AMBER Archive (2001) - By Subject1217 messages sorted by:
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About this archive
Starting: Tue Jan 02 2001 - 02:41:34 CST
Ending: Sun Dec 30 2001 - 21:24:17 CST
- "Goodness" of Trajectory
- (fwd)
- (no subject)
- (to "Xiaolin Chuang")
- ... error message
- 1-4 nonbonded interactions
- 2'-deoxy-uracil
- 2-Amino Purine Parameters
- 5-methyl deoxycytosine parameters
- 8-Oxo-G
- 90 degree phase offset in AMBER?
- ?s: Xeon vs. Athlon, latency
- [Amber]: Peptide torsions in Parm99.dat
- [charmm-bbs] Post-doctoral Position
- [charmm-bbs] Post-doctoral position available
- [Fwd: ?s: Xeon vs. Athlon, latency]
- a correction, sorry
- a few more questions
- a funny problem about output for sander_classic
- A request regarding AMBER postings with attached files
- A request regarding AMBER postings with attached files (fwd)
- About :ERROR TERMINATION DUE TO SHAKE OR TORCON
- About Delphi...
- about dials_and_windows
- about ion concentration in protein simulation
- about ion-amino group non-bonded distance
- about OWFEG
- about Owfeg in Amber 6.0
- about plevel in sander 6
- about prep input
- about pressure
- about radius of gyration
- About the input of GIbbs and parm98 and Monte Carlo
- About the input of GIbbs and parm98 and Monte Carlo (Sorry for my mistake)
- add counterions
- Add electric field
- adding atoms and amino acid residues
- Adding crystal water using tleap.
- Adding ions in xleap
- ADDING IONS USING EDIT
- adding water
- addions
- addions in leap
- addles
- Again Gibbs...
- AMBER
- Amber & F90
- Amber 6
- Amber 6 MDCRD Files > 2GB in 32 bit Linux.
- AMBER 6 on Linux - help
- Amber 6 on parallel SUN
- AMBER 6 on PME
- Amber 6.0 Benchmarks
- Amber 6.0 on Intel IA-64 Server
- Amber 6.0 on Linux Cluster
- Amber 6.0 on LINUX with absoft
- AMBER box
- AMBER compilation woes
- AMBER Compile Question
- Amber compiling on Alpha Clusters Redhat Linux
- AMBER enquiry
- Amber for SP
- Amber installation
- Amber installation on linux
- AMBER mail reflector archive
- AMBER on alpha
- AMBER on Hitachi SR8000
- AMBER on LINUX
- AMBER on mpi
- AMBER on SUN
- AMBER parameter database
- AMBER parameter for HCOO(-) and NCHCHNHC
- AMBER parameters
- AMBER vdW
- Amber Website - UK Mirror
- Amber, VMD and visualization
- amber-request@cgl.ucsf.edu
- amber5 and 77000 atoms ...
- amber5/6
- Amber6 by g77 and mpich
- amber6 compilation failure (fwd)
- amber6 in SGI Origin 2000
- AMBER6 on Alphas40
- AMBER6 on Alphas40 (fwd)
- Amber6 on AMD Athlon
- AMBER6 on IBMSP3
- AMBER6 on IBMSP3 (again)
- AMBER6 on IBMSP3 Installation
- Amber6 on SuSE Linux
- AMBER6/PME on Origin 2000
- AmberFFC version 1.2
- An Amber question
- An Invitation From The Middle East Chemical Industry
- ANAL
- ANAL (Amber6.0)
- anal ouput
- Analysis
- analysis of the results
- analysis problem
- Analysising the results
- Animating normal modes
- Announcing PyMOL v0.56 (+ Windows Installer)
- another error
- applying atom types
- Aqvist LJ parameters
- ask help
- Athlon 1GHz (was: Dual Origin vs dual Alfa)
- atom coordinates
- atom types for xleap
- ATP+Mg, P-tyrosine a P-threonine
- average structure
- Bang for the Buck
- batch mode
- begginer's question about RESP and GAMESS
- begginer's question.
- beginners problem (fwd)
- Belly Atonms
- Belly option in sander
- belly run
- belly with GB term
- Belly+Restraints
- benchmark on X-86
- benchmarks
- Best Topolgy for Linux Cluster
- Binary mdcrd
- block attachments?
