AMBER Archive (2006) - Sep 2006 By Subject371 messages sorted by:
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Starting: Fri Sep 01 2006 - 00:32:54 CDT
Ending: Fri Sep 29 2006 - 16:08:42 CDT
- [UCE]AMBER: Temperature not rising enough during simulated annealing
- Amber8: problem related to antechamber
- AMBER:
- AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package
- AMBER: 'lastrst' error for amber8
- AMBER: (no subject)
- AMBER: a ligand file
- AMBER: A question about Dynamics.
- AMBER: A script file for measuring the distance between 2 atoms during MD
- AMBER: About Lennard-Jones Parameters
- AMBER: about ligand charge
- AMBER: acidifying a water box
- AMBER: ACML and MASS/MASSV for sander and pmemd
- AMBER: addions default settings.
- AMBER: Amber parallel version
- AMBER: Amber8: problem related to antechamber
- AMBER: Amber9: Free Energy
- AMBER: angle between helices
- AMBER: bad atom type: Li
- AMBER: build a polymer with sequence command
- AMBER: Ca2+ polarizability
- AMBER: cAMP ligand charge
- AMBER: cAMP ligand file
- AMBER: Can salt effect be determined in GB medel?
- AMBER: center of mass dihedral restraints
- AMBER: change mdcrd file to pdb file
- AMBER: chemical shift restrains
- AMBER: coordinate files
- AMBER: cyclic AMP off and frcmod files?
- AMBER: Denaturing MD
- AMBER: distance between two atoms
- AMBER: DPPC Bilayer size
- AMBER: EGB term decomposition
- AMBER: Electrostatic Energy Constant
- AMBER: energy data for limited part of system
- AMBER: Error in compiling Amber 8 parallel
- AMBER: Error in reading RDC data
- AMBER: Error in Running Sander
- AMBER: Error: cannot run "$AMBERHOME/exe/divcon" of bcc() in charge.c
- AMBER: force fields for proflavine molecule
- AMBER: forrtl: severe (64): input conversion error, unit 9, file
- AMBER: from ADP-small protein complex to GTP-protein complex
- AMBER: Gaussian, antechamber, RESP
- AMBER: GPCR-membrane issue
- AMBER: have problems with restrained minimization
- AMBER: help with antechamber - creating ligand
- AMBER: how to feed dihedral angles of our choice to the linear sequence in amber8
- AMBER: How to get the ligand. ac file
- AMBER: hydronium ion parameters
- AMBER: implicit solovent model by adjusting the parameter EXTDIEL ?
- AMBER: Implicit Water - Force field parameters
- AMBER: improper torsion angle problem
- AMBER: installation error for pmemd in Amber 9/Opteron
- AMBER: Installing AMBER9 on cygwin (WinXP)
- AMBER: job crashes
- AMBER: kclust
- AMBER: LEAP - "could not find type: NH"
- AMBER: leap - how to recognize my structure
- AMBER: leap can't assign CALA
- AMBER: LENNARD_JONES_ACOEF & BCOEF prmtop changes
- AMBER: lib-4324 : UNRECOVERABLE library error
- AMBER: lifetime and maxocc
- AMBER: ligand file
- AMBER: Machine File for Intel Core 2 Duo E6400
- AMBER: MAXM in nmode
- AMBER: MD on protein-ligand interaction
- AMBER: mdcrd file
- AMBER: missing benchmark files
- AMBER: Mixed solvent?
- AMBER: mm-pbsa output
- AMBER: mm_pbsa segmentation faults
- AMBER: mm_pbsa snapshots for "three-trajectory"
- AMBER: Multiple Timestep MD
- AMBER: NAD parameters
- AMBER: new article on Amber force fields
- AMBER: nmode memory allocation error
- AMBER: on the rst file of the current ruuning
- AMBER: On the temperature increasement in the restriction MD in the tutorial 2 section 5
- AMBER: one question on MD
- AMBER: Oon Modeling the metalloprotein with GB model.
- AMBER: output file not generated
- AMBER: Parallel compile: ld: cannot find -lfmpi
- AMBER: PARAMETERISATION PROBLEM
- AMBER: Parameterization of ethidium - phenyl ring
- AMBER: parameters for Nickel and iron
- AMBER: parm*.dat
- AMBER: Parmchk problems (parm99.dat)
- AMBER: pbsa segmentation faults
- AMBER: Picking up water molecules around one molecule
- AMBER: pmemd error
- AMBER: pmf with respect to a surface
- AMBER: polarizable ff for ligand
- AMBER: post nmanal
- AMBER: potential energy
- AMBER: potential energy in the MD result
- AMBER: pqr from constant pH MD
- AMBER: Problem about installing amber9 on Mac OS X
- AMBER: problem to center solvateshell
- AMBER: Problem using antechamber
- AMBER: Problem with ptraj
- AMBER: Problems using rst distance constraints in Amber 8
- AMBER: Problems with a restrained minimization approach
- AMBER: proposed patch for ptraj/evec.c (Amber 9.0)
- AMBER: protein-ligand interaction
- AMBER: ptraj RMSD vs. RMSF
- AMBER: Question about free energy with mm_pbsa
- AMBER: Question about LEAP and twisting a dihedral angle
- AMBER: Question about Streptavidin/Biotin Tutorial.
- AMBER: Question about using PMEMD and GB
- AMBER: question on Lennard-Jones fitting in FF94 and 96
- AMBER: Questions
- AMBER: Questions/observations about Nudged Elastic Band (NEB)
- AMBER: RDC refinement
- AMBER: residence time of water molecules
- AMBER: resolving a bad initial model
- AMBER: resp
- AMBER: Restart problem on PMEMD with position restraint.
- AMBER: restraints and constant pressure
- AMBER: RMSd vs RMSf
- AMBER: running sander on several nodes
- AMBER: seg fault during test.serial
- AMBER: set a trucated octahedron box in Leap
- AMBER: strange values of the energy of "1-4 EEL" , "EAMBER" and the RMS
- AMBER: strange values of the energy of "1-4 EEL" , "EAMBER" andthe RMS
- AMBER: structure from MD
- AMBER: System in polarizable waters
- AMBER: Temperature fluctuation BIG with ntt=3
- AMBER: Temperature not rising enough during simulated annealing
- AMBER: the RMSD of MD
- AMBER: the sequence command in leap
- AMBER: the time length of the restricted MD
- AMBER: TI-FEP : strange result for different clambda values
- AMBER: trajout
- AMBER: WHAT IF CHeck after MD
- AMBER: WHATIF Check after MD
- AMBER: Which POPC Bilayer to start?
- AMBER: zzfft error for pmemd in Amber 9/Opteron
- AMBER: zzfft issue resolved -thanks!
- AW: AMBER: how to feed dihedral angles of our choice to the linear sequence in amber8
- FF problem: RG residue minimizes to non-planar structure
Last message date: Sat Dec 30 2006 - 07:20:23 CST
Archived on: Wed Feb 21 2007 - 22:44:16 CST
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