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AMBER Archive (2005) - May 2005 By Subject
393 messages sorted by: [ author ] [ date ] [ thread ]About this archive
Starting: Sun May 01 2005 - 16:00:59 CDT
Ending: Tue May 31 2005 - 22:41:42 CDT
- 75% Off for All New Softs Now! haberman
- A new rollax repliccas is in the mark. attitudinal
- AMBER:
- AMBER: *** Proper torsion parameters missing ***
- AMBER: 1-4 scaling factors
- AMBER: a nomenclature question
- AMBER: Amber 8 : installation problems : undefined reference to `mpi_allreduce_'
- AMBER: Amber 8 and LAM compilation problem
- AMBER: amber 8 REM possible test problem
- AMBER: amber code
- AMBER: AMBER Test
- AMBER: AMBER8 Build on Linux x64 running Opterons
- AMBER: amber8 test error
- AMBER: antechamber not working .. for thio residue..
- AMBER: Antechamber RESP failed for large organic molecule
- AMBER: antechamber, reference?
- AMBER: Asking how to creat alanine "dipeptide" in amber8
- AMBER: ATOM TYPE
- AMBER: average structure after MD
- AMBER: Bond angle restraints setting files
- AMBER: Bromelain PDF xleap load error
- AMBER: Bromelain PDF xleap load error (Proton Problems?)
- AMBER: Calculating of radius of gyration in Carnal
- AMBER: Can I add iodide anione?
- AMBER: Can we load prmtop and inpcrd files into xleap?
- AMBER: charges difference of atom in xleap and prmtop
- AMBER: Citing the PBSA module of AMBER8
- AMBER: compiling pmemd on dual xeon
- AMBER: conformational sampling of a peptide
- AMBER: Connecting two molecules
- AMBER: Copyright for PBSA
- AMBER: crashing xleap
- AMBER: crashing xleap; bugfix.44
- AMBER: creating residues - charge assign problems
- AMBER: density problem
- AMBER: density profiles in ptraj or carnal
- AMBER: dissolving micelle structure in water.. amber7
- AMBER: distance restraints between two centers of mass
- AMBER: DNA base-flipping: TI vs PMF
- AMBER: double counting of potentials
- AMBER: Dr. Cornell's calculation of Sulfur vdw epsilon value in parm94.dat?
- AMBER: error during MD run
- AMBER: error in chirality.c?
- AMBER: Error in minimization
- AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN
- AMBER: Error in sander: stack trace terminated abnormally.
- AMBER: Error on restrained MD equilibration (AMBER 7)
- AMBER: error with ptraj
- AMBER: Error: vlimit exceeded for step
- AMBER: External Field in AMBER?
- AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on"
- AMBER: fast 1/r methods
- AMBER: Force field modification problem
- AMBER: frcmod info for Nickel
- AMBER: GAFF angle parameters
- AMBER: gaff: ca-ca-c -o torsion parameter
- AMBER: GB - igb=1 versus dielc=?
- AMBER: GB with dipoles !
- AMBER: generating over 16 bps of DNA in nucgen
- AMBER: hbond analysis in ptaj/carnal
- AMBER: hbond detailed analysis over time?
- AMBER: How can I read parm99.dat file?
- AMBER: how to creat leaprc.gaff
- AMBER: How to create a parallel job for amber 8?
- AMBER: How to fix certain bond angles
- AMBER: How to fix the atom in NPT case?
- AMBER: how to generate frcmod file for using prepin file..
- AMBER: how to reduce box size and delete excess solvent
- AMBER: How to set constraint
- AMBER: How to set up dihedral constraints in amber
- AMBER: ibelly in nmode
- AMBER: Identifying water molecules with ptraj
- AMBER: if setting ntf=4, will it cause someproblem?
- AMBER: ipol=1 & use_pme= ??
- AMBER: Is Amber able to constrain(not restrain) certain angles at certain values?