- Blowup problem
- Box info after minimization
- box information
- box of water
- box size
- C DNA MONOMER UNITS
- C-terminal amide
- C8-methyl-guanine
- Ca2+ parameters and how ? ...
- calc free energy during dynamics
- Call for Papers: Special issue of MATCH
- Can amber calculate the gibbs perturb energy when a ligand added a group
- Can't compile Sander with parallel on Linux cluster
- Can't compile sander witk parallel on Linux cluster
- Can't run sander_classic with parallel machine
- CARNAL
- carnal error with crd files stripped of waters
- carnal problem
- Cavity solvation
- CCl4 charge problem...
- CCl4 charge problem... (part II)
- CCl4 ESP Grid problem with jaguar
- CCl4 ESP Grid problem with jaguar | 010628a (fwd)
- CCL:Date: Wed, 16 May 2001 13:47:15 +0200
- CCL:MEP with GAMESS or GAUSSIAN
- changing the g77 optimization for compiling sander_classic
- charge fitting
- charge on protein
- Charges for a 2-iodine-phenol
- Charges for methylated residue
- charges for non-standard AAs
- chlorine parameters
- Cl and H-bonding
- Cl and H-bonding (fwd)
- CMC/MD
- Code modification.
- color in xleap
- Combination of two solvents
- Combining trajectories
- Compilation of AMBER6
- Compilation of Amber6 in linux machine
- Compilation of LEaP on SP3
- compilation on linux6
- Compilation problem of AMBER6.0!
- compilation problems
- compile leap
- compiling amber6 in linux clusters
- computing order parameters from an MD trajectory
- Constant Pressure vs. Constant Volume
- Constraining backbone dihedrals
- constraining hydrogen bonds
- consult
- converting some files
- coordinate blowup in sander
- COORDINATE RESETTING
- coordinate resetting ?
- Correction: SP3 name list
- create a parm.top file
- creating a restrt file from frames of mdcrd and mdvel
- Creating capped peptides with AMBER
- curves
- CUT in AMBER6
- db4 with amber5.0
- Define flexible residues during MD simulation
- define the QM
- defining states in Gibbs
- Delphi Calculations
- DelPhi's manual
- density in equilibration?
- dG of wild type/mutant
- diffusion
- Diffusion constant
- dipolar couplings
- disk file larger than 2 GB
- dissociation of protein from DNA in MD
- Dist restraints + Belly Dyn
- distribution of Na+ around DNA
- DMSO ?
- DNA bend
- DNA force field
- DNA out of a box
- DNA Simulation
- DNA strand flying
- DNA strands separated...
- Drivers to support Stereo Viewing in VMD etc using Standard GeForce Cards
- dsp3 hybrid for P ?
- Dual Athlon
- Dual Origin vs dual Alfa
- Dual-processor performance.
- Dummy Atoms
- dynamic memory allocation
- E is not constant in NVE
- electrostatic point charge
- Emerging Technologies/COMP 2001
- emin after molecular dynamics
- energies for part of the protein
- Energy calculation
- energy decomposition
- equilibrating water in sander
- equilibration
- equilibriating LES
- Err in equilibration run
- ERR IN MD RUN!!
- error
- Error in Gibbs
- error in sander
- error message
- error message.
- error msg
- error msg in leap
- escaping atoms....
- esp with gamess-usB
- ESS Workshop - Flexibility and Function of Proteins
- Essential Dynamics
- ester
- ethidium bromide parms
- Ewalb bomb on SP3
- EWALD
- Ewald Bomb
- ewald bomb in amber 6
- Ewald error estimation
- Ewald sum
- f2c.h
- fatal error during equilibration of solvated system
- Fe4S4 cluster
- File format convert
- floating overflow in alpha Redhat 7.1
- Fluorescent dyes
- folding simulations
- Following Coordinates
- force fields
- free energy contribution of selected atoms vs. MM-PB/GBSA
- free energy method
- Freze solute molecules in AMBER
- GAMESS and RESP.
- gamess X resp : Conclusions. (fwd)
- Gaussian 98 to RESP
- Gaussian to Amber
- GB and Ions
- GB and Ions, 2nd try
- GB protein simulation
- gb with explicit water molecules
- GDP/GTP
- General install questions
- generalized born model on protein or peptide
- Generating C-DNA using nucgen!
