Amber Archive Sep 2006 by thread
370 messages
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Starting
Sun Sep 03 2006 - 06:07:18 PDT,
Ending
Sun Oct 01 2006 - 06:07:20 PDT
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Re: AMBER: Question about free energy with mm_pbsa
Thomas Cheatham
(Thu Aug 31 2006 - 23:23:59 PDT)
Re: AMBER: Question about free energy with mm_pbsa
William Wei
(Fri Sep 01 2006 - 06:32:29 PDT)
AMBER: Error: cannot run "$AMBERHOME/exe/divcon" of bcc() in charge.c
Jiten
(Thu Aug 31 2006 - 23:55:21 PDT)
Re: AMBER: Error: cannot run "$AMBERHOME/exe/divcon" of bcc() in charge.c
David A. Case
(Fri Sep 01 2006 - 07:34:10 PDT)
AMBER: force fields for proflavine molecule
sethl.gatech.edu
(Fri Sep 01 2006 - 10:49:00 PDT)
AMBER: output file not generated
bala
(Fri Sep 01 2006 - 08:35:40 PDT)
AMBER: Gaussian, antechamber, RESP
Ed Pate
(Sat Sep 02 2006 - 14:42:11 PDT)
Re: AMBER: Gaussian, antechamber, RESP
Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini)
(Sun Sep 03 2006 - 05:57:57 PDT)
AMBER: Question about LEAP and twisting a dihedral angle
Ilyas Yildirim
(Sat Sep 02 2006 - 18:52:45 PDT)
Re: AMBER: Question about LEAP and twisting a dihedral angle
David A. Case
(Sat Sep 02 2006 - 22:06:04 PDT)
Re: AMBER: Question about LEAP and twisting a dihedral angle
Ilyas Yildirim
(Sat Sep 02 2006 - 23:20:27 PDT)
Re: AMBER: Question about LEAP and twisting a dihedral angle
David A. Case
(Sun Sep 03 2006 - 08:55:16 PDT)
Re: AMBER: Question about LEAP and twisting a dihedral angle
Ilyas Yildirim
(Wed Sep 06 2006 - 01:46:57 PDT)
AMBER: Amber9: Free Energy
Franck_Vendeix.ncsu.edu
(Sun Sep 03 2006 - 16:11:44 PDT)
Re: AMBER: Amber9: Free Energy
David A. Case
(Sun Sep 03 2006 - 18:57:50 PDT)
Re: AMBER: Amber9: Free Energy
Franck_Vendeix.ncsu.edu
(Sun Sep 03 2006 - 19:27:13 PDT)
AMBER: ligand file
Fenghui Fan
(Mon Sep 04 2006 - 11:20:27 PDT)
Re: AMBER: ligand file
David A. Case
(Mon Sep 04 2006 - 12:02:34 PDT)
AMBER: cAMP ligand file
Fenghui Fan
(Mon Sep 04 2006 - 13:00:47 PDT)
AMBER: Implicit Water - Force field parameters
Ramdas Pophale
(Tue Sep 05 2006 - 12:22:49 PDT)
Re: AMBER: Implicit Water - Force field parameters
Fenghui Fan
(Tue Sep 05 2006 - 13:16:37 PDT)
Re: AMBER: Implicit Water - Force field parameters
Ilyas Yildirim
(Tue Sep 05 2006 - 13:22:13 PDT)
Re: AMBER: Implicit Water - Force field parameters
David A. Case
(Wed Sep 06 2006 - 08:54:15 PDT)
AMBER: a ligand file
Fenghui Fan
(Tue Sep 05 2006 - 13:18:51 PDT)
Re: AMBER: a ligand file
David A. Case
(Tue Sep 05 2006 - 13:55:26 PDT)
Re: AMBER: a ligand file
Fenghui Fan
