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AMBER Archive (2003) - By Subject
2933 messages sorted by: [ author ] [ date ] [ thread ]About this archive
Starting: Thu Jan 02 2003 - 04:37:41 CST
Ending: Fri Feb 06 2004 - 10:15:04 CST
- 'hot-solvent' and 'cold solute' problem
- (no subject)
- 1-4 vdw term in Glycam2000
- 10-12 H-bond terms
- 2 questions
- 2drms command in ptraj
- 3 simultaneous simulations in one computer
- [Fwd: AMBER: MM_PB/GB/SA]
- [Fwd: MPI problem in modi4.ncsa.uiuc.edu]
- a perl question for Hbond occupancies analysis
- A problem in opening the file
- A problem in Sander production dynamics
- A question about AMBER, leaprc.ff02EP
- a question about constructing a periodic box by PLEP.
- a question about scale factor
- a question about simulation at high temperature
- A question of how to choose a appropriate box size for imposing periodic boundary conditions in the simulations.
- A question of time
- a question~~
- A simple question about offset, want to make sure
- A weird antechamber error
- a-Helix direction?
- About antechamber
- About electrostatic force calculations
- about maxium number of residues read by xleap (fwd)
- about Mg++
- about molecular dynamics
- about the dielectric
- about the read error
- about urea and glycerol
- abt. Plastocyanin tutorial
- acetonitrile parameters
- Adding ACE to chopped protein
- adding hydrogens
- Adding missing parameters
- addles
- adjust virial
- ALA-scan problem with mm_pbsa.pl
- ALAscan of Proline
- Algorithm for the motion equations?
- AM1-BCC in Amber7
- AMBER
- Amber 7.xx installation on FreeBSD
- AMBER Cutoff
- Amber Documents
- Amber Installation on Octane
- amber installation problems (fwd)
- AMBER mail reflector archive
- Amber on Linux
- Amber on Parallel Sun?
- Amber on SGI with Itanium compilers for linux
- Amber on SGI with Itanium compilers for linux (fwd)
- AMBER parameters
- Amber parameters for Netropsin
- AMBER pdb help - lost atoms
- AMBER pdb help - lost atoms - Part 2
- AMBER question
- Amber tutorial crown-ether
- Amber under Linux
- AMBER water mediated contacts
- Amber web page
- Amber Web page.
- amber web site
- AMBER/FEP: RESP charges
- AMBER6 in Solaris 8
- Amber6 on RH 9
- AMBER6 problem in Solaris 8
- Amber7 & mpich
- AMBER7 & mpich : (no-attachment version)
- amber7 & mpich on sgi (fwd)
- Amber7 and mpirun on Linux
- AMBER7 on linux cluster
- Amber7 on Opteron
- amber7 on sgi
- AMBER:
- AMBER: "ATTN, need revision"
- AMBER: "irstrnt=1"in input file for RESP
- AMBER: 'high' temp. simulation!!
- AMBER: 'ho' vDW parameters
- AMBER: 'vlimit exceeded'
- AMBER: (no subject)
- AMBER: /exe/teLeap does not exist
- AMBER: 1 fs timestep for GB?
- AMBER: 2D periodic box
- AMBER: ?small bugs? - 2nd suggestion
- AMBER: a note on problems with MPI and sander
- AMBER: A problem about xleap
- AMBER: a problem with antechamber and leap
- AMBER: a problem with memory size
- AMBER: a problem with xleap
- AMBER: a question
- AMBER: a simple question about HBond energy...
- AMBER: about H-bond definition for TIP3P
- AMBER: about some of the cards in Sander 7
- AMBER: About Temperature Regulation
- AMBER: About the limitation of characters on one line in carnal input fi le
- AMBER: about the mopac7 installation.
- AMBER: about the npscal, box size changes and rms
- AMBER: absolute vs. relative binding free energy
- AMBER: Accuracy of PB solvation energy
- AMBER: add
- AMBER: Added water and mm_pbsa
- AMBER: adding extra salt
- AMBER: addions/xleap question
- AMBER: addition to: problem with a small system
- AMBER: Addles
- AMBER: altering mass in .top file
- AMBER: AM1-BCC in Amber7
- AMBER: Amber - compiler help
- AMBER: Amber 7 - bugfix 42 problem.
- AMBER: amber 7 for industrial application
- AMBER: AMBER 7_make install
- AMBER: AMBER and NAMD
- AMBER: AMBER Carnal files
- AMBER: Amber charge problem
- AMBER: AMBER error in CHALANGE
- AMBER: AMBER on LINUX ?? (fwd)
- AMBER: amber on mac cluster
- AMBER: Amber parallelisation
- AMBER: AMBER quasih question(s)
- AMBER: amber-on-cheetah-question
- AMBER: AMBER7 & mpich
- AMBER: AMBER7 & mpich : (no-attachment version)
- AMBER: AmberFFC v1.3 released
- AMBER: ambpdb
- AMBER: ambpdb and residue number
- AMBER: aminoacid mutation
- AMBER: anal - memory problem
- AMBER: ANAL component
- AMBER: ANAL/MMPBSA
- AMBER: antechamber
- AMBER: Antechamber & Ptraj/Rdparm
- AMBER: antechamber and bond type
- AMBER: Antechamber formal charges with Gasteiger method
- AMBER: Antechamber functionality, MOL2 files
- AMBER: antechamber mopac7 parameters
- AMBER: Antechamber problem
- AMBER: antechamber test failure
- AMBER: Antechamber:charges missing
- AMBER: Any correct way to image a molecule ?
