Amber Archive Feb 2003 By Thread
230 messages
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Starting
Sat Feb 01 2003 - 11:22:16 PST,
Ending
Sat Mar 01 2003 - 02:53:02 PST
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Gibbs stops after a finite number of window runs
Seongeun Yang
(Sat Feb 01 2003 - 11:22:16 PST)
Re: Gibbs stops after a finite number of window runs
David A. Case
(Sat Feb 01 2003 - 13:11:43 PST)
Re: Gibbs stops after a finite number of window runs
Seongeun Yang
(Sat Feb 01 2003 - 13:42:42 PST)
Re: Gibbs stops after a finite number of window runs
caldwell_at_heimdal.compchem.ucsf.edu
(Sat Feb 01 2003 - 14:42:54 PST)
Re: question about ligand
Lishan Yao
(Sat Feb 01 2003 - 18:24:57 PST)
gibbs input file
Patricia Burgess
(Sun Feb 02 2003 - 16:01:59 PST)
questions about AMBER
Guoxi Zhang
(Sun Feb 02 2003 - 18:57:21 PST)
How to calculate new force field?
k.watanabe
(Sun Feb 02 2003 - 23:22:31 PST)
Re: How to calculate new force field?
Jose Ramon Blas
(Mon Feb 03 2003 - 11:06:24 PST)
SASA calculation
Luis Gracia
(Mon Feb 03 2003 - 14:58:25 PST)
Re: SASA calculation
Michael Ford
(Mon Feb 03 2003 - 15:22:26 PST)
trajectory file in mm_pbsa
eric hu
(Mon Feb 03 2003 - 18:11:21 PST)
desolvation energy in mm_pbsa
eric hu
(Mon Feb 03 2003 - 18:36:44 PST)
Re: desolvation energy in mm_pbsa
Michael Ford
(Tue Feb 04 2003 - 06:21:15 PST)
Re: desolvation energy in mm_pbsa
eric hu
(Tue Feb 04 2003 - 12:38:18 PST)
Re: desolvation energy in mm_pbsa
Holger Gohlke
(Tue Feb 04 2003 - 12:59:21 PST)
Amber7 & mpich
FyD
(Tue Feb 04 2003 - 06:27:23 PST)
Re: Amber7 & mpich
Michael Crowley
(Tue Feb 04 2003 - 09:56:22 PST)
Re: Amber7 & mpich
Florian Barth
(Tue Feb 04 2003 - 15:39:51 PST)
How to do the image using ptraj?
Yuhui Cheng
(Tue Feb 04 2003 - 18:35:53 PST)
Re: Amber7 & mpich
FyD
(Wed Feb 05 2003 - 06:58:25 PST)
Acetonitrile parameters
N. Jiten Singh
(Mon Feb 03 2003 - 21:52:16 PST)
Re: Acetonitrile parameters
Pascal Bonnet
(Tue Feb 04 2003 - 07:22:04 PST)
ifc, gibbs and ewald
David Smith
(Tue Feb 04 2003 - 08:49:53 PST)
RESP charge derivation
Lepsa
(Tue Feb 04 2003 - 09:34:57 PST)
Fw: RESP charge derivation
Lepsa
(Wed Feb 05 2003 - 00:33:53 PST)
stacking energy
thenmalar rathinavelan
(Wed Feb 05 2003 - 02:19:06 PST)
[Fwd: Re: trajectory file in mm_pbsa]
Holger Gohlke
(Tue Feb 04 2003 - 09:47:08 PST)
MM-PBSA error
Bimo Ario Tejo
(Mon Feb 03 2003 - 21:56:34 PST)
Re: MM-PBSA error
Bimo Ario Tejo
(Tue Feb 04 2003 - 19:05:30 PST)
bond command
Craig A Bayse
(Tue Feb 04 2003 - 21:46:20 PST)
Re: bond command
David A. Case
(Tue Feb 04 2003 - 22:30:26 PST)
Re: bond command
Craig A Bayse
(Wed Feb 05 2003 - 13:30:36 PST)
Re: bond command
David A. Case
(Wed Feb 05 2003 - 22:13:22 PST)
Gibbs: DynamicWin and NSTMEQ?
Paula Petrone
(Thu Feb 06 2003 - 10:48:02 PST)
Re: Gibbs: DynamicWin and NSTMEQ?