(Wed Sep 06 2006 - 14:16:58 PDT)
Re: AMBER: a ligand file
David A. Case
(Wed Sep 06 2006 - 14:40:30 PDT)
AMBER: help with antechamber - creating ligand
sethl.gatech.edu
(Tue Sep 05 2006 - 14:10:08 PDT)
Re: AMBER: help with antechamber - creating ligand
Ilyas Yildirim
(Tue Sep 05 2006 - 14:26:11 PDT)
Re: AMBER: help with antechamber - creating ligand
David A. Case
(Tue Sep 05 2006 - 19:11:52 PDT)
AMBER: Amber parallel version
Franck_Vendeix.ncsu.edu
(Tue Sep 05 2006 - 23:05:20 PDT)
Re: AMBER: Amber parallel version
Jyh-Shyong Ho
(Tue Sep 05 2006 - 23:43:08 PDT)
Re: AMBER: Amber parallel version
Franck_Vendeix.ncsu.edu
(Thu Sep 07 2006 - 11:45:47 PDT)
AMBER: PARAMETERISATION PROBLEM
Claire Zerafa
(Wed Sep 06 2006 - 07:12:04 PDT)
Re: AMBER: PARAMETERISATION PROBLEM
David A. Case
(Wed Sep 06 2006 - 08:20:43 PDT)
AMBER: Question about using PMEMD and GB
H W
(Wed Sep 06 2006 - 10:41:12 PDT)
Re: AMBER: Question about using PMEMD and GB
David A. Case
(Wed Sep 06 2006 - 10:58:59 PDT)
Re: AMBER: Question about using PMEMD and GB
H W
(Wed Sep 06 2006 - 11:31:20 PDT)
AMBER: improper torsion angle problem
Fabian Alejandro Rodriguez
(Wed Sep 06 2006 - 14:52:40 PDT)
Re: AMBER: improper torsion angle problem
David A. Case
(Sun Sep 17 2006 - 16:52:38 PDT)
AMBER: trajout
Weihua Li
(Wed Sep 06 2006 - 20:22:28 PDT)
Re: AMBER: trajout
Carlos Simmerling
(Thu Sep 07 2006 - 04:04:02 PDT)
AMBER: Ca2+ polarizability
Martin LEPSIK
(Thu Sep 07 2006 - 02:02:38 PDT)
AMBER: mdcrd file
Jianhui
(Thu Sep 07 2006 - 07:15:45 PDT)
Re: AMBER: mdcrd file
Mark Williamson
(Thu Sep 07 2006 - 10:39:12 PDT)
Re: AMBER: mdcrd file
Brent Krueger
(Thu Sep 07 2006 - 19:55:27 PDT)
Re: AMBER: mdcrd file
David A. Case
(Thu Sep 07 2006 - 22:27:54 PDT)
Re: AMBER: mdcrd file
Joseph Nachman
(Fri Sep 08 2006 - 10:36:42 PDT)
Re: AMBER: mdcrd file
Carlos Simmerling
(Fri Sep 08 2006 - 13:54:34 PDT)
Re: AMBER: mdcrd file
Joseph Nachman
(Mon Sep 11 2006 - 11:00:21 PDT)
RE: AMBER: mdcrd file
Ross Walker
(Thu Sep 07 2006 - 15:52:28 PDT)
AMBER: Re: FF problem: RG residue minimizes to non-planar structure
David A. Case
(Thu Sep 07 2006 - 11:53:33 PDT)
AMBER: leap - how to recognize my structure
sethl.gatech.edu
(Thu Sep 07 2006 - 15:16:06 PDT)
Re: AMBER: leap - how to recognize my structure
Carlos Simmerling
(Thu Sep 07 2006 - 15:34:09 PDT)
AMBER: nmode memory allocation error
AYTUG TUNCEL
(Fri Sep 08 2006 - 01:41:35 PDT)
Re: AMBER: nmode memory allocation error
David A. Case
(Sat Sep 09 2006 - 21:17:54 PDT)
Re: AMBER: nmode memory allocation error
Cenk Andac
(Mon Sep 11 2006 - 02:48:30 PDT)
