBER9- error in LEaP while learning MMPBSA tutorial
- [AMBER] AMBER: error in reading namelist cntrl
- [AMBER] ambertools 1.2 compilation error on Debian Linux
- [AMBER] AmberTools 1.5 + Amber 11 installation - bugfixes conflicts?
- [AMBER] AmberTools 1.5 gnu compilation fails under FC15
- [AMBER] AmberTools 1.5 installation problem
- [AMBER] ambertools.1.5 installation errors on Linux
- [AMBER] Amoeba with water and ion
- [AMBER] Amoeba with water and ions (2)
- [AMBER] Antechamber
- [AMBER] Antechamber Error
- [AMBER] ANTECHAMBER/RESP
- [AMBER] Antechamber: Failure to calculate Mulliken partial charges using a Tripos MOL2 input file
- [AMBER] Architecture/compiler is not supported Error!
- [AMBER] Bfactor calculation in cpptraj
- [AMBER] bin size for rdf
- [AMBER] Binary reported data were wrong..
- [AMBER] Bug - AMBER Atom type - iodine
- [AMBER] Calculating energies
- [AMBER] Can Amoeba force field be used with divalent ions?
- [AMBER] Can I directly compare the PMF for two compounds with different size and chemical structures?
- [AMBER] CHAMBER and making PDB files
- [AMBER] CHAMBER prmtop
- [AMBER] Choosing the number of replicas in NEB
- [AMBER] Compile Python error
- [AMBER] concerted effect of the backbone movement
- [AMBER] CPPTRAJ- segmentation fault
- [AMBER] CUDA 4.0 RC
- [AMBER] Delete Solvatebox
- [AMBER] Detection of residues within a sphere
- [AMBER] DIELC constant for normal mode analyses in vacuum ?
- [AMBER] Dihedral parameters for sp carbon in GAFF
- [AMBER] dist restraint
- [AMBER] Does anyone know a screening program of hardware validity for GeForce GTX board?
- [AMBER] Energy decomposition
- [AMBER] Energy Decomposition Error using Perl Script (#RECMAP + #LIGMAP != #COMPRI)
- [AMBER] energy decomposition with mmpbsa.py
- [AMBER] energy of a single amino acid during minimization
- [AMBER] Entropy Decomposition
- [AMBER] Error compiling ambertools 1.5
- [AMBER] Error message for cpptraj
- [AMBER] Error mmpbsa
- [AMBER] error running mmpbsa
- [AMBER] Error While running RED III.4
- [AMBER] Estimation of free energy of solvation ?
- [AMBER] ff03 force field
- [AMBER] Force fields for DNA, what to choose?
- [AMBER] format error from mmpbsa.py
- [AMBER] forrtl: severe (64): input conversion error, unit 9
- [AMBER] Free energy perturbation of Ca2+ ion
- [AMBER] Frequency analysis of small molecule, constructing heterocyclic ring systems
- [AMBER] Fwd:
- [AMBER] Fwd: Interpreting the distance covariance matrix
- [AMBER] Fwd: warning in ptraj check coordinates()
- [AMBER] give_diff_runs
- [AMBER] Glycam Parameters for O-SIALIC ACID
- [AMBER] Gromacs to Amber trajectory
- [AMBER] Hairpin
- [AMBER] High-temperature output in REMD
- [AMBER] how to assess the convergence of the clustering
- [AMBER] how to interprete x.ss file
- [AMBER] How to prepare ATP with Antechamber?
- [AMBER] hydration number
- [AMBER] I want to add amide group at the end of my peptide ?
- [AMBER] Inquiry about installing AMBER
- [AMBER] Installation of Amber 9 : Problem
- [AMBER] Installation Problem
- [AMBER] Installation Problem : Amber 9
- [AMBER] installing ambertools
- [AMBER] interaction energies of DNA
- [AMBER] Interpreting the distance covariance matrix
- [AMBER] intra- and interstrand interaction energies of DNA
- [AMBER] Issues with Generating Prep File from Gaussian output using Antechamber
- [AMBER] keyword ref
- [AMBER] Kinetic energy in mdout file is not identical to that calculated from mdvel file.
- [AMBER] Leap adds atoms to pdb (tutorial B1)
- [AMBER] Leap question/suggestion for leap developers
- [AMBER] Ligand Minimization with Simulated Annealing
- [AMBER] Loadin AMBER9 in linux
- [AMBER] loadPdbUsingSeq command
- [AMBER] Methane with no surface area?
- [AMBER] missing residue
- [AMBER] MM-GBSA with QM/MM
- [AMBER] MM-PBSA/GBSA of charged molecules
- [AMBER] mm_pbsa.pl with Fe(III) ion
- [AMBER] MMPBSA
- [AMBER] mmpbsa-bad atom (metal ions)
- [AMBER] MMPBSA-binding energy calculation
- [AMBER] mmpbsa.py
- [AMBER] MMPBSA.py decomp
- [AMBER] MMPBSA: general question
- [AMBER] MPI_ABORT errorcode 1 for sander.MPI
- [AMBER] MPI_ABORT errorcode 1 sander
- [AMBER] Natural Language Angle Restraint
- [AMBER] Negative value of SASA calculated by surf command in cpptraj
- [AMBER] netcdf
- [AMBER] NETCDF Installation Error
- [AMBER] Nmode calculations using Amber 8
- [AMBER] Nmode with amber8
- [AMBER] NMR chemical shift restraints for an intrinsically disordered peptide
- [AMBER] NMR restraints file format
- [AMBER] noesy and dip Program error when testing Amber11 Parallel
- [AMBER] non-bonded cutoff in the case of REMD in explicit solvent
- [AMBER] Non-periodic behavior of NMR restraints upon restart in a periodic system
- [AMBER] Non-Standard Residues Problems
- [AMBER] Normal Mode Analysis
- [AMBER] Nucleic residues with methylphosphonates
- [AMBER] pairwise RMSD
- [AMBER] Parallel compilation of AmberTools1.5 failed
- [AMBER] Parallel compilation of AmberTools1.5 failed (2)
- [AMBER] PDB survey
- [AMBER] pH-dependent folding simulation
- [AMBER] PMEMD does not support intermolecular PRFs
- [AMBER] prep files ATP-MG++ and for phosphorylated threonine
- [AMBER] Prevent tleap to rearrange my ions?
