Amber Archive Apr 2005 by subject
- about run time in GB and PB
- Amber installation
- AMBER Test Error (Follow Up)
- AMBER:
- AMBER: a bimolecular reaction
- AMBER: A problem in TI approach - test case: meth2eth and eth2meth
- AMBER: a problem with mm_pbsa
- AMBER: A question on connecting residues in xleap
- AMBER: about equilibration dynamics
- AMBER: About Gaussian Key Words
- AMBER: About Gaussian Key Words (fwd)
- AMBER: About NAB
- AMBER: about run time in GB and PB
- AMBER: All the tests passed except prmtop and prepin...
- AMBER: AMBER 8.0 problems with impose (tleap) on linux
- AMBER: Amber compilation problem
- AMBER: Amber Installation
- AMBER: AMBER Test
- AMBER: AMBER Test Error
- AMBER: Amber8 installation on IBM (power4) with SUSE 9.1 Linux (IBM XLF compiler)
- AMBER: amber8/antechamber installation problem
- AMBER: Announcment: Nucleic Acid Builder (NAB) version 5 is released
- AMBER: Antechamber -reorders atom sequence
- AMBER: antechamber for cyano group
- AMBER: atommask error
- AMBER: ATTN REVISION
- AMBER: average structure-ptraj
- AMBER: big fluctuation in MM-PBSA/GA
- AMBER: breaking symmetry in minimization
- AMBER: Calculate vdw parameters for alkaline earth metal ions
- AMBER: capping
- AMBER: carnal problem
- AMBER: combine mdcrd using ptraj
- AMBER: Compile Error on Running Amber on AMD opterons in the Linux-based clusters
- AMBER: Compiling on dual-opteron with pathscale 2.1 on RHEL 4 AS
- AMBER: coordinates translation
- AMBER: dielectric constant
- AMBER: distance restraints
- AMBER: Disulfide bond
- AMBER: doble C and N terminal
- AMBER: Does anybody know the experimental solvation free energies of Efavirenz and some other DPC drugs
- AMBER: doesn't work in pmemd, and no output in parallel simulations
- AMBER: Dual Xeon EM64T Intel Fortran Compiler
- AMBER: error in pbsa calculation
- AMBER: Fail to load the trajectory file.
- AMBER: false bond created upon coordinate retrieval
- AMBER: ff02EP + pol3 (2)
- AMBER: force constant Unit used in TMD
- AMBER: Formatting a restraint file
- AMBER: Free energy
- AMBER: Free energy pertubation (thermodynamic intergration)
- AMBER: freee energy calculation without minimised structure
- AMBER: gaff atom types
- AMBER: GAFF: H type on carbon bearing a cyano group
- AMBER: GB and mm_pbsa.pl
- AMBER: GB dynamics
- AMBER: GB with Langevin dynamics - solution
- AMBER: GB with Langevin dynamics problem
- AMBER: GB with Langevin dynamics problem 2
- AMBER: Gibbs compilation problem
- AMBER: helical parameters obtaining
- AMBER: How to deal with the Non-standard residue
- AMBER: How to fix the torsion angles during energy minimization
- AMBER: how to get the parameters for modified amino acid residue?
- AMBER: how to make a nonsymmetric box around the solute
- AMBER: how to make the prepin file for dimer and clusters of organic molecule in Amber7
- AMBER: How to restart MM_PBSA or doing the statistics only
- AMBER: ibelly not working
- AMBER: implementing AMBER in NAMD
- AMBER: Induced dipole in AMBER8
- AMBER: interaction between residues
- AMBER: intramolecular nonbonded interactions in AMBER force field
- AMBER: ipol=1 & use_pme= ??
- AMBER: langevin, GB and simulated annealing - 2
- AMBER: langevin, GB and simulated annealing - 3
- AMBER: langevin, GB and simulated annealing - 4
- AMBER: langevin, GB and simulated annealing?
- AMBER: leap single precision
- AMBER: linit in mm-pbsa
- AMBER: local dielectric constant
- AMBER: makeDIST_RST ERROR
- AMBER: mean structure calculation
- AMBER: mixture solvent model
- AMBER: MM-PBSA in protein-Zn-ligand system
- AMBER: MM_PBSA error
- AMBER: mm_pbsa problem
- AMBER: Moil-view and Quicktime movie
- AMBER: New parametrs
- AMBER: No. of Snapshots in MM/GB/SA
- AMBER: Non-Bonded Cutoff vs PME
- AMBER: Nose-Hoover thermostat
- AMBER: nscm
- AMBER: Odd Antechamber Behavior
- AMBER: On the role of neutralizing ions in GB-MD and GBSA
- AMBER: oxo-heme
- AMBER: parameters in gaff.dat
- AMBER: PB Bomb in circle(): Stored surface points over limit
- AMBER: peptide side chain modification with LEAP
- AMBER: periodic boundaries and repeating structure
- AMBER: Problem when converting AMBER trajectories to CHARMM format
- AMBER: Problem with "Thermodynamic integration calculations" tutorial ,unsuspected error
- AMBER: problem with belly calculation restart
- AMBER: problem with input files when using ff02EP + pol3
- AMBER: problems with "protonate"
- AMBER: Problems with protonate on Linux
- AMBER: Protein With Structural Ions
- AMBER: ptraj, hbond problem
- AMBER: Pyranose pucker parameters
- AMBER: question about TGMD: vlimit exceeded for step
- AMBER: RADIOPT=1
- AMBER: radius parameter for F atom
- AMBER: rdparm
- AMBER: reference of Targeted MD
- AMBER: Rep Exch. suggestion
- AMBER: RESP charges - multiple conformations
- AMBER: RESP charges with Gaussian03 and Amber
- AMBER: rst file problems
- AMBER: Sander bomb - atom out of bounds
- AMBER: Sander minimization & dynamic question
- AMBER: Sander/Mpich2 error with mpd_singinit
- AMBER: scaleCharges with polarisable force fields
- AMBER: segmentation problem
- AMBER: serial and parallel
- AMBER: Silicon related parameters
- AMBER: single-stranded poly(rC) simulation
- AMBER: small target pressure in constant pressure dynamics
- AMBER: SollvateBox with ethanol
- AMBER: solvate water box
- AMBER: Solvate with mixture of ethanol and water(Newbie question)
- AMBER: solvateoct mymolecule CHCL3BOX 10 PROBLEM!!!
- AMBER: solvent accessible surface area
- AMBER: strange VDWAALS and EEL energies calculated by pbsa
- AMBER: surface area
- AMBER: The effect appling paches
- AMBER: the restart of replica exchange method (REM) simulations in AMBER8
- AMBER: the restarting error
- AMBER: tleap and water
- AMBER: trajectory alignment using ptraj
- AMBER: Two question about dielectric constant
- AMBER: value of SALTCON
- AMBER: vdw or center box dimensions, periodicity, and the jagged edge
- AMBER: Warning: Error opening "New" file from subroutine OPNMRG in pmemd
- AMBER: Warnings as a file
- AMBER: Watson-Crick restraints
- AMBER: what is wrong with my amber job or installation?
- AMBER: writing MASKs
- AMBER: xleap, lib file question
- AMBER:Bond lengths aren't reasonable after minimisation.
- AMBER:FAD can't be minimized.
- Gibbs compilation problem
- R.E.D. question
- single-stranded poly(rC) simulation
- system comparison for amber
- Last message date: Sat Apr 30 2005 - 14:53:00 PDT
- Archived on: Fri Nov 22 2024 - 05:53:24 PST