AMBER: hydronium ion parameters
Myunggi Yi
(Fri Sep 08 2006 - 07:15:32 PDT)
Re: AMBER: hydronium ion parameters
Myunggi Yi
(Fri Sep 08 2006 - 07:31:33 PDT)
Re: AMBER: hydronium ion parameters
Jiten
(Fri Sep 08 2006 - 08:12:03 PDT)
Re: AMBER: hydronium ion parameters
Myunggi Yi
(Fri Sep 08 2006 - 09:09:55 PDT)
Re: AMBER: hydronium ion parameters
Ilyas Yildirim
(Fri Sep 08 2006 - 13:41:17 PDT)
AMBER: Problem with ptraj
Gobind Singh Bisht
(Fri Sep 08 2006 - 14:00:19 PDT)
Re: AMBER: Problem with ptraj
Gobind Singh Bisht
(Fri Sep 08 2006 - 21:35:28 PDT)
Re: AMBER: Problem with ptraj
Thomas Cheatham
(Tue Sep 12 2006 - 19:47:46 PDT)
AMBER: LEAP - "could not find type: NH"
sethl.gatech.edu
(Fri Sep 08 2006 - 14:08:11 PDT)
Re: AMBER: LEAP - "could not find type: NH"
Ilyas Yildirim
(Fri Sep 08 2006 - 15:42:46 PDT)
AMBER: seg fault during test.serial
Lachele Foley (Lists)
(Fri Sep 08 2006 - 13:45:05 PDT)
Re: AMBER: seg fault during test.serial
David A. Case
(Fri Sep 08 2006 - 18:19:16 PDT)
AMBER: a ligand file
Fenghui Fan
(Fri Sep 08 2006 - 18:31:59 PDT)
Re: AMBER: a ligand file
David A. Case
(Fri Sep 08 2006 - 18:53:18 PDT)
Re: AMBER: a ligand file
Fenghui Fan
(Fri Sep 08 2006 - 20:06:49 PDT)
Re: AMBER: a ligand file
Ilyas Yildirim
(Fri Sep 08 2006 - 21:05:11 PDT)
Re: AMBER: a ligand file
Ilyas Yildirim
(Fri Sep 08 2006 - 19:23:48 PDT)
Re: AMBER: seg fault during test.serial
Lachele Foley (Lists)
(Mon Sep 11 2006 - 07:50:57 PDT)
Re: AMBER: seg fault during test.serial
David A. Case
(Mon Sep 11 2006 - 08:54:43 PDT)
AMBER: pmf with respect to a surface
Rahaman, Asif
(Fri Sep 08 2006 - 15:35:22 PDT)
Re: AMBER: pmf with respect to a surface
David A. Case
(Sat Sep 09 2006 - 21:14:30 PDT)
AMBER: post nmanal
杉森正道
(Fri Sep 08 2006 - 23:03:47 PDT)
Re: AMBER: post nmanal
David A. Case
(Sat Sep 09 2006 - 09:54:34 PDT)
Re: AMBER: post nmanal
杉森正道
(Sun Sep 10 2006 - 23:09:28 PDT)
AMBER: EGB term decomposition
backy
(Sat Sep 09 2006 - 02:00:08 PDT)
AMBER: EGB term decomposition
backy
(Sat Sep 09 2006 - 01:57:43 PDT)
AMBER: EGB term decomposition
backy
(Sat Sep 09 2006 - 02:01:34 PDT)
AMBER: protein-ligand interaction
Fenghui Fan
(Sat Sep 09 2006 - 09:59:51 PDT)
Re: AMBER: protein-ligand interaction
Ilyas Yildirim
(Sat Sep 09 2006 - 14:58:10 PDT)
AMBER: resp
Fenghui Fan
(Sat Sep 09 2006 - 18:03:06 PDT)
AMBER: resp
Fenghui Fan
(Sat Sep 09 2006 - 18:07:48 PDT)
Re: AMBER: resp
FyD
(Sun Sep 10 2006 - 00:46:11 PDT)
AMBER: Parmchk problems (parm99.dat)
Prashanth Athri
(Sun Sep 10 2006 - 17:23:25 PDT)
RE: AMBER: Parmchk problems (parm99.dat)
Junmei Wang
(Mon Sep 11 2006 - 13:48:51 PDT)