- [AMBER] problem about entropy calculation
- [AMBER] Problem in the energetics of the system Shake cannot be accomplished.
- [AMBER] Problem related to Missing amino acids in pdb
- [AMBER] Problem related to teh residue template and add ion
- [AMBER] Problem related to the load PDB
- [AMBER] Problem related to the load PDB/missing residues problem
- [AMBER] Problem related to the residue template and add ion
- [AMBER] Problem related with the Ptraj
- [AMBER] Problem with make test.serial Amber 9
- [AMBER] Problem with two jobs on one GPU
- [AMBER] problems ahout simulating a molecular crystal
- [AMBER] Problems Compiling Amber10
- [AMBER] Problems Compiling Amber11 Parallel GPU
- [AMBER] problems with relaxing a phosphonamide parametrizated with Antechamber
- [AMBER] production run duration
- [AMBER] ptaj: contacts
- [AMBER] ptraj cluster
- [AMBER] PTRAJ clustering
- [AMBER] ptraj error with *** glibc detected *** ptraj: free(): invalid next size (normal)
- [AMBER] ptraj in parallel
- [AMBER] ptraj, alignment, and rmsd
- [AMBER] ptraj: cluster
- [AMBER] ptraj: Could not find target 300.000000 in any of the replica trajectories
- [AMBER] query regarding void volume calculation in protein-ligand complex
- [AMBER] query with multocomponent system
- [AMBER] question about amber
- [AMBER] Question about INTRAmolecular restraint
- [AMBER] Question about the influence of trajectory format (ioutfm) on results
- [AMBER] Question about the influence of trajectory format (ioutfm) on results - part 2
- [AMBER] Question on the construction of a topology file
- [AMBER] R: forrtl: severe (64): input conversion error, unit 9
- [AMBER] R: R: forrtl: severe (64): input conversion error, unit 9
- [AMBER] RAM requirements
- [AMBER] RDF
- [AMBER] re-image
- [AMBER] Recompiling amber 8 on IBM
- [AMBER] RED
- [AMBER] regarding per residue decomposition of binding free energy using perl script
- [AMBER] regarding per residue wise free energy decomposition
- [AMBER] regarding pi-pi interaction
- [AMBER] Request for Amber Heme parameter file
- [AMBER] residual dipolar coupling restraints
- [AMBER] Residue numbering
- [AMBER] Resp charge
- [AMBER] Restart problems with pmemd.cuda
- [AMBER] Restraint Minimization
- [AMBER] restraint simulation
- [AMBER] restraints file
- [AMBER] rmsd calculation
- [AMBER] RNA duplex
- [AMBER] running a MD with a innert gas
- [AMBER] SANDER BOMB
- [AMBER] Sander Compilation Problem
- [AMBER] Sander Error
- [AMBER] sander terminates abruptly
- [AMBER] sander.mpi with amoeba?
- [AMBER] saving the first solvent shell molecules by Ptraj
- [AMBER] secondary structure plotting
- [AMBER] secstruct analysis
- [AMBER] Simulating a periodic System about Molecular Crystal
- [AMBER] simulation of small molecule with organic solvent and water
- [AMBER] single amino acid energies
- [AMBER] Sirius software
- [AMBER] sleap never worked anymore since AT 1.2
- [AMBER] sleap/tleap mol2 features
- [AMBER] small inconsistencies in parm99.dat and parm94.dat
- [AMBER] software assistance
- [AMBER] Solid surface simulation in Amber - the recommended approach ?
- [AMBER] Solution for frozen atom type
- [AMBER] Sorry again..this is right
- [AMBER] Steered Molecular Dynamics
- [AMBER] Structured water molecules with leap
- [AMBER] Suggestion for minor user manual clarification
- [AMBER] Suggestions for additions to AmberTools
- [AMBER] System temperature
- [AMBER] tleap error in reading structure generated from GLYCAM web
- [AMBER] trouble installing Amber 10
- [AMBER] unexpected behavior of ambpdb
- [AMBER] Units of SMD Simulation Output
- [AMBER] Uracil is not recognised as a nucleotide in Xleap - in FF99
- [AMBER] using Mg with ff99SB
- [AMBER] Using PQR files produced by PDB2PQR as input for tleap/xleap
- [AMBER] Using PQR files produced by PDB2PQR as input fortleap/x leap. .
- [AMBER] velocity auto correlation function; resident time;
- [AMBER] Velocity autocorrelation function
- [AMBER] Vibrational entropy with NAB
- [AMBER] VMD-Chamber interface
- [AMBER] warning in ptraj check coordinates()
- [AMBER] water test with pmemd.amba
- [AMBER] Where to send patches?
- [AMBER] Zotac GTX 580 3 GB
- Error While running RED III.4
- Last message date: Fri Jul 01 2011 - 02:00:03 PDT
- Archived on: Wed Dec 11 2024 - 05:54:13 PST