- AMBER: Apparent PMEMD bug -- NTWPRT > 0 & IWRAP = 1
- AMBER: atmtypenumbers for halogens
- AMBER: Atom type in prepin file
- AMBER: Atom type in prepin file - new problem
- AMBER: Atomic charges and internal H-bond
- AMBER: atomic clash or structure size?
- AMBER: atomtypenumber
- AMBER: average coordinates
- AMBER: Basic potential question:
- AMBER: basic questions
- AMBER: Benchmark of AMBER on Apple G5 machine
- AMBER: Big system in Gibbs
- AMBER: C-alpha RMS
- AMBER: Calculating solvation energies for MM-PBSA use
- AMBER: calculation of LJ 12-6 from .dat file (fwd)
- AMBER: calculation of LJ 12-6 from .dat file (fwd)-CORRECTION!!!
- AMBER: Can use mm_pbsa_statistics.pl to calculate each snapshot's Delta Delta G, then give the SD
- AMBER: Carbohydrate connectivity
- AMBER: carnal
- AMBER: Carnal Input file
- AMBER: carnal iteration deviation from original crd file
- AMBER: cd-c-os and c3-cd-c angle parameters
- AMBER: chage WATBOX216
- AMBER: change force constants
- AMBER: charge definition
- AMBER: charge fitting
- AMBER: charge method of antechamber
- AMBER: charge method of antechamber(it's ok)
- AMBER: charge of IRON in HEME!!
- AMBER: charmm force field in amber
- AMBER: chemical potential
- AMBER: combine prep files
- AMBER: Compaq Tru64 Unix
- AMBER: Comparing PE of different conformations
- AMBER: comparing versions 6.0 and 7.0 of AMBER
- AMBER: compile problem
- AMBER: compile problem?
- AMBER: Compiling 64-bit version on AIX
- AMBER: Compiling AMBER
- AMBER: compiling amber using gcc on SGI Unix machines
- AMBER: Compiling AMBER, ie, number of atoms limit
- AMBER: Compiling AMBER7 on Suse
- AMBER: Compiling antechamber on amber 8
- AMBER: Compiling on Suse 9 Pro with ifc...
- AMBER: Compiling sander with single precision
- AMBER: complete pdb structure
- AMBER: constant energy simulation
- AMBER: constant pressure in GB
- AMBER: Constant temperature
- AMBER: Coordinate resetting (SHAKE) cannot be accomplished
- AMBER: Correction [Separation of a Water molecules]
- AMBER: correlated motion
- AMBER: Could you please give me an example? Thanks!
- AMBER: curves nomenclature
- AMBER: Curves parameters UU and PP
- AMBER: Cutress %cmass error
- AMBER: density equilibrium & harmonic restrain
- AMBER: derive corresponding torsional parameters
- AMBER: dielectric constant for blends
- AMBER: dielectric in sander
- AMBER: Diffusion constant
- AMBER: distrance restraints for alpha carbons
- AMBER: DMSO box
- AMBER: DNA helix is not in z-direction
- AMBER: double bonds in prmtop
- AMBER: dual processor
- AMBER: Dynamics and Simulated Annealing
- AMBER: dynamics of isolated system
- AMBER: DYNAMICS RUN
- AMBER: ECC vs non-ECC (non-amber issue)
- AMBER: Energy map
- AMBER: error message is the same after I added a title
- AMBER: EWALD BOMB and solvent density problem
- AMBER: Ewald in Amber 7
- AMBER: Ewald problem
- AMBER: Ewald_Bomb
- AMBER: FEP problem
- AMBER: FF parameters for BOC - group
- AMBER: FILE UNITIO.C
- AMBER: fix some area
- AMBER: Fluorine in GBSA
- AMBER: following salt and waterbridges during a simulation
- AMBER: force field for hybrid systems
- AMBER: forces estimation
- AMBER: Freezing of water with TIP3P potential.
- AMBER: Freezing the residues
- AMBER: frequency analysis
- AMBER: frozen x unfrozen
- AMBER: frozen x unfrozen and the gibbs tragedy
- AMBER: Fwd: Minimizing after solvation
- AMBER: Fxnal form of NMR-style restraints
- AMBER: gaff atom types for phosphor compouds
- AMBER: gaff errors?
- AMBER: gaff parameters
- AMBER: GB/SA
- AMBER: GBSA problem
- AMBER: Generalized Born parameters
- AMBER: GIBBS - PMF problem: Lambda has not changed
- AMBER: GIBBS - PMF question: How to get <dV/d_lam> during TI calculations?
- AMBER: GIBBS - PMFquestion
- AMBER: gibbs pmf calculation
- AMBER: GLYCAM
- AMBER: GLYCAM/AMBER Configurator
- AMBER: GROUP
- AMBER: H-bond analysis
- AMBER: H-O-H angle in TIP3P water model during minimization
- AMBER: handling non neutral systems
- AMBER: HB dynamics in water and Ion solvation free energies
- AMBER: Hello
- AMBER: Heme and Zn parameters
- AMBER: high temperature, 498K, unfolding simulations
- AMBER: How can I set ntx=7, but exclude the velocity?
- AMBER: How to add new atom type.
- AMBER: how to calculate vibration frequency?
- AMBER: How to develop parameters for metallic atoms
- AMBER: How to estimate SD of the delta delta G between two mm_pbsa runs
- AMBER: how to measure the minor groove widths of a DNA?
- AMBER: how to mend the peptide with missing residues?
- AMBER: How to use quasih?
- AMBER: HT vs no HT
- AMBER: Hydrogen bond plot from carnal
- AMBER: iam a newbie !!!
