The following responses were culled from more than 4000 entries in the
Amber mail archives. They are still in chronological order, but the "find"
command in your browser may help. I have tried to "sanitize" all personal
information, except where people have expressly asked to be sent e-mails.
You can use Google to search this list: add "site:amber.scripps.edu" to your
keyword list to get just information from the Amber site.
- ewald and cutoff
- RE: RESP question
- OWFEG and other AMBER 6.0 manual issues
- AMBER PBC images
- Harmonic restraints on distances in sander
- IBELLY
- estimate entropy of dna using nmode
- trouble with NTR=1 and NMROPT=1
- Empty gap in the watbox at the beginning of MD
- GB parameters
- Ca2+ parameters
- Brief courses on AMBER 6
- converting MSI pdb files to Amber
- rdparm/ptraj
- Calcium bonds
- NMODE
- DMSO parameters
- nmode out of memory
- AmberFFC 1.0
- POL3 frcmod file
- Sander/MPI/redimension
- adding dummy torsion parameters
- question
- OWFEG documentation
- 2 questions
- dynamics with different pH conditions
- parameters for GB use
- Discover to AMBER trajectory utilities
- FW: INTPRT
- DNA flexibility
- Gibbs with Linux RH 7.0
- pressure regulation
- Typo's in the Parm99.dat
- Cavity solvation
- Belly option in sander
- RE: Lone Pairs.
- Ionic solutions
- RE: Ionic solutions
- Amber Parameters
- how to handle a metal ion
- AMBER mail reflector archive
- periodic box size
- imaging in amber6
- lipid bilayer MD simulations
- SHAKE
- sander VS sander_classic
- SHAKE
- RE: Xleap
- loading prmtop and inpcrd into leap
- Resp
- RE: saving a trajectory as individual pdb files
- RE: producing a post-ptraj prmtop
- Pairlist error
- RE: Windows version of AMBER?
- How to let IBELLY and NTR both on?
- tree names in group spec.
- RMSD calculation
- Residence time
- Amber, VMD and visualization
- Amber, VMD and visualization
- Amber, VMD and visualization
- summary: titratable amino acids and counter ions
- Adding crystal water using tleap.
- summary of Zn+2 van der Waals radii responses
- AmberFFC version 1.2
- RE: CCl4 charge problem...
- folding simulations
- AMBER parameter database
- RE: CCl4 ESP Grid problem with jaguar | 010628a (fwd)
- RE: CCl4 ESP Grid problem with jaguar
- gamess X resp : Conclusions. (fwd)
- ptraj diffusion
- ewald bomb in amber 6
- ewald bomb in amber 6
- ewald bomb in amber 6
- AMBER box
- dissociation of protein from DNA in MD
- solvation energy calculation
- adding atoms and amino acid residues
- adding atoms and amino acid residues
- GB and Ions, 2nd try
- RE: Binary mdcrd
- Temperature and pressure couplings
- Drivers to support Stereo Viewing in VMD etc using Standard GeForce Cards
- Drivers to support Stereo Viewing in VMD etc using Standard GeForce Cards
- RE: Drivers to support Stereo Viewing in VMD etc using Standard GeForce Cards
- RE: Drivers to support Stereo Viewing in VMD etc using Standard GeForce Cards
- R: color in xleap
- Amino acid unit "NHE" problem ?
- nmode memory requirements
- Latest parm + getting parm98 as default in LEaP
- "flags" in .lib files
- question regarding ntwv.
- AMBER logo citation
- Re Europium force field parms
- Re Europium force field parms
- scaleCharges
- combining trajectory file
- MM-PBSA philosophy
- GB model and belly
- What is the atoms limit for Amber 7?
- Amber6, GB (Memory, MATOM, nmr.h)/Folding (mutation)
- does PME function without charge neutralization?
- Amber7 and VMD
- GBSA with bromine
- INTPRT and PMF
- RESP tutorial
- generating left-handed A-DNA
- amber7 and tip5p
- Number of WATBOX
- PMF calculations
- PMF calculations
- PMF calculations
- parmjoin
- TIP4P parameters
- NTT=5?