David A. Case
(Fri Feb 07 2003 - 16:12:07 PST)
[Fwd: Re: Backbone torsional angles' format?]
Holger Gohlke
(Fri Feb 07 2003 - 16:23:15 PST)
Periodic Box
John Finke
(Fri Feb 07 2003 - 16:25:10 PST)
RE: Periodic Box
Xiang, Tian-Xiang
(Sat Feb 08 2003 - 08:52:49 PST)
energy calculation
thenmalar rathinavelan
(Sat Feb 08 2003 - 23:19:59 PST)
Re: energy calculation
Carlos Simmerling
(Sun Feb 09 2003 - 05:27:03 PST)
RE: energy calculation
Yong Duan
(Sun Feb 09 2003 - 08:36:28 PST)
Question about quasih
Lishan Yao
(Sun Feb 09 2003 - 15:18:38 PST)
Re: Question about quasih
CUI, Guanglei
(Sun Feb 09 2003 - 18:59:11 PST)
decrease a force const. for angle
Michal Otyepka
(Mon Feb 10 2003 - 04:47:35 PST)
Re: decrease a force const. for angle
David A. Case
(Mon Feb 10 2003 - 17:04:55 PST)
UCSF moving day.
caldwell_at_heimdal.compchem.ucsf.edu
(Mon Feb 10 2003 - 17:29:07 PST)
references
Ioana Cozmuta
(Mon Feb 10 2003 - 18:22:51 PST)
Itanium II
Jose Ramon Blas
(Tue Feb 11 2003 - 10:50:58 PST)
RE: Itanium II
Ross Walker
(Wed Feb 12 2003 - 15:46:27 PST)
RE: Itanium II
Scott Brozell
(Wed Feb 12 2003 - 16:21:06 PST)
Including the Peroidiic Box info ??
N. Jiten Singh
(Wed Feb 12 2003 - 19:21:41 PST)
About antechamber
k.watanabe
(Wed Feb 12 2003 - 21:32:18 PST)
Isotropic Solvent Box
N. Jiten Singh
(Thu Feb 13 2003 - 03:28:55 PST)
compatibility of amber with NAMD
Ioana Cozmuta
(Thu Feb 13 2003 - 10:42:41 PST)
Re: compatibility of amber with NAMD
Peter Gannett
(Thu Feb 13 2003 - 14:05:54 PST)
inter & intra-molecular interaction energies
Tian-Xiang Xiang
(Thu Feb 13 2003 - 14:10:07 PST)
Re: inter & intra-molecular interaction energies
David A. Case
(Thu Feb 13 2003 - 15:21:15 PST)
web page update
caldwell_at_heimdal.compchem.ucsf.edu
(Thu Feb 13 2003 - 15:34:45 PST)
RE: inter & intra-molecular interaction energies
Xiang, Tian-Xiang
(Thu Feb 13 2003 - 15:47:54 PST)
question about antechamber
Lishan Yao
(Thu Feb 13 2003 - 14:55:39 PST)
Re: compatibility of amber with NAMD
Andreas Svrcek-Seiler
(Fri Feb 14 2003 - 06:27:27 PST)
Re: compatibility of amber with NAMD
Luis Gracia
(Fri Feb 14 2003 - 10:16:12 PST)
charge determination for polariable ff02 force fields
Xiang, Tian-Xiang
(Fri Feb 14 2003 - 12:27:51 PST)
Fw: charge determination for polariable ff02 force fields
Lepsa
(Sat Feb 15 2003 - 08:12:02 PST)
TAUP and density problem
yuan bo
(Sun Feb 16 2003 - 01:29:34 PST)
RE: TAUP and density problem
case
(Sun Feb 16 2003 - 17:36:48 PST)
RE:RE: TAUP and density problem
yuan bo
(Mon Feb 17 2003 - 01:50:08 PST)
Re: RE: TAUP and density problem
David A. Case
(Mon Feb 17 2003 - 10:06:03 PST)
Number of water too large
kalyan_at_mbu.iisc.ernet.in
(Mon Feb 17 2003 - 08:10:52 PST)
Velocity
A. Hungie
(Mon Feb 17 2003 - 08:01:04 PST)
Re: Velocity
caldwell_at_heimdal.compchem.ucsf.edu
(Mon Feb 17 2003 - 08:10:06 PST)
Re: Velocity
Carlos Simmerling
(Mon Feb 17 2003 - 10:02:34 PST)
RE: Velocity
Yong Duan
(Mon Feb 17 2003 - 13:00:01 PST)
(no subject)
Majid moghaddam