- AMBER: ibelly
- AMBER: Ibelly and Ewald error message when ewald should be off
- AMBER: ibelly in AMBER 6
- AMBER: ibelly problem
- AMBER: IG value
- AMBER: image question
- AMBER: Implicit MD simulations in Amber7
- AMBER: Implicit precision in sander vs architecture
- AMBER: import pdb file in xleap
- AMBER: improper
- AMBER: Impropers from Amber parm files to NAMD
- AMBER: increase size of NATOM or NRES for "ambpdb"
- AMBER: infinitely long DNA & moil-view?
- AMBER: infinitely long DNA (to Yong Duan)
- AMBER: initial structures
- AMBER: initial velocity
- AMBER: input/output error
- AMBER: Insight pdb file in xleap
- AMBER: Installation Problem, xleap can't load pdb files
- AMBER: intermolecular force
- AMBER: Is NTC=2 correct for minimization when hydrogens are added?
- AMBER: is there a good program to quantitatively analyze hydration effect?
- AMBER: JAC on NCSA titan (Itanium 2 833MHZ)
- AMBER: large changes in xyz coordinates
- AMBER: large file for carnal
- AMBER: LEaP not compiling
- AMBER: leap/frcmod problem
- AMBER: length of deltaG calcs
- AMBER: lifetime in ptraj hbond
- AMBER: Lone pairs and resp
- AMBER: machine dependent?
- AMBER: make clean doesn't clean leap
- AMBER: MD
- AMBER: MD Equil
- AMBER: MD problem!
- AMBER: MD problem!!
- AMBER: MD simulation with ATP and MG
- AMBER: MD simulation: enzyme and its substrate
- AMBER: MD simulation: enzyme and its substrate!!
- AMBER: MD simulations on small molecules immersed in sparse water shell
- AMBER: MD: restrt
- AMBER: mddisplay
- AMBER: MeCNBOX
- AMBER: MeCNBOX & EWALD bomb
- AMBER: memory SC45
- AMBER: mfef90 - installation problem
- AMBER: Mg2+ parameters for RNA usage
- AMBER: mgbjsb radii in GBSA
- AMBER: minimization error
- AMBER: minimization on sander
- AMBER: minimization termination
- AMBER: minimize a covalently bounded protein-ligand complex
- AMBER: minimum image convention mystery
- AMBER: MIPS R14000 and Machine-file
- AMBER: missing of VdW Parameters for N3
- AMBER: MM-GB/PBSA:Main-chain/side-chain decomposition in ligands
- AMBER: MM-PBSA question
- AMBER: MM_PB/GB/SA
- AMBER: MM_pbsa
- AMBER: mm_pbsa - ?small bugs?
- AMBER: mm_pbsa and antechamber
- AMBER: mm_pbsa crg file
- AMBER: mm_pbsa example
- AMBER: mm_pbsa rna/dna charges
- AMBER: mm_pbsa with amber7
- AMBER: MM_PBSA(GBSA) Examples
- AMBER: modelling a Ca binding site
- AMBER: molsuf failure with too many intersecting cusps
- AMBER: monitor vdw along time
- AMBER: monte carlo
- AMBER: mopac
- AMBER: MOPAC from antechamber
- AMBER: MOPAC509mn test jobs on linux
- AMBER: more questions about igb
- AMBER: more than 100,000 atoms ?
- AMBER: mpi in mm-pbsa
- AMBER: mpich problem
- AMBER: mpprun: exec of '/usr/local/bin/sander7.0' failed: Not enough space
- AMBER: MSE
- AMBER: MSMS
- AMBER: N/C termini
- AMBER: NaCl ion pairs in TIP3P water box
- AMBER: NAD+ and NADH amber parameters
- AMBER: ndfmin in belly runs
- AMBER: neutral N- and C- termini !
- AMBER: Nitrated Tyr
- AMBER: nmanal in amber7
- AMBER: nmanal projection
- AMBER: nmanal's error message
- AMBER: nmanal's rvec file
- AMBER: Nmode analysis ptn-ligand complex
- AMBER: Nmode problem
- AMBER: nmode statistics
- AMBER: nmode, trajectory
- AMBER: no "Input orientation" in g98 log
- AMBER: no defined type for atom N atom
- AMBER: NO2-TYR
- AMBER: non-bonded cutoffs
- AMBER: Non-standard Residue
- AMBER: non-zero 10-12 coefficient
- AMBER: normal mode analysis
- AMBER: Not getting restrt file on running sanders
- AMBER: nstlim
- AMBER: NTT
- AMBER: NTX 5 or 7 after equilibration in constant pressure?
- AMBER: Odd Problem with PMEMD
- AMBER: one more line about the npscal, box size changes and rms
- AMBER: one more question
- AMBER: Online model of 2C9
- AMBER: order parameter
- AMBER: output frequency
- AMBER: overlap problem
- AMBER: pair-cutoff
- AMBER: parallelisation
- AMBER: Paramters for beta and gamma peptides
- AMBER: parm. and top. for sugars, charmm?
- AMBER: parmchk on MAC
- AMBER: parmscan
- AMBER: PARMSET problem
- AMBER: partial charge
- AMBER: performance vs number of processors
- AMBER: Phase for torsion angle different of 0 or 180 ?
- AMBER: plane angle.
- AMBER: please let me know if this is correct
- AMBER: pmemd
- AMBER: PMEMD 3.01 Update available
- AMBER: PMEMD 3.03 Update available
- AMBER: PMEMD 3.1 Release - High Scalability Update to PMEMD
- AMBER: PMEMD and EAMBER
- AMBER: PMEMD and sander from AMBER6 performances
- AMBER: PMEMD BUG ALERT!!!