RE: AMBER: Parmchk problems (parm99.dat)
Prashanth Athri
(Tue Sep 12 2006 - 08:54:08 PDT)
RE: AMBER: Parmchk problems (parm99.dat)
Prashanth Athri
(Tue Sep 12 2006 - 10:10:55 PDT)
RE: AMBER: Parmchk problems (parm99.dat)
Junmei Wang
(Tue Sep 12 2006 - 11:41:21 PDT)
RE: AMBER: Parmchk problems (parm99.dat)
Prashanth Athri
(Tue Sep 12 2006 - 12:30:02 PDT)
RE: AMBER: Parmchk problems (parm99.dat)
Piotr Cieplak
(Wed Sep 20 2006 - 20:46:19 PDT)
Re: AMBER: Parmchk problems (parm99.dat)
David A. Case
(Wed Sep 20 2006 - 21:22:56 PDT)
RE: AMBER: Parmchk problems (parm99.dat)
Junmei Wang
(Tue Sep 12 2006 - 13:44:30 PDT)
AMBER: (no subject)
Prashanth Athri
(Sun Sep 10 2006 - 17:23:05 PDT)
AMBER: Oon Modeling the metalloprotein with GB model.
wenfei Li
(Mon Sep 11 2006 - 00:41:16 PDT)
AMBER: mm_pbsa snapshots for "three-trajectory"
In Hee Park
(Thu Sep 14 2006 - 16:42:13 PDT)
AMBER: Error in Running Sander
Jianhui Tian
(Mon Sep 11 2006 - 06:52:39 PDT)
Re: AMBER: Error in Running Sander
David A. Case
(Mon Sep 11 2006 - 08:59:45 PDT)
Re: AMBER: Error in Running Sander
Jianhui
(Mon Sep 11 2006 - 10:10:55 PDT)
AMBER: set a trucated octahedron box in Leap
Vlad Cojocaru
(Mon Sep 11 2006 - 07:24:44 PDT)
AMBER: How to get the ligand. ac file
Fenghui Fan
(Mon Sep 11 2006 - 07:46:54 PDT)
Re: AMBER: set a trucated octahedron box in Leap
David A. Case
(Mon Sep 11 2006 - 08:56:59 PDT)
Re: AMBER: set a trucated octahedron box in Leap
Vlad Cojocaru
(Tue Sep 12 2006 - 01:30:06 PDT)
Re: AMBER: set a trucated octahedron box in Leap
Ilyas Yildirim
(Tue Sep 12 2006 - 01:48:56 PDT)
Re: AMBER: set a trucated octahedron box in Leap
David A. Case
(Tue Sep 12 2006 - 08:03:24 PDT)
AMBER: cAMP ligand charge
Fenghui Fan
(Mon Sep 11 2006 - 08:06:40 PDT)
Re: AMBER: cAMP ligand charge
David A. Case
(Mon Sep 11 2006 - 08:35:53 PDT)
AMBER: Parallel compile: ld: cannot find -lfmpi
Lachele Foley (Lists)
(Mon Sep 11 2006 - 08:38:00 PDT)
Re: AMBER: Parallel compile: ld: cannot find -lfmpi
David A. Case
(Mon Sep 11 2006 - 11:19:12 PDT)
Re: AMBER: Parallel compile: ld: cannot find -lfmpi
Lachele Foley (Lists)
(Mon Sep 11 2006 - 13:39:55 PDT)
AMBER: System in polarizable waters
Martin LEPSIK
(Mon Sep 11 2006 - 09:14:24 PDT)
Re: AMBER: System in polarizable waters
David A. Case
(Mon Sep 11 2006 - 11:12:04 PDT)
AMBER: angle between helices
张勇
(Mon Sep 11 2006 - 19:05:51 PDT)
AMBER: Installing AMBER9 on cygwin (WinXP)
HARADA Makoto
(Tue Sep 12 2006 - 02:38:19 PDT)
Re: AMBER: Installing AMBER9 on cygwin (WinXP)
Gobind Singh Bisht
(Tue Sep 12 2006 - 04:57:06 PDT)
Re: AMBER: Installing AMBER9 on cygwin (WinXP)