(Sun Feb 16 2003 - 05:57:21 PST)
Re: (no subject)
David A. Case
(Tue Feb 18 2003 - 14:16:34 PST)
RE: charge determination for polariable ff02 force fields
Xiang, Tian-Xiang
(Sun Feb 16 2003 - 10:19:39 PST)
Re: charge determination for polariable ff02 force fields
Lepsa
(Mon Feb 17 2003 - 00:16:07 PST)
question on EWALD
Sichun Yang
(Sun Feb 16 2003 - 15:54:49 PST)
Re: question on EWALD
David A. Case
(Mon Feb 17 2003 - 10:08:53 PST)
Re: question on EWALD
Sichun Yang
(Mon Feb 17 2003 - 11:16:25 PST)
Re: question on EWALD
Sichun Yang
(Mon Feb 17 2003 - 11:37:04 PST)
Amber Documents
Nicole A Rutkowski
(Mon Feb 17 2003 - 11:42:26 PST)
RE: question on EWALD
Yong Duan
(Mon Feb 17 2003 - 13:08:17 PST)
RE: question on EWALD
Sichun Yang
(Mon Feb 17 2003 - 14:12:42 PST)
RE: question on EWALD
Yong Duan
(Mon Feb 17 2003 - 14:54:14 PST)
RE: question on EWALD
Sichun Yang
(Mon Feb 17 2003 - 15:28:00 PST)
one time evaluation
Ioana Cozmuta
(Mon Feb 17 2003 - 16:14:32 PST)
question about partial charge
yuann
(Mon Feb 17 2003 - 18:43:48 PST)
Re: question about partial charge
Lepsa
(Mon Feb 17 2003 - 23:56:59 PST)
metallic ions
Marc Dobler
(Tue Feb 18 2003 - 01:10:29 PST)
interaction between ligand & protein
Lishan Yao
(Tue Feb 18 2003 - 08:59:56 PST)
Re: interaction between ligand & protein
Lepsa
(Tue Feb 18 2003 - 09:28:35 PST)
Gibbs: Electrostatic Decoupling
Paula Petrone
(Tue Feb 18 2003 - 09:31:41 PST)
adding hydrogens
CUI, Guanglei
(Tue Feb 18 2003 - 10:44:13 PST)
Re: adding hydrogens
Oliver Hucke
(Wed Feb 19 2003 - 00:02:30 PST)
Re: adding hydrogens
Lepsa
(Wed Feb 19 2003 - 00:26:36 PST)
How do NTC=2 recognize hydrogen atom?
yuan bo
(Wed Feb 19 2003 - 02:24:55 PST)
Re: How do NTC=2 recognize hydrogen atom?
David A. Case
(Thu Feb 20 2003 - 08:19:27 PST)
hexane parameters
pu xuemei
(Wed Feb 19 2003 - 04:06:50 PST)
RE: adding hydrogens
CUI, Guanglei
(Wed Feb 19 2003 - 06:06:27 PST)
Fw: adding hydrogens
Lepsa
(Wed Feb 19 2003 - 06:23:54 PST)
charge neutralization in DNA
Mahadevan Seetharaman
(Tue Feb 18 2003 - 11:08:55 PST)
Re: charge neutralization in DNA
David A. Case
(Tue Feb 18 2003 - 14:27:20 PST)
mm_pbsa
Yongmei Wang
(Tue Feb 18 2003 - 15:14:01 PST)
Re: mm_pbsa
Holger Gohlke
(Tue Feb 18 2003 - 16:13:51 PST)
Re: question about partial charge
sychen
(Tue Feb 18 2003 - 19:52:32 PST)
MAXINT problem
yuan bo
(Fri Feb 14 2003 - 21:51:13 PST)
charges, opt and iops
Lepsa
(Sat Feb 15 2003 - 07:59:44 PST)
xleap crash under Irix
FyD
(Thu Feb 13 2003 - 11:46:07 PST)
Re: xleap crash under Irix
David A. Case
(Thu Feb 13 2003 - 12:57:35 PST)
MM_PBSA Errors
Ramón Garduño-Juárez
(Tue Feb 11 2003 - 16:16:00 PST)
Re: MM_PBSA Errors
Pascal Bonnet
(Wed Feb 12 2003 - 01:50:23 PST)
hexane parameters
pu xuemei
(Wed Feb 12 2003 - 02:00:19 PST)
Error Massage in Sander amber7 in Linux
N. Jiten Singh
(Wed Feb 12 2003 - 05:07:26 PST)
Re: Error Massage in Sander amber7 in Linux
David A. Case
(Wed Feb 12 2003 - 05:22:55 PST)
NTC=3 for organic solvent and NTC=2 for soluter?