- AMBER: PMEMD NMR Restraints fix
- AMBER: PMEMD Performance on Beowulf systems
- AMBER: PMEMD Performance on IBM SP
- AMBER: PMEMD: dual XEON vs SGI cluster
- AMBER: PMF
- AMBER: PMF calculation
- AMBER: PMF calculation with gibbs
- AMBER: PMF calculations
- AMBER: PMF ethane example: Can someone correct the INPUT? Thanks.
- AMBER: polarizability and PME
- AMBER: prepin file
- AMBER: Pressure during MD
- AMBER: Pressure in NVT ensemble
- AMBER: prmtop file format
- AMBER: Problem generating .tpp and .rst files for a complex
- AMBER: problem in tleap
- AMBER: problem regarding surface
- AMBER: problem with file format
- AMBER: Problem with MPI_Finalize
- AMBER: problem with pdb files
- AMBER: Problems restarting with sander
- AMBER: Problems with extra points on parralellized linux and sgi machine
- AMBER: problems with periodic boundary conditions
- AMBER: problems with pmemd
- AMBER: problems with pressure control
- AMBER: processors
- AMBER: protein MD - problem
- AMBER: Protein Rotation
- AMBER: protonation states of small molecules
- AMBER: Pseudouridine force field parameters
- AMBER: ptraj and charmm files
- AMBER: ptraj problem
- AMBER: ptraj question
- AMBER: Ptraj-HBOND
- AMBER: question about ewald
- AMBER: question about input files for small molecule with fluorine
- AMBER: question about namelist
- AMBER: question about ptraj
- AMBER: question about ptraj?
- AMBER: Question about quasih analysis
- AMBER: question about quasih?
- AMBER: question on LJ parameters for molecules
- AMBER: question to calculate diffusion coefficient under periodic boundary conditions.
- AMBER: Questions about mm_pbsa and alanine scanning
- AMBER: Questions on Phi, Psi angles produced by pmemd/sander7
- AMBER: radial distribution-function by Ptraj
- AMBER: RADII in DELPHI
- AMBER: Radius of Gyration and RMSD
- AMBER: reduce box and delete excess solvent
- AMBER: Reference for Amber7 heme parameters
- AMBER: references about AMBER MD simulations
- AMBER: regarding trajectory input and output with ptraj or Carnal
- AMBER: Removal of Rotational and Translational Motion in AMBER6
- AMBER: reporting atoms clashed during simple energy minimization
- AMBER: residues and molecules
- AMBER: RESP calculation
- AMBER: RESP charge
- AMBER: RESP charge redistribution
- AMBER: RESP charges
- AMBER: Resp Esp charge Derive (RED v-1.0) release
- AMBER: RESP fitting limit?
- AMBER: Resp Problem
- AMBER: Restart a simulation
- AMBER: restart MD program
- AMBER: restarted MD and ptraj
- AMBER: Restarting MD amber7
- AMBER: restrain
- AMBER: Restrain of dihedral angle!
- AMBER: Restraints
- AMBER: restraints and reordering water
- AMBER: Restraints to maintain base pair planarity
- AMBER: Reverse TI run
- AMBER: RMSD and Radius of Gyration
- AMBER: RMSd per residue
- AMBER: RNA and Protein questions (also some general questions)
- AMBER: roar topology and coordinate files
- AMBER: rotation removal in sander GB
- AMBER: running AMBER on an IBM P690 cluster
- AMBER: Running Amber on MacOSX(XDarwin)
- AMBER: running sander_classic on multiple processors
- AMBER: Sander / Anal
- AMBER: sander lastist
- AMBER: sander minimization
- AMBER: sander on cygwin
- AMBER: sander output
- AMBER: sander: vlimit problem
- AMBER: sanderparallel
- AMBER: saveamberparm
- AMBER: saveamberprep and saveoff in xLeap
- AMBER: saveamberprep in xLeap
- AMBER: SC45
- AMBER: Scyld cluster amber 7 compile problems
- AMBER: secondary structure
- AMBER: segmentation fault
- AMBER: separate thermostats for different molecules
- AMBER: Separation of a Water molecules
- AMBER: shake constraint on all bonds
- AMBER: SHAKE for TIP4P!
- AMBER: SHAKE poblem with dummy atoms
- AMBER: SHAKE Problem
- AMBER: SHAKE question
- AMBER: simulating a crystal using the unit cell
- AMBER: Simulation of small protein
- AMBER: Simulation of small protein (MD Display tips)
- AMBER: slow simulation
- AMBER: slower simulation
- AMBER: Slower simulation and pair-range cutoff?
- AMBER: Small problems
- AMBER: solute images
- AMBER: solvatebox-solvateshell
- AMBER: Spartan and AMBER7
- AMBER: special gaff atom types available?
- AMBER: stable protein
- AMBER: strange problem with a small system
- AMBER: STREAM problems : segmentation fault with CARNAL
- AMBER: structure refinement using CNS vs. AMBER
- AMBER: Suggestion regarding long simulation.
- AMBER: surface code in Amber
- AMBER: surften value in mm_gbsa/mm_pbsa calculations
- AMBER: Taisung Lee/San Diego/Accelrys is out of the office.
