AMBER Archive (2000) - By Subject884 messages sorted by:
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About this archive
Starting: Mon Jan 03 2000 - 11:28:16 CST
Ending: Sat Dec 30 2000 - 23:44:00 CST
- Polarizabilities
- "Protonate" errors
- (no subject)
- ..and also getcor.f....
- 1-4 interactions
- 2 questions
- 2parts ehanol, 1 part water
- 3-botton emulat
- 4096wat running problem
- 4096wat runnning problem
- 6-12 nonbonded function
- 6.0 shipping status
- :trouble shooting in amber
- [pavan@bnpi.com: 'Coordinate resetting in amber6']
- A problem with "inhomogeneous'
- a question about compiling amber6
- a question about compiling amber6 (fwd)
- a question about the setting to contrain kinetic energy
- a question regarding ISCHARGE=1
- A thought in the mind
- a6 sander gb breaks on smallmol
- About "Nukit"!
- about constraints
- about defining disulfide bond
- About periodic box & modification of sander(5.0)
- About PME neutralization
- about PMF
- About Retinal
- about temperture
- absoft and AMBER6
- Acetonitrile
- adding atom types in leap
- adding counter ions
- Adding divalent metal ions to libraries
- Adding metal parameter
- addition to prev. mail
- Additional Water Potentials
- amber
- AMBER 5.0 MPI and IBM RS6000
- AMBER 5.0 on IBM SP2!
- AMBER 5.01 on Linux
- AMBER 6
- Amber 6 - license agreement
- AMBER 6 and residual dipolar coupling
- AMBER 6 crash
- amber 6 note
- Amber 6.0 build under Solaris 2.6
- AMBER 6.0 on parallel IBM SP system.
- AMBER data file for program DOT
- AMBER forcefield and thioglycosides
- AMBER installation
- Amber on a Linux box
- amber on alpha
- amber on AMDs cluster
- Amber on Linux
- AMBER on Linux- prob' solved----- thanks
- amber parameters
- amber parameters request
- Amber paramters
- AMBER PBC images
- AMBER PC-linux/O2 SGI
- AMBER performance with g77
- amber problem
- Amber2curves
- Amber5 RESP (fwd)
- AMBER501 on linux
- amber6
- amber6 and redhat 6.2
- amber6 and redhat 6.2 (
- amber6 and redhat 6.2 (thank you all)
- amber6 CD's
- Amber6 documentation
- Amber6 environment error
- AMBER6 on a CRAY SV1-B
- Amber6 on a ES40/4CPUs
- amber6 on HP N-4000 Complex
- Amber6 on SGI with IRIX6.5
- AMBER6 RESP
- AMBER6.0 on t3e
- amber6.0 timing
- Amber6/Compaq
- AMBER: Linux box
- AmberFFC 1.0
- ambpdb input format
- ambpdb problem
- ANAL
- ANAL question
- anal.in format
- analysis tool for water and stacking?
- Angle parameters
- Anglerfreunde - Einladung zum kostenlosen Fischfraß
- animation of normal modes
- anions of NAB's
- Annealing with rigid body
- Announcement of interest to your user group
- announcing mdxvu MD aanalysis code
- Another xleap problem?
- ANTECHAMBER
- ATP parameters for MD simulation
- Attachment
- automatic/semi-automatic type assignments
- babel
- Baic MD simulation
- basic minimisation
- basis set in RESP calculations
- belly
- Benchmarking AMD CPUS
- Benzamidine
- bond order
- book on molecular design
- Brazilian Symposium on Medicinal Chemistry
- Brief courses on AMBER 6
- C=C
- Ca2+ parameters
- Calcium bonds
- calcium parameter
- calculation time
- Call for Papers - ACS Symposium: "Artificial Intelligence in Computational Chemistry"
- calsium parameter
- Can amber6.0 do the implicit sovation model?
- Can I create a prmtop file without unwanted H atoms?
- Can I use heme prameters with param94 ?
- Can I...?
- Cannoct connect to Amber Home Page
- carbohydrate minimisation
- carbohydrates
- carnal
- CARNAL Code
- Carnal NORM
- carnal script
- carnal:TORSION phipsi BACKBONE error
- CATFEE Announcement
- CCL:AMBER6 and MPICH
- CCL:froce field parameters
- CCL:Performance of Compaq ES vs IBM or ORIGIN servers
- center of mass with gibbs ?