- generating parameters for a small molecule ligand
- generation of small organic molecules on xleap
- GFP chromophore force field parameters
- Gibbs
- Gibbs and cutoff!
- GIBBS error
- Gibbs input
- GIBBS on Cray
- Gibbs with Linux RH 7.0
- Gibbs, PME, DynModW, ISDX0, etc.
- Gibbs/non-bonded pairs
- gibbs_restrt
- GIBSS pertType
- gradual warming + partial solvation
- group input
- h-bond energy
- helix analyse
- help
- help for restrained minimization
- Help with Leap!
- Help with new residue
- high density spot
- histidines normal-modes
- how do I turn on the verbose option?
- How is the random number used to generate random velocities?
- How tleap does not add missing H atoms?
- how to add Zn Ca parameters
- How to calculate energy from mdcrd output file
- how to create a bond
- how to create a bond (fwd)
- How to deal with the little molcule?
- how to form ljp-files for PROFEC ?
- how to get dials_and_windows
- how to handle a metal ion
- How to let IBELLY and NTR both on?
- How to minimization of Average structure?
- how to pay
- How to remove CIO from prmtop & crd
- How to turn off PME?
- how to write out ...
- how to write out...
- Hritz
- hybridization
- hydorgen bond life time
- i need help!
- I'm upset !
- ice cube flying through space
- idsx0 parameter
- igb=1 error message: Unable to find bonded partner for atom 239
- image command of ptraj
- imaging in amber6
- Implicit solvent MD with small RNA's
- Important Address change
- IMPORTANT Amber mail list announcement
- Incomplete coord file after crash
- Info
- Info about LEaP
- Informations
- input parameter for amber5
- installing amber6
- Interface
- Interface and Sander_classic
- Interface program installation
- Internal Restraints in Sander Problem
- internal variables in ptraj
- Intprt in PMF calculations
- intprt option in Thermodynamics integration
- ion analysis
- Ionic solutions
- is parm98 the same as parm99? (fwd)
- Is there a potential for speedup in the GB-code ?
- isotropic scaling of coordinates during MD
- ISTAR option and performance
- ISTAR2 and 64-bit sander
- iwrap
- iwrap & TIP3P model water
- L-J mixing rules?
- LAPACK required by Amber
- LEAP
- LEaP adding an extra hydrogen to N-terminus
- leap adding terminal phosphates
- LEAP and crystal waters
- Leap and parm/pert!
- leap and SP2 nitrogen
- LEaP compilation
- leap compile on alpha linux
- leap not reaing torsion from frcmod file
- LES analysis
- library files in leap
- LIE method
- limit in xleap
- limit the distance
- LINMIN Failure
- Linux 2.2.19 Compil. Amber 4.1 with gcc 2.95.4
- Linux 6.2 install problems
- Linux stability
- Linux-cluster performance
- Linux-cluster performance)
- lipid bilayer MD simulations
- list filter
- loading prmtop and inpcrd into leap
- Lone Pairs.
- lower_bound and upper_bound
- Machine file for sgi
- machine/OS on which make test.all crashes in AMBER
- Machine_g77_lam-mpi
- make test.all
- make test.all crashes in AMBER
- makeDIST_RST
- matrix diagonalizing subroutines
- MAX_RSTACK
- MAXGRP parameter
- Maxwell-Boltzmann distribution of velocities
- MD in vacuo
- MD integrator
- MD of DNA
- MD run with constantly decreasing total energy
- MD run with constantly decreasing total energy (fwd)
- MD with 'Solvated Ions'
- MD without SHAKE
- Measuring rigid-body rotation with AMBER
- Membrane
- MEP with GAMESS or GAUSSIAN
- Methane in water box FEP
- Methane minimization using Interface
- minimization
- Minimization and NSNB
- Minimization inputs in AMBER6!!
- Minor correction (I think) on RESP input
- Missing "ASH" parameters
- MM-PBSA
- MM-PBSA; E(internal)
- MM-PGBSA Question!!
- mm_pbsa
- mm_pbsa on single structure
- Model(l)ing 2001 in Erlangen/Germany: Bursaries and Awards available!
- Model(l)ing 2001 in Erlangen/Germany: Speaker list
- modified aminoacids using Leap
- movie for subset of atoms
- MPI version of Gibbs
- My input problem in amber6 !
- Mystery protons!