- AMBER: target MD simulation
- AMBER: TEMP is not reaching 300K
- AMBER: Temperature dependent properties of TIP4P and TIP5P
- AMBER: temperature does not reach to temp0
- AMBER: temperature problem
- AMBER: TFE solvent box
- AMBER: The FCAP parameter in amber7
- AMBER: The lost velocities in the restart file generated by Ptraj
- AMBER: The restart file generated by Ptraj
- AMBER: TIP5P
- AMBER: tleap under amber6
- AMBER: Toolchest
- AMBER: torsion problems of dummy atoms
- AMBER: torsional restraints for groups of atoms
- AMBER: tru64 alpha
- AMBER: TTF parameters
- AMBER: umbrella sampling with AMBER
- AMBER: united atom weiner force field
- AMBER: update of BOX dim.
- AMBER: update to answer about solvateShell
- AMBER: usability of mm_pbsa with ligand - membrane protein - complex
- AMBER: Using NWCHEM for esp?
- AMBER: using sander without SHAKE
- AMBER: variable not in namelist for Sander input
- AMBER: Vibration frequency of nucleobases
- AMBER: vlimit?
- AMBER: Water as part of protein in mm_pbsa calculation
- AMBER: water box problem
- AMBER: water mediated contacts
- AMBER: water model
- AMBER: water neighborhood of amide hydrogens
- AMBER: water prep file needed
- AMBER: what can't I use ibelly?
- AMBER: What does this error message mean?
- AMBER: what is the unit for the energy calculated from MM_PBSA?
- AMBER: Why I get the same TSTRA for different strucutures from Nmode calculation?
- AMBER: xleap memory issue
- AMBER: xLEAP Problem
- AMBER: xleap-N/C terminus
- AMBER: xplor2amber
- AMBER: zero free energy change for nonbond leg of electrst. decoupling
- AMBER: Zinc parameters
- AMBER: Zn in antechamber
- ambpdb
- ambpdb and protonate in AMBER7
- AMD opteron
- ANAL in AMBER
- anal question
- anal, amber7 and resnum 0
- Analysis of close waters
- Analysis of Curves program output
- angle violation in SANDER simulation
- Annealing blown up
- Another mm_pbsa problem
- Antechamber
- antechamber -rn keyword
- antechamber and gamess
- antechamber and its prepin files
- Antechamber atom types
- Antechamber Manual
- Antechamber questions
- antechamber read gaussian file
- any one has references to parallelization aspects of AMBER
- any tool to know what functions are being called while sander is being run??
- anyone have AMBER benchmarks with gigabit ethernet?
- apparent PMEMD bug -- NTWPRT > 0 & IWRAP = 1
- Ar as a solvent
- atom position restraints
- atom type
- atomic charges and internal H-bond
- atomic positional fluctuation
- Automated response
- average structure generated by carnal
- AW: AMBER: Problem with MPI_Finalize
- Backbone torsional angles' format?
- Backbone torsional angles' format?]
- bad atom type f(fluorine) in MM-PBSA?
- Bad atom type: f
- barium
- belly vs. position restraints
- best force field for Protein+DNA
- Beyond 1,000,000 atoms
- Beyond 1,000,000 atoms...
- big changes coming
- Binary output switch (IOUTFM=1) broken in sander? (AMBER7)
- bond command
- boron parameters
- Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold
- bugfix ptraj-6.4 (need to confirm)
- bugfix.33 not online
- Bugfixes
- building molecules by script files for leap
- Calcium in proteins
- calculated b-factor higher than x-ray
- can not minimize
- can you give me more advice about: vlimit exceeded when sander calculate free energies using TI
- CARNAL
- Carnal DECLARE of TORSION problem
- carnal hbond
- carnal in big systems
- Carnal problem...
- Carnal processing of binary mdcrd files (IOUTFM=1) Sander 7
- CCL: Amber free energy equation
- CCL:electrostatic potential calculations
- CCL:MEAD on SuSE 8.1
- CCL:MPI run problem
- center command
- CFP: Informatics Approaches in Structural Genomics at PSB 2004
- characteristics of nucleic acids homopolymers
- charge determination for polariable ff02 force fields
- charge fitting for c-term homocysteine.
- charge neutralization in DNA
- charges, opt and iops
- CHARMm force field for AMBER
- Chloroform Parameters
- chloroform, dichlormethane f.f.
- clustering trajectories
- CMC/MD
- Comparative MD
- compatibility of amber with NAMD
- Compilation error of Amber 7 using pgi and mpich on Linux Cluster
- compiling amber on myrinet
- Compiling Amber7 for linux
- compiling amber: Machine file for new 64 bit HP-Itanium II CPU
- conformational sampling
- constant volume
- constraint + restraint
- converting amber to gromos format
- coordinate files from carnal
- coordinates for quasih
- correction to location of the PMEMD program
- crystal structure of DNA/RNA homopolymers
- current AMBER citation?
- CYS and HIS
- debug leap
- debug sander
- decrease a force const. for angle
- delphi and charge file
- delphi on linux
- delphi with amber 7
- DelphiLinux V. 4 Segmentation Fault
- Description of ATOM type in GLYCAM
- desolvation energy in mm_pbsa
- Diferences in gibbs
- difference between iwrap and image?
- diffusion coefficients
- diffusion in ptraj
- distance-dependent dielectric function
- Distribution Min with truncated octahedron box
- Disulphide bridges
- DNA base-step distortion
- Does Anyone Have a Working MACHINE File for Solaris/SPARC?
- Does Leap has a problem with Isoleucines?
- Domain/Helix movement/MD
- DON'T DELETE THIS MESSAGE -- FOLDER INTERNAL DATA
- doubts
- Dummy atoms in free energy calculation
- Dummy-parameters in Amber?