- valine to alanine example
- NTT=5?
- NTT=5?
- heterochirical peptides ?
- NTT=5?
- Amber7 nmode
- NMR refinement
- this is a test of the amber reflector. Please ignore. Marcela
- antechamber
- again about sander_classic Amber 6.0
- PME & cutoff
- MPich error
- xLeap problem
- Intel Kernel Math Library
- RE: Reorder water in amber7
- RE: minimization probs
- vlimit exceeded
- Periodic water box
- j3 coupling
- ptraj problem
- SHAKE (actually: new atom types)
- Problem in amber
- taupt: time constant for heat bath coupling for the SOLUTE
- van der Waals, hydrogen bond energy
- md equilibration in chloroform
- eedmeth variable in AMBER7
- Announcement: Optimally Partitioned Electric Properties - OPEP
- Question about error message about "lastist" and "virtual box"
- counter-ions in FEP
- are there inconsistencies in anal?
- LEaP gives "no sp2 improper torsion term" warnings
- Problem with LEAP
- prmtop file question.
- The 216 water box
- electrostatics truncation in AMBER
- correction about solvateOct
- Questions about xleap and mm_pbsa]
- Questions about xleap and mm_pbsa(cont.)
- several questions
- several questions
- "crd" file created with VMD
- am1-bcc charges, antechamber
- am1-bcc charges, antechamber
- SS bond
- increase lastist
- Umbrella sampling in AMBER
- water box size
- mol2 with antechamber
- RE: ptraj
- parallel jobs die with no error message from sander
- SANDER documentation for nmropt
- a water jumps
- RE: AM1-BCC sensitivity to AM1 charges
- periodic box
- Potential Energy and RMS-Deviation Issues
- reorder water with nmropt
- FWD: RE: Including explicit waters in GB dynamics
- water box-nonperiodic
- Please give me a hand on understanding AMBER/MPI and locmem.
- problems with parallel sander on linux clusters?
- Import of CHARMM force field and GB potential parameters into Amber7
- MD in alcohol
- Generalized Born and OPLS potential
- "number of processors must be a power of two"
- protonation pH dependent
- RE: trajectory file limit???
- PMF with sander module
- Antibody residue numbering
- RE: Antibody residue numbering
- adding_hydrogens_to_pdb (fwd)
- ewald bomb in md equilibration (fwd)
- Gibbs (FEP) (fwd)
- how to make mpeg files from amber trajectories
- [ can carnal do the job as anal to break down the energy?]
- IMIN=5 ? (Was: Re: [Re: can carnal do the job as anal ...)
- water box size
- trajectory problem?
- carnal averaging
- compiling amber on a linux box using DMEM-ALLOC
- RE: cut-off question
- who to address this to?...
- sander.LES questions
- Distace dependent dielectric constant
- Dynamic Movement of Molecule
- vlimit and vmax
- mol2 file format in the future of amber
- mm_pbsa
- expression of V(lambda) in GIBBS
- watershell in ptraj
- Question about Antechamber
- mm_pbsa and statistic program
- Request for help with Antechamber
- MM-PBSA basics
- antechamber web page
- Different numbers on different architectures.
- Dielectric constant for interior of proteins
- loss of disulfide bonds
- Compiler & Hardware requirement of AMBER7 ?
- Error in Antechamber program in ammber7
- How to convert oldparmtop to newparmtop?
- IGB =4 with GAFF and bugfix24 incomplete?
- dummy torsional parameters again.
- cutoffs in GB
- Carnal table output
- Is H-bonding really there?
- MM-PGBSA Question!!