David A. Case
(Tue Sep 12 2006 - 08:01:41 PDT)
AMBER: forrtl: severe (64): input conversion error, unit 9, file
Ilyas Yildirim
(Tue Sep 12 2006 - 14:09:34 PDT)
RE: AMBER: forrtl: severe (64): input conversion error, unit 9, file
Ross Walker
(Tue Sep 12 2006 - 14:35:47 PDT)
RE: AMBER: forrtl: severe (64): input conversion error, unit 9, file
Ilyas Yildirim
(Tue Sep 12 2006 - 15:49:33 PDT)
AMBER: about ligand charge
Fenghui Fan
(Tue Sep 12 2006 - 20:16:27 PDT)
AMBER: how to feed dihedral angles of our choice to the linear sequence in amber8
priya priya
(Wed Sep 13 2006 - 02:02:33 PDT)
AW: AMBER: how to feed dihedral angles of our choice to the linear sequence in amber8
Hannes Barsch
(Wed Sep 13 2006 - 06:54:54 PDT)
Re: AMBER: how to feed dihedral angles of our choice to the linear sequence in amber8
Ilyas Yildirim
(Wed Sep 13 2006 - 10:59:10 PDT)
AMBER: 'lastrst' error for amber8
Arvind Marathe
(Wed Sep 13 2006 - 05:52:07 PDT)
Re: AMBER: 'lastrst' error for amber8
michael crowley
(Wed Sep 13 2006 - 08:14:08 PDT)
Re: AMBER: 'lastrst' error for amber8
Robert Duke
(Wed Sep 13 2006 - 08:28:16 PDT)
Re: AMBER: 'lastrst' error for amber8
Arvind Marathe
(Thu Sep 14 2006 - 06:08:08 PDT)
Re: AMBER: 'lastrst' error for amber8
David A. Case
(Thu Sep 14 2006 - 08:05:25 PDT)
Re: AMBER: 'lastrst' error for amber8
Arvind Marathe
(Fri Sep 15 2006 - 13:01:43 PDT)
Re: AMBER: 'lastrst' error for amber8
David A. Case
(Sat Sep 16 2006 - 09:50:31 PDT)
Re: AMBER: 'lastrst' error for amber8
Arvind Marathe
(Sun Sep 17 2006 - 05:02:09 PDT)
Re: AMBER: 'lastrst' error for amber8
Arvind Marathe
(Sun Sep 17 2006 - 23:50:41 PDT)
Re: AMBER: 'lastrst' error for amber8
David A. Case
(Mon Sep 18 2006 - 08:44:49 PDT)
Re: AMBER: 'lastrst' error for amber8
Arvind Marathe
(Mon Sep 18 2006 - 09:25:33 PDT)
Re: AMBER: 'lastrst' error for amber8
David A. Case
(Mon Sep 18 2006 - 09:41:56 PDT)
Re: AMBER: 'lastrst' error for amber8
Arvind Marathe
(Mon Sep 18 2006 - 10:44:11 PDT)
AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package
Zhihong Yu
(Wed Sep 13 2006 - 05:57:44 PDT)
Re: AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package
David A. Case
(Wed Sep 13 2006 - 09:32:39 PDT)
Re: AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package
Zhihong Yu
(Wed Sep 13 2006 - 20:21:07 PDT)
Re: AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package
David A. Case
(Wed Sep 13 2006 - 22:53:50 PDT)
Re: AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package
Zhihong Yu
(Wed Sep 13 2006 - 23:47:07 PDT)
AMBER: On the temperature increasement in the restriction MD in the tutorial 2 section 5