- Charge Neutrality using PME
- charges for new compound
- ChemInt2000 - July 1 Early Registration Deadine
- ChemInt2000 hotel rooms
- cion & LINMIN failure
- Cl and NO2
- CMC
- cobalt
- compilation errors
- Compilation of AMBER 6.0 on Origin 2000
- compilation of Amber6 on IBM SP3
- Compilation of parallel sander on Origin 2000
- compilation of sander
- compilation problem
- compile error
- compile in linux
- compile on ibm
- compile on linux
- compile on linux RH 6.2
- Compile problem
- Compile Problem ptraj with PGI compiler
- Compiler Bug?
- Compiling AMBER in LINUX
- compiling AMBER on IBM 44P
- Compiling Amber on win 2k
- compiling AMBER5.0 on Beowolf cluster
- Compiling AMBER6 under OCTANE DUO
- compiling leap on a linux box
- compiling problems
- Compressibility of water at 348 K
- Configuring AMBER program
- constrained MD
- content of amber output:mden
- continue running
- Coord. reset. not accomp.: Set-up vs. Soft/Hardware issue?
- coordinate averaging
- Coordinates in Leap
- correlation matrix
- crd file input for ptraj
- Crosslink in Leap
- CYM residue
- Cysteine with negative charge
- d-uridine
- Decreasing PE during MD
- delphi
- density decreases
- Density value in sander output
- DEVIATION IS TOO LARGE
- DFT parital charges
- DHFR - MTX
- Did MM/PBSA runs on linux also?
- dielectric constant
- dimer
- Discover to AMBER trajectory utilities
- distance-dependent dielectric in nmode
- DMSO parameters
- DNA bending
- DNA dissociation in Ewald simulation
- DNA flexibility
- docking
- Does AMBER include effects from pH?
- DOUBT IN AMBER5 PTRAJ DOCUMENTATION (fwd)
- doubt in constant pressure simulations
- DOUBT IN PTRAJ DOCUMENTATION
- dummy atom as anchor in gibbs ?
- dynamics with different pH conditions
- edit.out
- Element
- Elements
- Emerging Technologies/COMP 2001
- Empty gap in the watbox at the beginning of MD
- energy decomposition along MD trajectory
- ENTER to WIN a beautiful 1969 Z/28 Camaro for $1.00
- entropy estimation from harmonic analysis
- entropy estimation of dna with car.
- equilibration of CH2Cl2 box
- erfcfun.c for Alpha
- error 76
- error compiling
- Error in minimization and MD...
- error in restrt file
- error message in compiling amber6
- error of allocation pair array
- Error with GB
- estimate entropy of dna using nmode
- ewald and cutoff
- EWALD BOMB
- Ewald bomb ?
- EWALD parameter range problem
- Ewald parameters
- excluded atoms in prmtop files
- extract energies
- Field delegate for MidasPlus
- File /usr/lib/libI77_mp.a
- file format question
- filter?
- finding average
- first Amber 6 bug-fixes and manual updates are now available....
- FIX: amber6 ptraj compile
- force constants
- Force field
- formamides
- Forwarded mail....
- frcmod file format in amber 6.0
- frcmod polar
- Free Energy Calculation with Potential of Mean Force
- froce field parameters
- Fwd: question about sensitivity of DNA free energy simulations
- GB parameters
- GB source code question
- GB vs. GB/SA
- gb/sa
- GB/SA question
- gibbs
- Gibbs / Torcon problem
- Gibbs and PME simulation with DNA
- gibbs ile->val energies
- gibbs in sodium
- gibbs output
- GTP Parameters
- H+ parameters
- H-bond angles
- H2PO4(1-) parameters
- Harmonic restraints on distances in sander
- HBOND analysis after CARNAL
- Hello
- HEllo!
- Help
- help with amber 41 on linux redhat 6.2
- Help with polynucleotide building
- help! simulation of membrane protein
- hi
- How to
- How to creat new force field parameter for Mg++?
- how to get unusual topology in leap
- how to justify the size of a periodic box.
- How to make pdb"q" files easily?
- how to retrieve the average structure of MD?
- how to set up free energy perturbation
- how to turn off self repulsion
- I can't run sander6 with lam-mpi : is mdread.f wrong ??