yuan bo
(Wed Feb 12 2003 - 01:57:21 PST)
NTC=3 for organic solvent and NTC=2 for solute?
yuan bo
(Wed Feb 12 2003 - 01:57:42 PST)
mm_pbsa energy unit
eric hu
(Mon Feb 10 2003 - 11:22:38 PST)
Re: mm_pbsa energy unit
Holger Gohlke
(Mon Feb 10 2003 - 11:48:51 PST)
Carnal problem...
Andrei Leitão
(Thu Feb 06 2003 - 14:17:49 PST)
Misaligned Coords from Alanine Scanning
Robert J. Woods
(Fri Feb 07 2003 - 07:54:07 PST)
Re: Misaligned Coords from Alanine Scanning
Holger Gohlke
(Fri Feb 07 2003 - 08:00:31 PST)
essential dynamics
Lishan Yao
(Fri Feb 07 2003 - 08:31:05 PST)
Re: essential dynamics
Yongxing Liu
(Fri Feb 07 2003 - 10:13:09 PST)
Carnal DECLARE of TORSION problem
William Wei
(Fri Feb 07 2003 - 10:20:37 PST)
Re: Carnal DECLARE of TORSION problem
Holger Gohlke
(Fri Feb 07 2003 - 10:34:07 PST)
Re: essential dynamics
David A. Case
(Fri Feb 07 2003 - 13:19:04 PST)
mpi/sander help
Thu Zar Lwin
(Fri Feb 07 2003 - 14:01:05 PST)
Re: mpi/sander help
Michael Crowley
(Fri Feb 07 2003 - 14:05:10 PST)
Backbone torsional angles' format?
William Wei
(Fri Feb 07 2003 - 15:35:56 PST)
Re: Backbone torsional angles' format?
Bill Ross
(Fri Feb 07 2003 - 20:01:26 PST)
Re: bond command
Craig A Bayse
(Wed Feb 12 2003 - 13:36:29 PST)
Re: bond command
David A. Case
(Thu Feb 13 2003 - 22:38:09 PST)
Postdoctoral position available in Molecular Modeling
Nicolas Le Novere
(Fri Feb 14 2003 - 02:27:56 PST)
Ptraj problem with small molecules
Dvira Segal
(Tue Feb 04 2003 - 06:18:11 PST)
Re: Ptraj problem with small molecules
David A. Case
(Tue Feb 04 2003 - 07:20:54 PST)
some questions in gibbs calculation
Xiang, Tian-Xiang
(Mon Feb 03 2003 - 05:46:39 PST)
Re: some questions in gibbs calculation
David A. Case
(Tue Feb 04 2003 - 07:16:40 PST)
question about temperature
Lishan Yao
(Mon Feb 03 2003 - 09:02:13 PST)
Re: question about temperature
Carlos Simmerling
(Mon Feb 03 2003 - 09:31:28 PST)
boron parameters
Fabian Boes
(Mon Feb 03 2003 - 09:51:20 PST)
Neutral ARG
Osmar Norberto de Souza
(Mon Feb 03 2003 - 09:19:02 PST)
Re: acetonitrile parameters
Jose Ramon Blas
(Tue Feb 04 2003 - 11:21:39 PST)
about Mg++
Lishan Yao
(Wed Feb 05 2003 - 09:17:12 PST)
noninteger charge
eric hu
(Wed Feb 05 2003 - 10:03:08 PST)
Re: noninteger charge
David A. Case
(Wed Feb 05 2003 - 10:59:32 PST)
Internal dielectric in MM-GBSA
Robert J. Woods
(Mon Feb 10 2003 - 11:29:36 PST)
Re: Internal dielectric in MM-GBSA
David A. Case
(Mon Feb 10 2003 - 12:29:44 PST)
AMBER mail reflector archive
Jarrod Smith
(Mon Feb 10 2003 - 12:37:09 PST)
force field problem
Bayly, Christopher
(Mon Feb 10 2003 - 12:01:37 PST)
URGENT UPDATE .
