AMBER Archive (2009) - Nov 2009 By Subject539 messages sorted by:
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Starting: Sun Nov 01 2009 - 11:59:34 CST
Ending: Mon Nov 30 2009 - 23:59:05 CST
- [AMBER] -np not 2^x a problem w/ sander???
- [AMBER] -np not 2^x a problem w/ sander??? update
- [AMBER] 60 giga output file .mdcrd file
- [AMBER] about divcon
- [AMBER] About zinc parameters ?
- [AMBER] amber 10 test failures...
- [AMBER] amber 9 compilation
- [AMBER] amber parameter file creation and usage
- [AMBER] amber9 compilation
- [AMBER] AMBER: segmentation fault when running parmchk
- [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala
- [AMBER] AmberTools 1.3 has a likely release date?
- [AMBER] ambr parameter file creation and usage
- [AMBER] analyzeMatrix: cannot find a match in the matrixInfoStack
- [AMBER] Antechamber and Parmchk problems
- [AMBER] Asking help for parallel installation of Amber9
- [AMBER] Atomic radii assignment for WAT molecules
- [AMBER] build up solvate box
- [AMBER] Calculaiton stop ?
- [AMBER] Can I get an average trajectory?
- [AMBER] check MAXPR in locmem.f error on minimization
- [AMBER] coarse-grained MD
- [AMBER] combining parameter files of ligand and enzyme
- [AMBER] compilation problem of amber
- [AMBER] compilation problem of amber9
- [AMBER] conversion of kelvin to kcal/mol
- [AMBER] Creating new residue with tleap.
- [AMBER] difference between two inputs
- [AMBER] distance-dependent dielectric constant minimization
- [AMBER] enquiry regarding parameter file to be used
- [AMBER] error in kclust of MMTB_tool set
- [AMBER] error in reading namelist cntrl
- [AMBER] error reading namelist cntrl
- [AMBER] errors on leap for a RNA + Non-Standard molecule pdb structure
- [AMBER] errors on leap for a RNA+Adenine pdb structure
- [AMBER] errors on leap for a RNA+Adenine pdb structure with antechamber
- [AMBER] errors on leap for a RNA+Adenine pdb structure withantechamber
- [AMBER] Etot positive
- [AMBER] ff fitting ?
- [AMBER] fillratio
- [AMBER] Fortran error in standard simulation
- [AMBER] Fortran error in standard simulation 2
- [AMBER] Fortran error in standard simulation 3
- [AMBER] Gaussian log file error
- [AMBER] GB and Atom Type
- [AMBER] Getting minimized .pdb file without non-polar hydrogens
- [AMBER] Gly -> Ala mutation
- [AMBER] have a question
- [AMBER] HB for each snapshot
- [AMBER] hbond analysis by ptraj- segmentation fault
- [AMBER] Hbond analysis output giving no hbonds
- [AMBER] heme (united-atom)
- [AMBER] High-temperature simulation ?
- [AMBER] How to change the input matrix for "analyze matrix" instruction?
- [AMBER] How to compile and recompile ptraj?
- [AMBER] How to get total energy of asystem
- [AMBER] How to split mdcrd files
- [AMBER] how to use amber to verify the reason for difference in affinity
- [AMBER] how to use GLYCAM04 for carbonhydrate in amber9?
- [AMBER] Hydrogen bond analysis for protein dna complex using ptraj
- [AMBER] i-APBS and apbs
- [AMBER] implicit_run_error
- [AMBER] Increase Temperature to 550 K
- [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala
- [AMBER] Is it possible to simulate transmembrane protein with GB model ?
- [AMBER] Is it taking too much time
- [AMBER] is rst file the last structure?
- [AMBER] Is the integral value from RDF the same as average number of atoms?
- [AMBER] ligand parameterization
- [AMBER] linux version for Amber10
- [AMBER] Lisp library for amber analysis?
- [AMBER] LJ parameters for HO and HW
- [AMBER] looking for parameters for DHFR substrates and inhibitors...
- [AMBER] Low frequency Raman spectra
- [AMBER] LYS-ASP
- [AMBER] matrixInfoStack
- [AMBER] MD snapshots of most probable protein conformations in Amber
- [AMBER] MM-PB/GBSA NMODE
- [AMBER] MM-PBSA NMODE
- [AMBER] MM_PBSA energy per residue
- [AMBER] MM_PBSA enquiries
- [AMBER] MM_PBSA error
- [AMBER] MMTSB tool set PDF
- [AMBER] MPI process terminated unexpectedly after cluster upgrade
- [AMBER] MSD of ligand??
- [AMBER] NAD - mmpbsa
- [AMBER] non standart residue library creation with tleap (Zn atom)
- [AMBER] Not able to compile pmemd with openmpi in Amber9
- [AMBER] Output Does Not Match in Tutorial B1
- [AMBER] PCA analysis with ptraj
- [AMBER] Phosphorylated Threonine
- [AMBER] Phosphothreonine
- [AMBER] pmemd failure
- [AMBER] pmemd vs sander.MPI
- [AMBER] Polarizable simulation of the slab
- [AMBER] problem with FAD in tleap
- [AMBER] ptraj script for H bond for protein (explicit )
- [AMBER] R.E.D. resp error
- [AMBER] R.E.D. too small charges
- [AMBER] read substrate into leap
- [AMBER] reagarding Dihedral PCA
- [AMBER] rectangular box with PME problem
- [AMBER] reg. GBA
- [AMBER] regarding Dihedral PCA
- [AMBER] Regarding rigid bond
- [AMBER] Regarding Urey-Bradley term in amber calculation
- [AMBER] request
- [AMBER] RESP using antechamber with Se atom
- [AMBER] retinal lib file, params?
- [AMBER] rings getting planar
- [AMBER] rmsd
- [AMBER] sander.APBS install problem
- [AMBER] sander.mpi. mdfil: Error unknown flag: sander
- [AMBER] Scripting tleap
- [AMBER] Segmentation Fault
- [AMBER] Segmentation fault in antechamber
- [AMBER] sleap fastbld error
- [AMBER] sleap fastbld error is not an error
- [AMBER] slope
- [AMBER] slope {no reply}
- [AMBER] solvent
- [AMBER] Some queries about pH simulation
- [AMBER] standard way to upload a lipid bilayer
- [AMBER] Task is running on supercomputer without any output
- [AMBER] The decreasing MSD of ligand??
- [AMBER] the different RMSD?
- [AMBER] The MSD and periodic boundary condition
- [AMBER] the problem of nucgen.dat
- [AMBER] three trials to create topologies with sleap and tleap
- [AMBER] tleap maximum coordination exceeded
- [AMBER] total number of hydrogen bonds of the system as a function of time
- [AMBER] trajout problem
- [AMBER] trouble with antechamber
- [AMBER] unable to find mopac charges in mopac.out
- [AMBER] varying positional restraints with PMEMD
- [AMBER] Verlet update time in explicit water Replica Exchange MD
- [AMBER] where to get leaprc.ff99sb?
- [AMBER] which is the best intel complier for amber 10?
- [AMBER] zeros in excluded atom list in topology file
- [AMBER]Amber10 + g95
- Etot positive
- How to compile and recompile ptraj?
- MM_PBSA error
- question
- RESP with -a and witout -a flag
- Verlet update time in explicit water Replica Exchange MD
- 回å¤ï¼š [AMBER] the different RMSD?
Last message date: Thu Dec 31 2009 - 22:57:46 CST
Archived on: Thu Dec 31 2009 - 22:58:33 CST
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