- ibelly
- ibelly and ntr
- Ibelly and sander6
- ibelly in nmode
- IBM SP
- igb=1 and atom ordering
- imaging problem in moil-view
- improper density in constant pressure md
- Improper Dihedrals
- improvements to force field
- information
- information on troubleshooting in Amber
- initial density generated by solvatebox
- input error?
- inquire about the cost of the license.
- installation help
- installing AMBER on Linux
- interaction energy
- INTERNATIONAL PIANO MASTER CLASS 2001
- INTPRT
- intprt on gibbs
- is leap compatible?
- Is PME MPI-parallelized in v.6.0?
- isoxazole force constants
- Issues with compiling AMBER6 (MPI) on Linux
- Issues with Trunc. Oct.
- ISTAR2
- LAM Mpi not efficient for sander ?
- last message continued
- leap
- Leap compilation
- leap problem about periodic boundary box
- leap problems
- Leap problems with Zn, DNA
- LEaP question
- LGFIL and other outputs for OWFEG calcs
- libcss for SP2
- library entry for amidated c-terminus
- LINMIN
- linmin failure
- linmin failure?
- Linux
- List of force field parameters_II
- Loading CRD or RST files into Leap
- Location of /doc directory?
- Looking for a PREP input file
- MACHINE file for DEC Alpha!
- Machine file for SV1
- Machine file....
- make install
- make off file from minimized coordinate.
- manganese ions
- Md at NVE
- MD error
- MD namelist error with new Sander
- md toolchest
- MD-problem
- MDEN output file format
- mdextract
- mdtoolchest
- Merz-Kollman atomic radii for Cu and Fe
- message in minimisation
- min error
- minimization from the average structure of MD simulation
- minimization of many structures
- missing angle parameters
- Missing opls_parm.dat
- missing parameters
- MM-PB/SA with MSI-Delphi
- MM-PBSA
- MM-PBSA trajectory file
- MM_GBSA and DNA methylation
- modeling GPCRs
- modify topology file
- MOIL-View and Quicktime Recap
- Moilview and Quicktime movies
- Molecular Dynamics Problem
- Molecular Modelling example
- Monte-Carlo
- movie file
- MPI gibbs
- MPI on SUN
- MPI Sander on a 5 node SMP cluster
- Myrinet + Beowulf for AMBER?
- NAD parameters
- NADH FF parameters
- namelist
- NAMOT
- NAN
- NAN (
- NARI'2K - Novel Approaches in RNA Informatics
- NATOMS > 99999
- NATOMS > 99999 for sander 6.0
- need help
- new book
- new residue in leap
- NMODE
- nmode out of memory
- nmode-error message
- NMR restrained MD
- non-aqueous solvent; ethanediol
- nonbonded pairlist update
- normal modes
- NRUN in input file
- NSER
- ntwxm,ntwvm,ntwem
- Oct box and ptraj
- omit non-bonded energy in Amber 6
- one question
- One question about praj
- OpenMP parallelization in AMBER6
- opls_parm.dat
- Organic solvents with Leap
- OWFEG and other AMBER 6.0 manual issues
- OWFEG documentation
- pairlist
- parallel computing of amber 6
- parallel problem ?
- parallel sander
- Parallelization on SGI for AMBER5
- Parallelization on VPP700 for AMBER5
- parameter for azido (-N=N(+)=N(-))
- parameter for mm_pbsa
- Parameter-Web Page
- parameters for a tetrazole
- parameters for GB use
- parameters for GFP cro
- Parameters for pTyr
- parametrization
- Paramters for sulfate and methanol
- Parm File
- Parm98 parameters
- Parm99
- partial solvation
- partially solvate the protein
- pdb files
- pdb_MD
- pdbgen
- Performance of Compaq ES vs IBM or ORIGIN servers
- Periodic Boundary Condition
- periodic boundary conditions
- perturbed topology file
- perturbing charge
- Ph.D. thesis in Strasbourg-France
- Pl. fwd to your users group
- Please tell me calcium parameter
- Plotting Hbond info from Carnal
- PME
- PME group decomposition
- PME on cluster on linux
- PME on SP2 for AMBER5
- PME with charged system
- PMF and PME with DNA
- POL3
- Polarizabilities
- Porphyrin/porphycene
- PostDoc Position available
- prep file
- pressureS
- problem in AMBER
- problem in GIBBS
- problem of compilation of roar-cp
- problem of translation - rotation
- problem on launching xleap
- Problem with AMBER installation
- problem with Interface script
- problem with leap
- problem with makeDIST_RST
- Problem with PME test
- Problem with Protonate
- problem with rdparm
- problems in sander
- Problems on Alpha: Too slow
- Problems using IBELLY in AMBER6
- problems with MD
- Problems with memory for large systems
- processing of carnal output
- Profec
- Profect visualization
- progesterone parameter
- Program to convert CHARMM force field file to AMBER format
- Protein and Ligand in Leap
- protein capping
- Protein-Protein docking
- protonated adenine and cytosine?