- min output
- 64-bit Compilation SUN's forte compiler
- time correlation function
- xleap and modified sugar residues
- molsurf reference
- RE: P4_GLOBMEMSIZE problem
- average and runningaverage in ptraj
- residue cross-correlation
- Sander: check COM velocity, temp: 0.000000
- limit of RMSD value
- RE: PARMSET
- PARMSET
- ion distances
- Restraint Ambiguities
- solvateOct
- gB vs. explicit
- CCL:ion concentration in protein simulation
- solvating a protein with large cavity
- SUMMARY: solvating a protein with large cavity
- protein is compressed upon equilibration
- Are ewald and belly compatible?
- one way to create a box of solvent
- Linux cluster Amber7 sander mpi error -- Null communicator, IOT
- free energy perturbation (Gibbs/Amber 5)?
- chloroform, dichlormethane f.f.
- script for Potential/kinectic energy
- Dummy-parameters in Amber?
- conformational sampling
- terminal phosphate group in RNA
- Zn2+ parameters
- RE: Intramolecular H-bonds in charge fitting
- RE: script for H-bonds extracting
- MM_PBSA
- Quasi-harmonic analysis
- Gibbs, ewald and ifc
- Amber7 & mpich
- The image command of ptraj of Amber 6 is not working.
- RE: failure of minimization
- Compilation error of Amber 7 using pgi and mpich on Linux
- Leap to prep
- end of namelist options for IBM
- Notes: Compiling Amber 7 on Mac OS X (fwd)
- Side-chain/main-chain decomposition in MM-GBSA
- addles
- question about MM-PBSA?
- Request for Amber7 (xleap problem)
- Description of ATOM type in GLYCAM
- Ewald: coeff, error estimate
- Etot is not constant in NVE ensemble
- Etot is not constant in NVE ensemble
- H-O-H angle
- Mainchain.dat
- jarrod
- LEAP compiling problem
- GAFF in GUI MD apps
- your mail (IBM runtime problem)
- Valdiation of Latest Amber parameters
- AMBER: methylphosphonate
- AMBER: question about quasih?
- AMBER: AMBER and NAMD
- AMBER: question about ptraj
- FW: dynamics of isolated system (loops are not closed at all!)
- AMBER: derive corresponding torsional parameters
- AMBER: machine dependent?
- AMBER: question to calculate diffusion coefficient under periodic
- AMBER: simulating a crystal using the unit cell
- AMBER: modelling a Ca binding site
- Re[2]: AMBER: antechamber problem
- AMBER: Using NWCHEM for esp?
- AMBER: solvatebox-solvateshell
- AMBER: Calculating solvation energies for MM-PBSA use
- AMBER: NaCl ion pairs in TIP3P water box
- molecule definition
- AMBER: frozen x unfrozen and the gibbs tragedy
- AMBER: Simulation of small protein (MD Display tips)
- AMBER: mddisplay
- RE: AMBER: Simulation of small protein
- AMBER: mddisplay
- RE: AMBER: aminoacid mutation
- AMBER: aminoacid mutation
- AMBER: ibelly problem
- AMBER: mddisplay
- AMBER: a problem with antechamber and leap
- AMBER: GB/SA
- AMBER: GIBBS - PMF problem: Lambda has not changed
- amber-developers: Pmemd vs sander
- AMBER: MOPAC from antechamber
- AMBER: no "Input orientation" in g98 log
- RE: AMBER: atom type CM
- AMBER: leap - orientation of sequenced residues
- AMBER: positive binding free energy
- AMBER: rdparm/ptraj writeparm
- AMBER: amber98 with amberffc+INSIGHT II
- AMBER: About RESP Calculation
- AMBER: About RESP Calculation
- AMBER: About RESP Calculation
- AMBER: About RESP Calculation
- AMBER: INtel Fortran 90 compiler
- AMBER: INtel Fortran 90 compiler
- AMBER: hbond analysis in ptraj(%occupied>1)
- AMBER: PMEMD and myrinet trouble
- AMBER: pmemd speedup and interactions
- AMBER: test output of amber8
- AMBER: installing amber8 on a dual processor single box
- AMBER: installing amber8 on a dual processor single box
- AMBER: question about image
- AMBER: question about image