- N-terminal and C-terminal hydrogens
- NAN errors during production runs
- Need some help with Amber/Linux
- New product creates custom e-mail lists!
- Newton-Raphson minimization!
- NFFT
- Nitro group
- nmode analysis
- no. of processors decrease
- Non-standard DNA bases
- Nonbonded Pair List
- Not able to do parallel run
- not using SHAKE
- Npairs Exceeds Max
- NPSCAL parameter
- NPT restart problem
- NPT to NVE ensemble
- NRUN in AMBER 6
- NSCM in periodic simulations
- NSCM setting to remove center of mass motion
- nstlim in sander
- ntc in sander6
- nucgen
- Nucleic acid notation within Toolchest
- number of atoms for large system
- O6-methyl-guanine parameters
- OCCO in parm99
- octahedral box in AMBER6
- Octahedral Box?
- odd display of ambpdb generated files
- One article
- opinion about buying linux clusters.
- opinions on supercomputer platforms
- P-N-parameters
- P4 benchmarks posted
- Pairlist error
- parallel gibbs
- parallel load difference under linux (long)
- parallel sander
- param CT-CT-CT-OH
- parameter
- Parameter for abasic nucleotide
- parameter regarding S-O
- parameters
- parameters for 5'-phosphate GUA
- Parameters for DMSO solvent
- parameters for NADH
- parameters for neutral amino acids
- Parameters for phosphonate available?
- parameters forms
- params - ADP, neutral ARG
- parm warnings
- parm94
- parm94.dat vs parm99.dat
- parm96
- Parm98 for amino acids?
- parm99
- PARMSCAN
- Parmscan and iron parameters
- partial solvation using delphi
- PBC box problems
- PDB old to new
- peek_ewad_inpcrd
- peek_ewald_inpcrd
- Pentium 4
- Pentium IV compiler in MD
- periodic box size
- Perturbed internal coordinate parameters
- Peter Kollman
- Peter Kollman memorial
- Phosphorylated residues.
- phosphotyrosine
- plotting MD results for DNA
- PME
- PME model
- PME with octahedral box
- PMF calculations
- PMF input file
- PMF-input file
- polarization
- porphyrin parameters
- possible bug in carnal in AMBER5
- Possible error in AMBER parm94 file?
- Post-doctoral Position
- Post-doctoral position available
- post-processing of energy analysis
- Postdoctoral position
- potentials
- Prep.in
- pressure regulation
- pressure with polarizable potentials
- Principal component analysis
- problem in a short MD with protein fixed
- Problem in adding solvent other than water ...
- Problem in GIBBS!
- problem in Leap
- Problem in MD!
- problem in xleap
- problem in xleap (fwd)
- Problem minimizing on SGI (SHOULD NOT BE HERE).
- Problem of running sander on Linux cluster
- problem processing stripped RST/CRD files
- problem using xleap and tleap
- Problem with
- problem with ambpdb
- problem with anal
- Problem with carnal ...
- problem with carnal on linux
- Problem with compilation of AMBER on IBM Power3 SP
- problem with Leap
- problem with xleap
- problem with xleap and sander! (fwd)
- Problem, setting up AMBERHOME!
- Problems with AMBER
- Problems with analin
- process problem
- producing a post-ptraj prmtop
- PROFEC
- program req
- Program versoins
- protein ionization
- protonate database
- Protonated Water
- prowat test difficulties
- PSC BIOMEDICAL WORKSHOPS 2001
- ptraj
- ptraj correlation command
- ptraj diffusion
- ptraj image for octahedral box
- ptraj resolved; irest=1?
- ptraj to re-associate protein+DNA
- ptraj Vector command
- ptraj: principal axes
- pyridoxal phosphate parameters
- Q about RESP
- QM/MM in roar
- quasih
- quasih again
- query
- query (fwd)
- Question
- question about implicit solvation model with AMBER
- Question about installing AMBER
- question about mm-pbsa
- Question about prep file
- question about RESP calculation
- Question...
- questions about Sander
- questions for group specification...
- R: color in xleap
- RDF figure
- recommended vs. default values
- references
- reflector back on.
- reflector limitations
- Regarding MD
- Regarding the construction of gris in insightII
- REMD
- Request
- Request.
- Residence time
- residue numbering in dimers and trimers
- Residue wise RMSD using carnal
- Resp
- RESP charges
- RESP charges (correction)
- RESP charges!