- Protophorphyrin IX
- purine partial charges
- query
- question
- question about 2DRMSd made by rdparm.
- question about imaging
- QUESTION ABOUT SANDER
- Question about TEMP and PRESS on Sander AMBER 5.1
- question about using SUN machine for amber?
- question in compiling amber6 on linux.
- question of running sander on sp2
- Question on DNA Simulation Using PME!
- question on expanding nphb
- Question on Parallel Sander AMBER 6.0
- Question?
- questions about AMBER_SERVER
- Questions on the definition of parameters
- radius of gyration
- rdparm/ptraj
- re Yanni Wang's compile problem
- re-assign velocity
- Re. calcium parameter
- read coordinates file
- reading back into leap
- reading in residues
- reassigning temp. during MD
- regarding edit option
- removing rotation during MD
- REPEATED LINMIN FAILURE
- repeated linmin failures
- request
- Request for using AMBER server
- RESP
- resp fit
- RESP question
- restart MD
- Restarting production runs
- Restraint and topology mismatch error
- restraints + potential
- Restraints in Amber6
- Review a sample issue of the Journal of Applied Spectroscopy (eu20)
- Rigid Body Analysis
- rms in rdparm
- ROAR-CP calculation on axp machines
- RST file for non-standard residue
- run sander on shared memory sgi
- Running tests on SP2 machine
- Sander compilation problem on HP
- sander compile error with MPICH compiled by PGI compiler
- Sander error in AMBER5
- Sander error solved
- sander minimization
- sander on sgi O2/R5k--workaround
- sander test /Amber6
- Sander/MPI/redimension
- Sander: crash if nmropt=1. HELP!!!!!!!
- Sander_classic to Sander switch
- sander_pme.MC examples
- saveamberparm problem of new molecule
- Saving coordinates with sander_classic
- scaling on ibm sp power3 machine
- self diffusion of water at equilibrium T=300K P=1atm
- server down
- SGI
- SGI+MPICH
- SGI_MP and sander 6
- SGI_MP and sander 6] input files
- Shake and a new computer system
- shake/potential function
- SHAKE/TORCON failure in Gibbs
- shared mem
- shared memory sander
- showing density map?
- Side chain mobility
- Simulation of DNA
- site mutation with xLeap
- sizes.h for sander
- Small Molecule Paramaterisation
- sodium_gibbs_pme test
- soft repulsion option
- Solute temp
- SOS from Italy
- sulfur parameters
- Surface accessible area and hydrogen bonds
- Surface areas
- sysdir
- TAUP
- temperature and pressure control
- test - NM
- Testing problems with SGI Irix 6.5.5!
- thanks
- the topology file in mutant MM-PBSA calculation?
- TIP3P water in Amber6
- TIP4P water
- To Cray t3e users
- Too many atoms
- topology/coordinate files
- trajectory file
- transition metal ions parameters
- trouble with NTR=1 and NMROPT=1
- Trying to compile Amber 6 on Intel/linux
- two questions: (1)dihedral, (2) movies
- unable to extract trajectory of MD simulation with sander_classic
- unit
- units
- units of force constant
- unsuscribe
- urgent
- Using CARNAL to compute per-residue RMSD between PDB files
- VdW numbers in Amber
- vdw parameter
- vdW parameter for S atom
- Visualization
- VRAND
- water and ions
- water density around the molecule
- wcleap
- Wee Problems.
- What can I get from docking?
- What does this mean?
- Where to download mm5_car1.Z for example1 of mmpbsa?
- where to specify parm98.dat + has AMBER been compiled on HP N-4000 complex
- xleap
- xleap problem
- xmgr
- Xtal Waters and SolvateBox
- your mail
- Z-dna
- Zinc potential?
Last message date: Sat Dec 30 2000 - 23:44:00 CST
Archived on: Thu May 05 2005 - 14:17:08 CDT
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