frankikpendu_at_hknetmail.com
(Mon Feb 17 2003 - 13:02:33 PST)
Final energy minimization step
Andrei Leitão
(Tue Feb 18 2003 - 12:30:08 PST)
Re: Final energy minimization step
David A. Case
(Tue Feb 18 2003 - 14:25:05 PST)
restrained atoms NTR
Sichun Yang
(Tue Feb 18 2003 - 13:45:33 PST)
Re: restrained atoms NTR
David A. Case
(Tue Feb 18 2003 - 20:16:50 PST)
Re: restrained atoms NTR
Sichun Yang
(Wed Feb 19 2003 - 09:27:18 PST)
no statistics.out in mm_pbsa binding energy calculations
eric hu
(Wed Feb 19 2003 - 10:27:10 PST)
Re: no statistics.out in mm_pbsa binding energy calculations
Holger Gohlke
(Wed Feb 19 2003 - 10:48:59 PST)
File in the tutorial
Alexei Valiaev
(Tue Feb 18 2003 - 15:18:05 PST)
Re: File in the tutorial
David A. Case
(Tue Feb 18 2003 - 14:19:24 PST)
antechamber and its prepin files
Steve Seibold
(Wed Feb 19 2003 - 11:11:23 PST)
Re: antechamber and its prepin files
David A. Case
(Wed Feb 19 2003 - 13:08:55 PST)
Energy calculation
Sichun Yang
(Wed Feb 19 2003 - 14:25:45 PST)
Re: Energy calculation
Holger Gohlke
(Wed Feb 19 2003 - 14:54:30 PST)
Re: Energy calculation
Sichun Yang
(Wed Feb 19 2003 - 18:51:11 PST)
Web site problems.
caldwell.heimdal.compchem.ucsf.edu
(Wed Feb 19 2003 - 13:47:11 PST)
Minimization after dynamic?
Andrei Leitão
(Wed Feb 19 2003 - 16:13:31 PST)
Nmode
thenmalar rathinavelan
(Wed Feb 19 2003 - 22:21:03 PST)
Re: Nmode
Holger Gohlke
(Thu Feb 20 2003 - 10:35:57 PST)
probelms with antechamber
Yongmei Wang
(Thu Feb 20 2003 - 12:09:44 PST)
Re: probelms with antechamber
David A. Case
(Thu Feb 20 2003 - 17:19:24 PST)
AMBER6 problem in Solaris 8
S.Swaminathan
(Fri Feb 21 2003 - 11:18:19 PST)
Re: AMBER6 problem in Solaris 8
David A. Case
(Thu Feb 20 2003 - 23:56:21 PST)
Re: AMBER6 problem in Solaris 8
S.Swaminathan
(Wed Feb 26 2003 - 10:10:56 PST)
Re: AMBER6 problem in Solaris 8
Sanjeev B.S.
(Tue Feb 25 2003 - 21:03:55 PST)
about urea and glycerol
Nikolai Smolin
(Fri Feb 21 2003 - 03:04:33 PST)
minimization with fixed UC dimensions
Ioana Cozmuta
(Fri Feb 21 2003 - 11:38:01 PST)
Re: minimization with fixed UC dimensions
David A. Case
(Fri Feb 21 2003 - 12:00:09 PST)
Re: minimization with fixed UC dimensions
Ioana Cozmuta
(Fri Feb 21 2003 - 17:24:32 PST)
failure of minimization
Ioana Cozmuta
(Fri Feb 21 2003 - 17:10:37 PST)
RE: failure of minimization
Yong Duan
(Fri Feb 21 2003 - 18:34:04 PST)
RE: failure of minimization
Ioana Cozmuta
(Mon Feb 24 2003 - 11:33:58 PST)
RE: failure of minimization
Ioana Cozmuta
(Mon Feb 24 2003 - 15:11:23 PST)
RE: failure of minimization
Yong Duan
(Mon Feb 24 2003 - 17:42:14 PST)
new-style prmtop file
chernhoe
(Sun Feb 23 2003 - 19:45:46 PST)
Re: new-style prmtop file
David A. Case
(Sun Feb 23 2003 - 21:38:29 PST)
Re: new-style prmtop file
chernhoe
(Sun Feb 23 2003 - 22:48:47 PST)
Binary output switch (IOUTFM=1) broken in sander? (AMBER7)
John D. Chodera
(Sun Feb 23 2003 - 20:49:56 PST)
GB/SA
Franck Chevalier
(Mon Feb 24 2003 - 01:04:22 PST)
Re: GB/SA
David A. Case
(Fri Feb 28 2003 - 18:29:29 PST)
Force field ?