- resp charges: ccl4 jag vs. g98
- RESP demo files
- RESP fit: ivary -1 ?
- Resp input confusion.
- RESP X GAMESS Dummie Question
- restarting gibbs (fwd)
- restraint
- restraints and type
- Result: Dist restraints + Belly
- rigid body motion
- RMS calculations
- RMS matrix with CARNAL
- RMSD calculation
- Roar
- roar-cp crashed
- running Amber on dual processor machine
- running Sander in 4 CPUs
- sader-classic
- Sander
- sander 6 warming up
- sander compilers
- sander crash / linux cluster
- sander energy data
- sander input in Amber 6
- Sander minimization
- sander minimization problems with igb=3, ntb =0
- sander on SP3
- Sander parallel compilation
- sander VS sander_classic
- sander6/Linux compiled with pgf77 + mpipro
- sander_classic
- sander_classic no mdcrd
- sander_classic NPAIRS limit
- sander_classic: bellyrun with constraints
- sander_classic: bond energy problem
- saving a trajectory as individual pdb files
- secondary structure
- Segmentation fault (core dumped)
- Selection
- sense of justice
- Serious Problem with parm99.dat
- setting random velocities
- SGI_MP (was "your mail")
- SHAKE
- shake comparison
- shake tricks?
- shared memory
- simulating membranes with AMBER
- simulating membranes with AMBER (fwd)
- software
- software to build molecules
- solvate cap
- solvatebox
- solvation energy calculation
- sorry for the virus.
- SP3 benchmark
- SP3 MACHINE file
- SP3 name list
- spam
- SPC water
- special belly minimization
- starting MD from t=0
- stop COM motions in AMBER 5.0.1 question
- Strange density behavior with tr. octahedral box and constant pressure
- structure verification
- Structure with coordinates of C-alpha atoms only
- substracting of MM nonbondeb potential from QM curve
- sugguestion!
- SUMMARY for GAMESS/GAUSSIAN MEP
- summary of Zn+2 van der Waals radii responses
- summary: AMBER6 on IBMSP3
- summary: lipid bilayer MD simulations
- summary: titratable amino acids and counter ions
- supercritical water
- Temperature and pressure couplings
- terminal base pair opening
- terminal base pair opening 2
- Test Group - swarm.ca
- test run
- Test run for gb_rna on AMBER6 (IBM SP3)
- the molecule rotates during the MD run
- the program and references
- TIP3P
- TIP3P/SPC VdW radius
- TIP4P
- titratable amino acids and counter ions
- tleap but no xleap on IBM SP3
- tleap input format
- topology description
- TOPOLOGY FILE PROCESSING
- torsion parameters needed
- torsional profile
- torsional profile with MD
- trajectory analysis
- trajectory-problem
- tree names in group spec.
- Trosion parameters
- Trouble compiling amber on an Indy, R4400, running IRIX 6.5.10
- Typo's in the Parm99.dat
- Unit of force constant
- unusual parameters
- update to 1GHz Athlon
- update to files
- using "radial" in PTRAJ
- Utilizing Amber6 on Linux Cluster
- variable NTWXM in Sander
- varying cartesian restraint
- vdW parameters for our friend, vanadium (fwd)
- vdw parameters for:THR-HG1, TYR-HH
- Velocity information in CARNAL generated restart files
- velocity-output
- Wallclock on Intel/Linux sander
- Water Box ...
- water cap
- water density and rdf calculations
- water model
- water molecules in a periodic box
- water parameters+TIP3 water model
- weights for DNA and ions
- What do the exit codes mean?
- what should change in the parameter?
- Where to Start working in AMBER from?
- Why does water leak!?
- WHY NOT TRY IT?
- why the slowdown?
- Windows version of AMBER?
- Windows Virus
- Wrong compilation artifacts on ES40s?
- X-ray vs. MD
- Xeon vs. Athlon, latency
- Xleap
- xleap crashing on sgi's
- xleap for windows 98?
- xleap silly thing
- Xleap, PDB file format
- xleap: japanese keyboad
- your mail
- zinc
- Zn+2 van der Waals radii
Last message date: Sun Dec 30 2001 - 21:24:17 CST
Archived on: Thu May 05 2005 - 14:17:15 CDT
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