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AMBER Archive (2004) - Feb 2004 By Subject
360 messages sorted by: [ author ] [ date ] [ thread ]About this archive
Starting: Mon Feb 02 2004 - 07:31:51 CST
Ending: Sun Feb 29 2004 - 13:43:24 CST
- AMBER:
- AMBER: (no subject)
- AMBER: A general question
- AMBER: add Na+
- AMBER: adding ions to nucleic acids
- AMBER: Aldo's PMEMD bug
- AMBER: AMBER 5 (sander) Parallel PME on IBM p630
- AMBER: Amber on Redhat Enterprise
- AMBER: ANAL problem.
- AMBER: antechamber + FAILED TO ACHIEVE SCF
- AMBER: antechamber + mopac + MAXIMUM NUMBER OF ATOMIC ORBITALS EXCEEDED
- AMBER: antechamber + mopac +scf failed
- AMBER: antechamber + mopac error
- AMBER: antechamber error
- AMBER: antechamber error in test / differences in prmtop files
- AMBER: atom type for GBSA
- AMBER: averaged structure with unknown elements
- AMBER: bad crd file
- AMBER: Box of mixed solvant
- AMBER: Build a H+ ion in Leap?
- AMBER: Can anybody help me with CHARMM
- AMBER: Can you write me how can I add the ACE and NMe groups in the Xleap?
- AMBER: carnal
- AMBER: cell dimensions
- AMBER: center of mass in CARNAL
- AMBER: check unit + saveamberparm
- AMBER: Close contact warnings
- AMBER: compiling software(RESP)
- AMBER: compiling software(RESP) on MAC G5
- AMBER: contributed parameters
- AMBER: contributed parameters (modified base - PSU)
- AMBER: convert restart to mdcrd?
- AMBER: Defining residues
- AMBER: DIELC
- AMBER: dipole moment in ptraj
- AMBER: distance-aromatic ring
- AMBER: DNA
- AMBER: Errors when running tleap
- AMBER: flexible water potential
- AMBER: GBSA frequency update
- AMBER: GLYCAM web site
- AMBER: histidine and its various forms
- AMBER: How to add ACE and NME groups?
- AMBER: how to add force field parameters
- AMBER: How to add H+ ion in leap?
- AMBER: How to remove Cl- ions
- AMBER: how to use prep file
- AMBER: IFC COMPILER
- AMBER: image in ptraj
- AMBER: Installing Amber on IBM AIX cluster
- AMBER: Installing AMBER on SGI Octane 2-CPU - erfcfun.c compile prob.
- AMBER: ions94.lib file
- AMBER: Lattice structures in xleap
- AMBER: LCPO parameters in gbsa
- AMBER: leap - orientation of sequenced residues
- AMBER: LEaP- Error reading frcmod parameters.
- AMBER: LES
- AMBER: LES methodology question
- AMBER: LES question
- AMBER: MCSS
- AMBER: MD simulations with 2 molecules
- AMBER: minimizating complex-protein with AMBER
- AMBER: minimization output
- AMBER: MM-PBSA: molecular charges and active site water
- AMBER: MM-PBSA:??Decomposition of receptor energies??
- AMBER: mm_pbsa question
- AMBER: mmpbsa qustion
- AMBER: moil-view question
- AMBER: multiple messages on the amber reflector
- AMBER: neutrality of charge in AMBER 7
- AMBER: Nitrogen vdw type
- AMBER: Nmode convergence
- AMBER: NMODE for protein via MM-PBSA-cntd
- AMBER: NMR restraints-Floating point exception
- AMBER: nucleic acid bases nonplanar during LES sim
- AMBER: NVE&polarizable force field
- AMBER: off-subject ROCKS/Qbank
- AMBER: PB in mm-pbsa
- AMBER: PGA
- AMBER: pka calculation
- AMBER: PMEMD and nmropt=1
- AMBER: pmf calculation using gibbs
- AMBER: pmf calculation using gibbs.
- AMBER: prep files for modified bases
- AMBER: problem with frcmod file
- AMBER: problem with tleap in Amber
- AMBER: Problems with xleap
- AMBER: protein - fractional native contacts
- AMBER: protonation
- AMBER: ptraj
- AMBER: ptraj & LES
- AMBER: ptraj and dipoles
- AMBER: ptraj and dipoles....
- AMBER: question about the average structure from ptraj
- AMBER: questions parm94/99 ff secondary structure
- AMBER: R.E.D.
- AMBER: RESP charges for protein fragment
- AMBER: rstdip
- AMBER: Run calculations for protein in Amber
- AMBER: Run calculations for protein in Amber-distance dependent dielectric function
- AMBER: sander + ewald bomb
- AMBER: sander + vlimit exceed...
- AMBER: sander and mpich (which compilers/mpich work)
- AMBER: sander output
- AMBER: saveamberparm warning in leap?
- AMBER: Segmentation fault in SaveAmberParm
- AMBER: SIGSEGV
- AMBER: size.h error
- AMBER: Star like (branching) molecule
- AMBER: temperature in DelPhi for MM-PBSA calculation
- AMBER: Temperature in Nmode
- AMBER: TER in amber
- AMBER: The charge given by xleap from amber 5
- AMBER: the uses for Amber FFs
- AMBER: Thermostat comparison ?
- AMBER: TI, angle parameters for nitrogen, frcmod
- AMBER: TIP4P
- AMBER: TIP4P extended
- AMBER: tmd question
- AMBER: water as a "ligand" in GBSA and MM-PBSA?
- AMBER: What does this error message mean?
- AMBER: xleap & antechamber
- AMBER: xleap don't recognize my residue/atom
- ANAL problem
- To David Case
Last message date: Thu May 05 2005 - 14:26:38 CDT
Archived on: Thu May 05 2005 - 14:29:59 CDT
360 messages sorted by: [ author ] [ date ] [ thread ]
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