- AMBER: Is the MD simulation normal
- AMBER: keeping two domains closed together during a simulation
- AMBER: langevin, GB and simulated annealing - 5
- AMBER: leap problem: savepdb
- AMBER: loading pdb
- AMBER: Loading pdb-residue (re)numbering in leap
- AMBER: maximum number of processors
- AMBER: MD on surface
- AMBER: Meaning of induced dipole moments for atom pairs?
- AMBER: meaningful tax for sander question
- AMBER: Message in .out file
- AMBER: MM-PBSA calculation
- AMBER: mm/pbsa error
- AMBER: MM_PBSA for NMR restrained structures
- AMBER: MMPBSA calculations on Highly charged systems
- AMBER: modeller
- AMBER: Mol2 to prepin file conversion
- AMBER: molsurf error
- AMBER: my frcmod file created using parmchk
- AMBER: my prepin file in lowe-case
- AMBER: nmode in mmpbsa
- AMBER: No vdW parameters for HO..
- AMBER: NOE constraints
- AMBER: output of force field info
- AMBER: pairwise energy decomposition using MM-PBSA
- AMBER: Parameter for alpha-lactose
- AMBER: parameter for sulfur in thio-glucoside residue
- AMBER: parameter for sulfur in thio-octyl-glucopyranoside
- AMBER: PARMSCAN program
- AMBER: platinum atom in Xleap
- AMBER: problem with gb md
- AMBER: Problem with xleap
- AMBER: ptraj - hbond detailed analysis over time?
- AMBER: quadrupole in resp
- AMBER: question about initial conditions for amber
- AMBER: question about loadiing pdb file of a molecule complex
- AMBER: radial distribution function
- AMBER: radius parameter for F atom
- AMBER: rborn(i) in egb.f
- AMBER: read pdb back to xleap after solvation of chloroform
- AMBER: Reference (?) for normal-mode analysis in nmode
- AMBER: Relative stability with MMPBSA
- AMBER: Representation of cations in MD
- AMBER: RESP charge fitting for N-methylguanine cation
- AMBER: rotating and repositioning molecules in xleap
- AMBER: runtime error in sander?
- AMBER: SANDER BOMB: volume of ucell too big
- AMBER: Sander Restart Problem
- AMBER: sander run
- AMBER: Setting Amber force field parameters
- AMBER: setting up Parallel processing
- AMBER: Solute-solvent boundary in pbsa
- AMBER: stack terminated abnormally
- AMBER: STOP 0
- AMBER: strange mm_pbsa.pl bug
- AMBER: the out put I get... parameter for sulfur in thio-glucoside residue
- AMBER: the restraint MD fail with amber8,but success with amber7
- AMBER: Trouble with example tutorial
- AMBER: Tutorial #1 ptraj/sander problem
- AMBER: Unexpected stop of Sander run
- AMBER: Using AMBER for Carbon nanotubes
- AMBER: Using amber4 generated prep files in amber8?
- AMBER: using antechamber ... to get prepin file
- AMBER: Which forcefield?
- AMBER: Which source file determine the initial value of IX XX arrray in AMBER8?
- AMBER: why is snaupe.f is empty?
- AMBER: Working with a nickel-organometallic compound
- AMBER: Workshop Tutorials Downtime this weekend.
- AMBER: write format of restart crd in sander/pmemd
- AMBER:Sander errors: Unit 6 Error on OPEN: mdout
- antechamber not working .. for thio residue..
- Installing PMEMD on IBM machine (CPU power4) running SUSE_9.1
- Office XP - 60 dolars! coagulate
- R.E.D. question
- The new ganaration of repliccas is here capella
- Tutorial#1 ptraj/sander problem
- We can send you disccounted errection mads party
- You wont believe these pr1ces on name-brannd soft's! kerchief
Last message date: Sat Dec 31 2005 - 12:51:27 CST
Archived on: Sat Dec 31 2005 - 12:51:45 CST
393 messages sorted by: [ author ] [ date ] [ thread ]
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