AMBER Archive (2003) - Apr 2003 By Subject234 messages sorted by:
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Starting: Tue Apr 01 2003 - 06:08:59 CST
Ending: Wed Apr 30 2003 - 14:57:31 CDT
- (no subject)
- A problem in opening the file
- A problem in Sander production dynamics
- A weird antechamber error
- a-Helix direction?
- About electrostatic force calculations
- about molecular dynamics
- Adding ACE to chopped protein
- addles
- ALA-scan problem with mm_pbsa.pl
- AMBER
- Amber on Linux
- Amber on Parallel Sun?
- AMBER pdb help - lost atoms
- AMBER pdb help - lost atoms - Part 2
- Amber7 and mpirun on Linux
- ambpdb
- ambpdb and protonate in AMBER7
- anal question
- Annealing blown up
- any one has references to parallelization aspects of AMBER
- anyone have AMBER benchmarks with gigabit ethernet?
- atom position restraints
- Beyond 1,000,000 atoms
- Bugfixes
- carnal hbond
- CCL:MPI run problem
- characteristics of nucleic acids homopolymers
- converting amber to gromos format
- CYS and HIS
- debug leap
- Description of ATOM type in GLYCAM
- diffusion coefficients
- Examples for Energy Minimisation methods
- force field parameters for phosphoserine
- frcmod file
- frcmod file for Free energy perturbation tutorial of valine to alanine
- free energy calculations
- free energy in sander
- Future of structural biology conference
- GB/SA
- general minimisation methods
- Groups defenition
- growing side chains
- how to restrain base pair
- How to use GLYCAM force field in AMBER
- Hydrogen bond energy
- ibelly and ntr
- id_torus(): Could not find torus for atoms 1878 and 1894
- job stopped
- leap problem
- makeDIST_RST
- MD went crazy
- Metalloprotein
- MM-GBSA question
- mm_pbsa & nmode
- mm_pbsa nmode calculation
- mm_pbsa_statistics.pm
- MPI run problem
- mutating residues
- New Machine.sgi_mpi file
- Nitro group introduction in tyrosine residue
- nmode and mm_pbsa questions?
- nmode for S calculation
- No statistical output for MM-PBSA?
- non bonded pair list
- old prmtop format in AMBER 6 differs from what is presented in AMBER 7 manual
- Organic Solvents
- Periodic Boundary Condition in AMBER7 (the sander module)!
- phi and psi angles analysis
- please kindly help
- PME box information
- Polarizable simulation2
- Problem Finishing Tutorial
- Problem of Hbond in CARNAL
- problem with tleap
- problem_namelist_reading
- Problem_to_open_PROTON_INFO_file
- Proper Restraint usage
- Protein - DNA complex simulation - protocol
- protonate
- PSC Summer Workshop: Modeling from Protein Sequence to Structure
- ptraj problem
- quasih
- question about H-bond in carnal?
- question about MM-PBSA?
- Question: Nmode with counter ions.
- Request for Amber7 (fwd)
- Request for Amber7 (xleap problem)
- Residual dipolar couplings
- sander & prmtop file generated from antechamber input ?
- SANDER Source Code Documentation
- Side-chain/main-chain decomposition in MM-GBSA
- size of a simulation system
- solvents aren't loading
- SSBonds and charge problems
- The error in the trajectory file
- Tleap
- Tleap-metalloprotein
- topology file in large systems
- Trouble with AMBER 7
- trouble with OFF files
- troubles on RS6000
- Trying to understand parm99.dat
- Unit of velocity
- Using MPI, PBS
- velocity auto-correlation function
- very important
Last message date: Fri Feb 06 2004 - 10:15:04 CST
Archived on: Thu May 05 2005 - 14:17:44 CDT
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