- dynamics of isolated system (fwd)
- effect of forcing neutrality
- EGB problem in MMPBSA
- electrostatic interaction energ. /delphi
- electrostatic potential calculations
- Energy calculation
- equilibrated solvent box
- Error in minimization using sander_classic of AMBER6
- Error Massage in Sander amber7 in Linux
- errors in MD trajectories
- essential dynamics
- Etot is not constant in NVE ensemble
- EWALD
- EWALD BOMB
- Ewald error
- Ewald: coeff, error estimate
- Examples for Energy Minimisation methods
- EXTRA_PTS: frtype 2 Should not be here
- extract coord and velocities
- Extracting structures
- failure of minimization
- File in the tutorial
- Final energy minimization step
- Flag for antechamber
- Fluorine atom type in mm_pbsa?
- Force field ?
- force field parameters for phosphoserine
- force field parameters for torsions
- force field parameters for torsions (I am away)
- force field problem
- Force Fields
- format of 'mask' in ptraj
- Forwarded mail....
- Forwarded mail.... (fwd)
- Fourth European Workshop in Drug Design
- frcmod file
- frcmod file for Free energy perturbation tutorial of valine to alanine
- free energy calculations
- free energy in sander
- free energy perturbation (Gibbs/Amber 5)?
- freeware to visualize RMSD matrices creatde with Carnal
- From Dr. Ekaterina Nikitina
- Future of structural biology conference
- GAFF in GUI MD apps
- GB model
- GB simulation on protein (fwd)
- GB vs. explicit solvent calculations
- GB/SA
- general minimisation methods
- GIBBS - Non periodic simulations.
- GIBBS - Routine TORCON failed. Required change is too large.
- gibbs calculation
- Gibbs dummy atom
- gibbs input file
- gibbs run
- Gibbs stops after a finite number of window runs
- Gibbs tutorial question
- Gibbs, ewald and ifc
- Gibbs: DynamicWin and NSTMEQ?
- Gibbs: Electrostatic Decoupling
- glycam force field with amber
- Glycerol Parameters
- GRASP (fwd)
- Groups defenition
- growing side chains
- H-O-H angle
- Has anyone ever used MEAD?
- Hbond analysis with Carnal
- HBOND energies in sander
- Heat of Vaporization
- Helical Drift
- helix axis for A-RNA
- helix movement
- help me switching from amber5 to amber6
- help on solvatecap
- Help with Sander test output error
- hexane parameters
- High temperature MD
- How do I perform an Nmode calculation on a big protein-ligand complex?
- How do NTC=2 recognize hydrogen atom?
- How much is minimum distance
- How to calculate new force field?
- How to control box size
- how to convert the amber force field files to any proper format that can be used by gaussian98
- How to do a rigid solvent model?
- How to do the image using ptraj?
- How to do with two MG2+ ions?
- how to generate FF of DNA complex?
- How to put the outside atoms back to the truncated octahedron box?
- how to restrain base pair
- how to restrain water
- how to set up a carbon nanotube pdb file
- how to stop mapping of N- and C-terminal residues in xleap
- how to stop mapping of N- and C-terminal residues in xleap (The RTFM solution)
- How to use GLYCAM force field in AMBER
- how to use profec???
- how to validate ff parameters obtained from antechamber
- Hybdrogen bonds and LJ 10-12
- hydration site
- Hydrogen bond energy
- hydrogen bonding
- I still have problems with parm99.dat
- ibelly and ntr
- id_torus(): Could not find torus for atoms 1878 and 1894
- IDSX0 in free energy calculations
- ifc, gibbs and ewald
- improper torsion for X -CB-CB-X
- Including the Peroidiic Box info ??
- Increase lastist in the &cntrl namelist
- Info request: Amber on 64-bit CPUs
- information
- initial structures
- initial velocity
- input problem
- Install Amber 7
- Install Amber7 in linux cluster
- install amber7 on Linux (fwd)
- install problem
- installing AMBER 7
- intel ifc amber5 and mpich-1.2.5
- inter & intra-molecular interaction energies
- interaction between ligand & protein
- Internal dielectric in MM-GBSA
- intra-perturbed group (fwd)
- Intramolecular H-bonds in charge fitting
- IR6 and makeDIST-RST
- Isotropic Solvent Box
- Itanium II
- JACS 125th and PAK
- jarrod
- job stopped
- keeping pdb residues numbers ?
- LAM-MPI, Oscar and Amber compile Machine.g77_lam-mpi
- lanes when solvating in LEAP (fwd)
- lastrst
- Latest Leap Compile Errors
- LEAP compiling problem
- leap complains!
- leap problem
- leap remove command
- Leap to prep
- Lennard-Jones A and B coefficients
- LES analysis tool other than Moil-view
- Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap
- Lipids
- looking for 'pdb_to_mass'
- Machine file available for ICC compiler ?
- Machine for IBM Horizon
- mail reflector
- mail reflector address is changing
- Mainchain.dat
- makeDIST_RST
- Max residues (fwd)
- Maximum molecular size for Amber?
- MAXINT problem
- May I get you help from new user of amber?
- May I get you help from new user of amber?(xmkmf)
- May I get your help?
- MD input file for MM-PBSA calculations
- MD problem
- MD problem!!
- MD steps limit in sander (Amber 6)
- MD went crazy
- MEAD on SuSE 8.1
- MeCNBOX
- memory problem
- memory shortage with mm_pbsa
- memory shortage with mm_pbsa - some more thoughts
- metallic ions
- Metalloprotein
- methylphosphonate
- Mg++ polarizability
- Mg2+ ion parameters
- MGB RADII PARAMETRIZATION
- Minimisation - peek_ewald_inpcrd: SHOULD NOT BE HERE
- minimizaiton in vacuum
- Minimization after dynamic?