Subba.Raju
(Mon Feb 24 2003 - 02:17:54 PST)
adjust virial
Ioana Cozmuta
(Tue Feb 25 2003 - 00:15:45 PST)
problem patch files
chernhoe
(Tue Feb 25 2003 - 00:15:44 PST)
ptraj residue number out of range
Giulio Rastelli
(Tue Feb 25 2003 - 09:20:30 PST)
Re: ptraj residue number out of range
Holger Gohlke
(Tue Feb 25 2003 - 08:24:00 PST)
Re: ptraj residue number out of range
Giulio Rastelli
(Tue Feb 25 2003 - 15:35:24 PST)
Re: ptraj residue number out of range
Holger Gohlke
(Tue Feb 25 2003 - 09:31:14 PST)
Compilation error of Amber 7 using pgi and mpich on Linux Cluster
Fabrice Yerly
(Tue Feb 25 2003 - 05:02:00 PST)
Re: Compilation error of Amber 7 using pgi and mpich on Linux Cluster
Tormod Skauge
(Tue Feb 25 2003 - 07:00:19 PST)
Info request: Amber on 64-bit CPUs
Daniel Svozil
(Tue Feb 25 2003 - 05:34:57 PST)
Re: Info request: Amber on 64-bit CPUs
Chuck Schneider
(Tue Feb 25 2003 - 07:02:49 PST)
Re: Info request: Amber on 64-bit CPUs
Carlos P. Sosa
(Tue Feb 25 2003 - 09:43:23 PST)
(no subject)
Robert Cave
(Tue Feb 25 2003 - 11:55:51 PST)
Re: Amber under Linux
Scott Brozell
(Tue Feb 25 2003 - 13:13:11 PST)
EXTRA_PTS: frtype 2 Should not be here
Artem Mamonov
(Tue Feb 25 2003 - 14:09:56 PST)
Re: EXTRA_PTS: frtype 2 Should not be here
Artem Mamonov
(Tue Feb 25 2003 - 15:49:42 PST)
mm_pbsa
Layi Adekoya
(Wed Feb 26 2003 - 02:05:35 PST)
Re: mm_pbsa
Lepsa
(Wed Feb 26 2003 - 04:41:47 PST)
Analysis of close waters
Markus Drumm
(Wed Feb 26 2003 - 04:23:25 PST)
Namelist READ error
Thomas Steinbrecher
(Wed Feb 26 2003 - 04:54:46 PST)
Re: Namelist READ error - solved
Thomas Steinbrecher
(Wed Feb 26 2003 - 06:54:54 PST)
nmode on Linux : another memory question
E.S.
(Thu Feb 27 2003 - 14:42:15 PST)
Beyond 1,000,000 atoms...
Vlad
(Thu Feb 27 2003 - 17:45:14 PST)
seperate one trajectory file into two
eric hu
(Thu Feb 27 2003 - 19:02:58 PST)
Re: seperate one trajectory file into two
Holger Gohlke
(Thu Feb 27 2003 - 19:45:50 PST)
protein dna simulation
chernhoe
(Thu Feb 27 2003 - 20:13:58 PST)
how to validate ff parameters obtained from antechamber
Jiyoung Heo
(Thu Feb 27 2003 - 21:27:54 PST)
Last message date
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Sat Mar 01 2003 - 02:53:02 PST
Archived on
: Mon Mar 15 2010 - 05:58:04 PDT
230 messages
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