AMBER Archive (2009) - Oct 2009 By Subject482 messages sorted by:
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Starting: Thu Oct 01 2009 - 06:31:51 CDT
Ending: Sat Oct 31 2009 - 23:59:38 CDT
- (files attached) RESP with -a and witout -a flag
- [AMBER] "Cannot open file ATOMTYPE.INF, exit" when using antechamber
- [AMBER] "extra points" incompatibility with pmemd
- [AMBER] (no subject)
- [AMBER] [amber10] atom groups used in torsion constrain
- [AMBER] [Fwd: ligand exiting a protein cavity]
- [AMBER] [Fwd: problem with minimization]
- [AMBER] A bug in LEaP ?
- [AMBER] A bug in LEaP II ?
- [AMBER] Add the hydrogen to the carboxyl of the GLU residue?
- [AMBER] AMBER 11.
- [AMBER] AMBER FF and NAMD
- [AMBER] amber parallel test fail
- [AMBER] amber8 pmemd trajectory coordinates problem
- [AMBER] Analyzing per-residue decomposition data
- [AMBER] Any tutorial on the proper way to merge a ligand and protein?
- [AMBER] B-factor
- [AMBER] binding energy
- [AMBER] building quadruplex with NAB
- [AMBER] can I run EVB in other ensemble than NVE?
- [AMBER] Can I use other ntb options in constant pH simulation
- [AMBER] Centering and reimaging with ptraj- stop rotating.
- [AMBER] charges for heme-cys in p450
- [AMBER] Circular RNA topology file
- [AMBER] Combine and rename group of residues in xleap
- [AMBER] Compiling Amber with gfortran-4.5.0 on a mac
- [AMBER] Computing an Hessian matrix using NAB
- [AMBER] contradictive hydrogen bonds using ptraj
- [AMBER] Conversion of Gaussian output file into mol2
- [AMBER] Conversion of Gaussian output file to mol2
- [AMBER] cross correlation analysis with ptraj
- [AMBER] decomposing energies
- [AMBER] decomposition and calculation of entropy
- [AMBER] DG improper torsion problem, two missing parameters
- [AMBER] Different optimized structures with HF and B3LYP
- [AMBER] Different results for different computers
- [AMBER] Dihedral energy profile in a single molecule
- [AMBER] Dipole moment visualization.
- [AMBER] Distance Replica Exchange
- [AMBER] DMF solvent box
- [AMBER] eigenvalues add up to more than trace of matrix
- [AMBER] Energy-from-MM/PBSA-VS-experiment
- [AMBER] Environment Variables in Cygwin Don't Remain
- [AMBER] error in AMBer distance constraint
- [AMBER] error in distance restraint
- [AMBER] error message from iAPBS
- [AMBER] Error: unable to find mopac charges in mopac.out
- [AMBER] ff03 parameter for GDP and GTP
- [AMBER] File format for reading in charges in antechamber
- [AMBER] Fwd: Group specification
- [AMBER] GAFF parameter
- [AMBER] Gaussian log file error
- [AMBER] HBOND analysis
- [AMBER] How create PRMTOP and INCPRD for surface?
- [AMBER] How to add a hydrogen to the residue?
- [AMBER] How to create FF for diamond.
- [AMBER] how to get hold of older versions of MKL ?
- [AMBER] How to introduce the second protein molecule into simulation box?
- [AMBER] How to prepare the acetate ion file in leap?
- [AMBER] iAPBS - how to set the right grid dimensions
- [AMBER] inhibitor prepin not recognized in xleap
- [AMBER] installation of Amber on OSX
- [AMBER] Is it the way to do simulation in vacuum
- [AMBER] Is iwrap mapping water molecules to my protein cavity?
- [AMBER] Large File Support
- [AMBER] Lennard Jones Potential A and B coefficients in Topology file
- [AMBER] LES and NEB problem
- [AMBER] Ligand covalent bonds appear to be broken
- [AMBER] ligand exiting a protein cavity
- [AMBER] man pages?
- [AMBER] mean square displacment
- [AMBER] method used to determine partial charges?