Fenghui Fan
(Wed Sep 13 2006 - 07:23:33 PDT)
Re: AMBER: On the temperature increasement in the restriction MD in the tutorial 2 section 5
Thomas Cheatham
(Wed Sep 13 2006 - 08:48:54 PDT)
AMBER: MAXM in nmode
William Wei
(Wed Sep 13 2006 - 13:24:14 PDT)
Re: AMBER: MAXM in nmode
William Wei
(Wed Sep 13 2006 - 14:07:52 PDT)
Re: AMBER: MAXM in nmode
David A. Case
(Wed Sep 13 2006 - 14:17:29 PDT)
AMBER: RDC refinement
Young-Tae Lee
(Wed Sep 13 2006 - 08:13:30 PDT)
Re: AMBER: RDC refinement
David A. Case
(Wed Sep 13 2006 - 08:35:07 PDT)
AMBER: energy data for limited part of system
Tanya Johannsen
(Wed Sep 13 2006 - 10:57:15 PDT)
Re: AMBER: energy data for limited part of system
David A. Case
(Sun Sep 17 2006 - 16:56:23 PDT)
AMBER: potential energy
Fenghui Fan
(Sun Sep 17 2006 - 17:38:44 PDT)
RE: AMBER: potential energy
Ross Walker
(Mon Sep 18 2006 - 08:52:23 PDT)
Re: RE: AMBER: potential energy
linfu
(Mon Sep 18 2006 - 18:44:18 PDT)
Re: [UCE]Re: RE: AMBER: potential energy
Thomas Cheatham
(Mon Sep 18 2006 - 19:16:20 PDT)
Re: [UCE]Re: RE: AMBER: potential energy
Fenghui Fan
(Mon Sep 18 2006 - 19:41:09 PDT)
RE: [UCE]Re: RE: AMBER: potential energy
Ross Walker
(Mon Sep 18 2006 - 21:01:04 PDT)
Re: RE: AMBER: potential energy
Thomas Cheatham
(Tue Sep 19 2006 - 09:57:47 PDT)
AMBER: residence time of water molecules
venditti2.unisi.it
(Wed Sep 13 2006 - 07:56:34 PDT)
Re: AMBER: residence time of water molecules
Angelo
(Thu Sep 14 2006 - 01:57:38 PDT)
AMBER: the time length of the restricted MD
Fenghui Fan
(Wed Sep 13 2006 - 12:38:59 PDT)
AMBER: Mixed solvent?
Mingfeng Yang
(Wed Sep 13 2006 - 12:44:32 PDT)
AMBER: Error in reading RDC data
Lee, Young-Tae
(Wed Sep 13 2006 - 13:09:42 PDT)
Re: AMBER: Error in reading RDC data
David A. Case
(Wed Sep 13 2006 - 14:44:14 PDT)
AMBER: LENNARD_JONES_ACOEF & BCOEF prmtop changes
Michael Mazanetz
(Wed Sep 13 2006 - 13:42:02 PDT)
Re: AMBER: LENNARD_JONES_ACOEF & BCOEF prmtop changes
Michael Mazanetz
(Thu Sep 14 2006 - 01:15:43 PDT)
AMBER: pqr from constant pH MD
harianto
(Wed Sep 13 2006 - 14:43:13 PDT)
AMBER: MD on protein-ligand interaction
Fenghui Fan
(Thu Sep 14 2006 - 07:04:20 PDT)
Re: AMBER: MD on protein-ligand interaction
Ilyas Yildirim
(Thu Sep 14 2006 - 12:09:14 PDT)
AMBER: potential energy in the MD result
Fenghui Fan
(Thu Sep 14 2006 - 07:39:12 PDT)
AMBER: pmemd error
bala
(Thu Sep 14 2006 - 08:34:12 PDT)
Re: AMBER: pmemd error
Robert Duke
(Thu Sep 14 2006 - 09:46:40 PDT)
Re: AMBER: pmemd error
Robert Duke
(Thu Sep 14 2006 - 09:46:30 PDT)
AMBER: addions default settings.