- Minimization does not converge.
- Minimization problem w/ counter-ion !
- minimization with fixed UC dimensions
- minimization with restraints
- Misaligned Coords from Alanine Scanning
- MM-GBSA question
- MM-PBSA error
- mm-pbsa error message
- mm-pbsa problem & possible solution
- MM-PBSA results
- mm_gbsa error message
- mm_gbsa question
- mm_gbsa: Unit 5 Error on OPEN: sander_com.in
- mm_pbsa
- mm_pbsa & nmode
- MM_PBSA (Amber7) and delphi
- mm_pbsa -- COMPT must be specified (correctly)
- mm_pbsa and ALA scan
- mm_pbsa and B/Z DNA relative stabilities
- mm_pbsa energy unit
- mm_pbsa error message
- MM_PBSA Errors
- MM_PBSA for Linux
- mm_pbsa nmode calculation
- MM_pbsa prmtop file
- mm_pbsa problem
- mm_pbsa question
- mm_pbsa Stop at statistics
- mm_pbsa with PBCAL = 0
- mm_pbsa_statistics.pm
- Moil-view
- morse potential
- Move the atom with specific velosity
- MPI run problem
- mpi/sander help
- mpirun problem!
- mpirun problem: no rsh
- multiple timesteps
- mutating residues
- nab compilation
- Namelist READ error
- Namelist READ error - solved
- namelist read: variable not in namelist
- Nancy's leaving
- naphthalene, anthracene force field
- nasty npt md problem (fwd)
- Need help recompiling
- Neutral ARG
- Neutral Arginine
- new amino acid residues
- New location for the Amber web site
- New Machine.sgi_mpi file
- New program available: PMEMD (Particle Mesh Ewald Molecular Dynamics)
- new tutorial available: introduction to ptraj
- new-style prmtop file
- Newton-Raphson minimization for large systems
- Nitro group introduction in tyrosine residue
- Nmanal
- nmanal & quasih question
- Nmode
- nmode and mm_pbsa questions?
- Nmode doesn't work ?
- nmode for S calculation
- nmode on Linux : another memory question
- Nmode problem
- Nmode query
- Nmode recompilation
- Nmode recompilation)
- no MD output
- No statistical output for MM-PBSA?
- no statistics.out in mm_pbsa binding energy calculations
- NOESY restraints
- non bonded pair list
- non bonded pairlist?
- non-periodic system
- noninteger charge
- Notes: Compiling Amber 7 on Mac OS X (fwd)
- npscal
- nscm
- NTC=3 for organic solvent and NTC=2 for solute?
- NTC=3 for organic solvent and NTC=2 for soluter?
- NTX / INIT inconsistency
- ntx in sander
- nucgen.dat
- nucleic acid structures
- Number of water too large
- NVT system implosion!!!
- octahedral volume
- off-diagonal VDW term
- old prmtop format in AMBER 6 differs from what is presented in AMBER 7 manual
- one question
- one time evaluation
- Opteron Experience
- Order parameters
- Organic Solvents
- parallel sander jobs die with error: "MPI_COMM_RANK : Null communicator"
- parallel version amber installation problem
- parallelisation
- Parameters for Cy3 and Fluorescein
- Parameters for Hyddantoin derivatives?
- parameters for nitro group
- parameters GB/SA
- Parameters: additive, lone pair
- parm99
- PBC without solvent
- pdb_to_mass
- Periodic Boundary Condition in AMBER7 (the sander module)!
- Periodic Box
- perl question
- phi and psi angles analysis
- Phosphorylated Serine Library
- Phosphotyrosine parametrization
- pi-pi in AMBER
- Pi-Pi stacking
- Please help on xleap: FATAL ERROR
- please kindly help
- PME
- PME box information
- PME cutoff box size
- PMF
- pol_h
- Polarizable simulation2
- polarization + ewald
- Polarization charges -geometry
- Polarization simulation
- Polymers
- posphinic acid parameters
- Postdoctoral position available in Molecular Modeling
- Predefined Water_cap with xleap
- Preparation of RESP input from GAUSSIAN output
- pressure variation control
- pressure variation control (fwd)
- Probelm with the generation of topology file
- probelms with antechamber
- problem about virtual box?
- Problem Finishing Tutorial
- Problem in separating LES copies into different trajectory
- Problem of Hbond in CARNAL
- problem of mass center
- problem on MD simulation of damage DNA
- problem patch files
- problem with "Example 3" tutorials
- Problem with a library
- problem with antechamber
- Problem with CMC/MD
- Problem with LES topology file
- PROBLEM WITH LIBRARY
- Problem with Snader
- problem with tleap
- Problem with XLEaP in Mandrake 9.1
- problem_namelist_reading
- Problem_to_open_PROTON_INFO_file
- problems in equilibrating NaCl solution
- problems with anal in amber7
- profec
- Proper Restraint usage
- Proper torsion parameters missing?
- Protein - DNA complex simulation - protocol
- protein dna simulation
- Protein Reorientation
- Protein Reorientation (fwd)
- Protein-Inhibitor binding afinity
- protonate
- protonate problem
- PSC Summer Workshop: Modeling from Protein Sequence to Structure
- ptraj
- ptraj and rdf help
- ptraj distanse question
- ptraj generated PDB files
- ptraj html documentation still available?