- [AMBER] minimization error
- [AMBER] Missing X11 Libraries
- [AMBER] MM/PBSA: NaN, Infinity and ************* in snapshot_com.all.out
- [AMBER] MM_PBSA decomposition pair question
- [AMBER] mm_pbsa- Decomposition: bad atom type
- [AMBER] MM_PBSA: abnormal VDW interaction energy
- [AMBER] MMPBSA: No radius found for F
- [AMBER] MMTSB cluster analysis versus ptraj cluster analysis
- [AMBER] nab normal mode analysis has imaginary frequencies
- [AMBER] nasty memory bug in calculatePrincipalAxis
- [AMBER] new process_mdout.pl script????
- [AMBER] NMR restraint
- [AMBER] OpenMP
- [AMBER] pairwise per-residue decomposition
- [AMBER] Parallel sander & polarisability
- [AMBER] parameters for O2 molecule
- [AMBER] part of the protein escaped from the water box
- [AMBER] PEMD
- [AMBER] pmemd ifort problem
- [AMBER] Possible bug in "com" group torsion angle constrain? Thanks!
- [AMBER] Preparing distance restraints
- [AMBER] probelm-APBS
- [AMBER] Problem with memory in nmode analysis
- [AMBER] problem with minimization
- [AMBER] Problem with running anal module in amber
- [AMBER] Protein and charged surface
- [AMBER] ptraj and prmtop
- [AMBER] Ptraj Segmentation Fault
- [AMBER] pucker calculation for six member rings
- [AMBER] Question about distance restraint ?
- [AMBER] question with hbond in carnal
- [AMBER] question with pucker in six member ring
- [AMBER] R.E.D.-III.3 tools release - q4md-forcefieldtools.org
- [AMBER] RDC and alignment tensor
- [AMBER] red problem
- [AMBER] RESP charges with -a and without -a flag
- [AMBER] resp_problem
- [AMBER] rms fit of mutant with respect to wild type structure
- [AMBER] RMSD vs time and RMSD vs residues
- [AMBER] S-S problem-in protein
- [AMBER] Salt bridge time scale
- [AMBER] Simulated annealing
- [AMBER] Simulating transmembrane protein.
- [AMBER] simulation blown up
- [AMBER] six member pucker calculation
- [AMBER] software to hydrate protein pockets
- [AMBER] solvent accessible surface area
- [AMBER] Some queries about pH simulation
- [AMBER] some queries on -states flag in constant pH simulation
- [AMBER] SPC/E HOH angle
- [AMBER] stacking clusters
- [AMBER] surface binding protein
- [AMBER] The -c option in Sander
- [AMBER] the criterion of equilibrium
- [AMBER] The hydrophobic contribution
- [AMBER] Thermodynamic Integration calculation on an artificial anion receptor
- [AMBER] Time scale of the Protein domain motion ?
- [AMBER] TiO2 modeling
- [AMBER] too many undefined parameters in frcmod
- [AMBER] translate multiple residues
- [AMBER] trouble using iAPBS
- [AMBER] Unable to correctly identify element when running QM/MM in amber10
- [AMBER] unit converter for force constants
- [AMBER] unit convertion for force constants
- [AMBER] units of measures
- [AMBER] Using idecomp=3 with igb=10 (PB)
- [AMBER] using RESP program
- [AMBER] vlimit
- [AMBER] why is TAUTP scaled by "e" ?
- [AMBER] Why the calculation ofen stop with the calculation process not end?
- [AMBER] xleap editing window icons inactive
- [AMBER] xleap not reconizing inhibitor prepin
- [AMBER] xleap-does not work
- [AMBER] xleap-does not work(Being solved!)
- [AMBER] XServe cluster
- [Amber]AMBER: MM_PBSA problems in AMBER10
- AMBER: periodic bondary condition
- AW: [AMBER] Add the hydrogen to the carboxyl of the GLU residue?
- Help required in Amber10 Installation
- Missing X11 Libraries
- RDC and alignment tensor
- VDW and TI for free energy
- 回å¤ï¼š [Amber]AMBER: MM_PBSA problems in AMBER10
- 回å¤ï¼š [Amber]AMBER: MM_PBSA problemsin AMBER10
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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