asli ertekin
(Thu Sep 14 2006 - 08:37:47 PDT)
Re: AMBER: addions default settings.
Bill Ross
(Thu Sep 14 2006 - 10:14:18 PDT)
AMBER: acidifying a water box
Eric Shamay
(Thu Sep 14 2006 - 11:36:11 PDT)
Re: AMBER: acidifying a water box
David A. Case
(Thu Sep 14 2006 - 15:21:01 PDT)
Re: AMBER: acidifying a water box
Thomas Cheatham
(Thu Sep 14 2006 - 15:56:32 PDT)
Re: AMBER: acidifying a water box
Eric Shamay
(Fri Sep 15 2006 - 01:49:15 PDT)
AMBER: DPPC Bilayer size
Akshay Patny
(Thu Sep 14 2006 - 11:47:45 PDT)
AMBER: Denaturing MD
Fenghui Fan
(Thu Sep 14 2006 - 15:58:35 PDT)
Re: AMBER: Denaturing MD
Thomas Cheatham
(Thu Sep 14 2006 - 16:55:59 PDT)
AMBER: on the rst file of the current ruuning
Fenghui Fan
(Thu Sep 14 2006 - 20:33:50 PDT)
RE: AMBER: on the rst file of the current ruuning
Ross Walker
(Mon Sep 18 2006 - 08:58:01 PDT)
AMBER: Temperature not rising enough during simulated annealing
Adam Pelzer
(Thu Sep 14 2006 - 20:30:12 PDT)
Re: [UCE]AMBER: Temperature not rising enough during simulated annealing
Thomas Cheatham
(Thu Sep 14 2006 - 21:33:42 PDT)
AMBER: cyclic AMP off and frcmod files?
Daniel Lee
(Thu Sep 14 2006 - 20:52:33 PDT)
Re: AMBER: cyclic AMP off and frcmod files?
Fenghui Fan
(Fri Sep 15 2006 - 06:44:49 PDT)
AMBER: have problems with restrained minimization
Abhilash
(Fri Sep 15 2006 - 11:10:50 PDT)
Re: AMBER: cyclic AMP off and frcmod files?
Daniel Lee
(Sun Sep 17 2006 - 19:10:28 PDT)
AMBER: restraints and constant pressure
Joshua
(Thu Sep 14 2006 - 22:44:09 PDT)
Re: AMBER: restraints and constant pressure
Thomas Cheatham
(Thu Sep 14 2006 - 23:22:02 PDT)
Re: AMBER: restraints and constant pressure
Joshua
(Fri Sep 15 2006 - 02:09:44 PDT)
Re: AMBER: restraints and constant pressure
Myunggi Yi
(Fri Sep 15 2006 - 12:52:21 PDT)
Re: AMBER: restraints and constant pressure
Thomas Cheatham
(Sat Sep 16 2006 - 21:38:06 PDT)
Re: AMBER: restraints and constant pressure
Myunggi Yi
(Sat Sep 16 2006 - 23:29:38 PDT)
Re: AMBER: restraints and constant pressure
Carlos Simmerling
(Sun Sep 17 2006 - 07:01:54 PDT)
Re: AMBER: restraints and constant pressure
Myunggi Yi
(Sun Sep 17 2006 - 07:23:33 PDT)
AMBER: About Lennard-Jones Parameters
Jianhui
(Fri Sep 15 2006 - 14:08:13 PDT)
Re: AMBER: About Lennard-Jones Parameters
David A. Case
(Fri Sep 15 2006 - 17:07:35 PDT)
AMBER: distance between two atoms
Fenghui Fan
(Fri Sep 15 2006 - 13:49:11 PDT)
AMBER: Problems with a restrained minimization approach