- ptraj on Methane in water box
- ptraj problem
- Ptraj problem with small molecules
- ptraj question
- ptraj rdf help
- ptraj residue number out of range
- pyroglutamic acid (PCA)
- Q) vdw radii & GBSA error
- Quasi-harmonic analysis
- quasih
- quasih problem
- question about antechamber
- Question about BELLY NMODE
- Question about defining force field
- Question about defining force field (followup)
- question about dummy atoms? (fwd)
- question about H-bond in carnal?
- question about ligand
- question about lysine?
- question about MM-PBSA?
- question about mm_pbsa
- question about mm_pbsa?
- question about partial charge
- Question about quasih
- question about temperature
- question on EWALD
- question on ptraj
- Question: about restarting Energy
- Question: Nmode with counter ions.
- questions about AMBER
- Questions about output archive and micromolecules
- Questions about statistics output of mm_pbsa?
- Questoin about temperature
- RDPARM problems (ptraj)
- reduce the disk space
- reducing restrains
- references
- Refining a docked protein complex
- reflector text - please ignore
- reg. problem with SM and ICE libraries
- Regarding the quotation for AMBER 7 Programme
- Request
- Request for Amber7 (fwd)
- Request for Amber7 (xleap problem)
- Residual dipolar couplings
- RESP charge derivation
- Resp Charges for large ligand.
- resp for charged molecule?
- RESP, constraining Dipole Moment
- RESP-group constraint
- restart MD
- Restrain of dihedral angle!
- restrained atoms NTR
- results of MD comparison
- RMS in carnal
- RMSD fluctuation too much
- RMSF problem
- roar-cp : input for QM part ; output for CM2 charges
- rotational and translational motion
- run sander?
- Running MD
- sander & prmtop file generated from antechamber input ?
- Sander box error and thanks on previous mdin error
- Sander error
- Sander help
- sander outputs
- Sander problem
- SANDER Source Code Documentation
- SANDER vs GIBBS equilibration
- sander,ntt=5
- Sander_classic output: NAN
- SASA and H-bond over trajectories
- SASA calculation
- saveAmberParm problems in xleap
- saving trajectory of solute only
- Script and MPICH
- script for H-bonds extracting
- script for Potential/kinectic energy
- scripts for compiling UHBD/MEAD with amber 7.0
- SCSL
- seperate one trajectory file into two
- sequence
- serine/tyrosine in charged states
- shake and belly
- shake and H-O-H angle
- Shake problem in organic solvent
- shake problem?
- Side-chain/main-chain decomposition in MM-GBSA
- Simple math of memory calculation for nmode
- Simple question about sander parameter set
- Simulation under physiological conditions
- single point mutations to investigate the conformational change
- size of a simulation system
- Small organic molecules
- Software Sales
- Solaris Benchmark for Amber7
- solvatecap
- solvent free energy, GB
- solventbox at constant pressure
- solvents aren't loading
- some questions in gibbs calculation
- SPC/E model -LJ parameters
- SPC/E water model
- SSBonds and charge problems
- stacking energy
- Strange F.E.P. behavior
- stress - strain - pressure
- structure image
- Summary: mm_pbsa -- COMPT must be specified (correctly)
- Summary: Protein-Inhibitor binding affinity
- Superimposed trajectory
- surface accesible area
- T in MD vs. T in wet experiments
- TAUP and density problem
- tautp in gibbs
- teleap
- Temperature control
- terminal phosphate group in RNA
- TFE input
- The error in the trajectory file
- The gblambda parameter
- The image command of ptraj of Amber 6 is not working.
- the unit of velocity
- three digits in the charges of extPDB
- tip5p water model
- Tleap
- tleap in large systems
- Tleap-metalloprotein
- topology file in large systems
- torsional energy
- trajectory file in mm_pbsa
- trajectory file in mm_pbsa]
- translational and rotational motion (more information)
- Trouble with AMBER 7
- trouble with OFF files
- troubles on RS6000
- Trying to understand parm99.dat
- UCSF moving day.
- UCSF Network changes to affect Amber Web site.
- unifying trajectory files
- unit of energy
- unit of output velocity
- Unit of velocity
- unit of vlimit?
- unsubscribe
- upper limited of memory for nmode
- Use of Mg2+ in AMBER 7
- using antechamber
- using distance restraints in Sander (AIX 4.3 RS6000)
- Using GLYCAM in sander with a non-zero 10-12 coefficient
- Using MPI, PBS
- using xleap
- Valdiation of Latest Amber parameters
- van der Waals term
- VdW in FEP
- velocities
- Velocity
- velocity auto-correlation function
- very important
- viewing movie with VMD
- virtual box
- vlimit exceeded
- vlimit exceeded when sander calculate free energies using TI
- VXllig Legal geld Verdienen Ohne Risiko!
- water box distortion
- Water density and force output questions
- water reordering in sander
- water residence time analysis
- waterbox
- web link for PLEP is not available.
- web page update
- Web site problems.
- What kind of interactions are ignored for end group interactions
- which AMBER program to use to get the e-density output?
- Why the NMA discrepancies?
- writing mol2 files using antechamber
- Xleap adding torsions
- xleap crash under Irix
- xleap crashes
- xleap in Amber7
- xLEAP Problem
- Xleap: 'triangular' and 'square' bond
- your mail
- your mail (IBM runtime problem)
- Zn2+ parameters
- 永嘉瓯北上明阀门厂
Last message date: Fri Feb 06 2004 - 10:15:04 CST
Archived on: Thu May 05 2005 - 14:17:43 CDT
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