Abhilash
(Fri Sep 15 2006 - 12:35:34 PDT)
Re: AMBER: Problems with a restrained minimization approach
David A. Case
(Fri Sep 15 2006 - 17:41:04 PDT)
AMBER: new article on Amber force fields
Carlos Simmerling
(Fri Sep 15 2006 - 12:47:34 PDT)
AMBER: change mdcrd file to pdb file
Fenghui Fan
(Sat Sep 16 2006 - 22:02:54 PDT)
Re: AMBER: change mdcrd file to pdb file
Ilyas Yildirim
(Sat Sep 16 2006 - 22:17:21 PDT)
Re: AMBER: change mdcrd file to pdb file
Jianhui
(Sun Sep 17 2006 - 07:16:29 PDT)
Re: AMBER: change mdcrd file to pdb file
Fenghui Fan
(Sun Sep 17 2006 - 08:30:02 PDT)
Re: AMBER: change mdcrd file to pdb file
Fabian Alejandro Rodriguez
(Sun Sep 17 2006 - 09:04:22 PDT)
AMBER: lib-4324 : UNRECOVERABLE library error
Vasu Chandrasekaran
(Sun Sep 17 2006 - 00:36:26 PDT)
Re: AMBER: lib-4324 : UNRECOVERABLE library error
Robert Duke
(Sun Sep 17 2006 - 05:30:08 PDT)
Re: AMBER: lib-4324 : UNRECOVERABLE library error
Vasu Chandrasekaran
(Sun Sep 17 2006 - 10:23:24 PDT)
AMBER: parameters for Nickel and iron
Rachel
(Mon Sep 18 2006 - 06:02:39 PDT)
Re: AMBER: parameters for Nickel and iron
Fenghui Fan
(Mon Sep 18 2006 - 19:45:24 PDT)
Re: AMBER: parameters for Nickel and iron
Rachel
(Tue Sep 19 2006 - 09:00:45 PDT)
Re: AMBER: parameters for Nickel and iron
Ken Merz
(Tue Sep 19 2006 - 13:00:51 PDT)
Re: AMBER: parameters for Nickel and iron
Rachel
(Thu Sep 21 2006 - 04:50:23 PDT)
RE: AMBER: parameters for Nickel and iron
Junmei Wang
(Tue Sep 19 2006 - 09:16:26 PDT)
RE: AMBER: parameters for Nickel and iron
Junmei Wang
(Tue Sep 26 2006 - 14:38:08 PDT)
Re: AMBER: parameters for Nickel and iron
Rachel
(Wed Sep 27 2006 - 06:53:45 PDT)
AMBER: A script file for measuring the distance between 2 atoms during MD
Fenghui Fan
(Wed Sep 27 2006 - 08:14:23 PDT)
Re: AMBER: A script file for measuring the distance between 2 atoms during MD
Fenghui Fan
(Wed Sep 27 2006 - 10:49:53 PDT)
Re: AMBER: A script file for measuring the distance between 2 atoms during MD
Carlos Simmerling
(Wed Sep 27 2006 - 10:59:33 PDT)
Re: AMBER: A script file for measuring the distance between 2 atoms during MD
Thomas Cheatham
(Wed Sep 27 2006 - 11:05:25 PDT)
Re: AMBER: A script file for measuring the distance between 2 atoms during MD
Carlos Simmerling
(Wed Sep 27 2006 - 11:26:35 PDT)
AMBER: WHATIF Check after MD
Fenghui Fan
(Wed Sep 27 2006 - 19:24:39 PDT)
Re: AMBER: WHATIF Check after MD
FyD
(Wed Sep 27 2006 - 21:06:30 PDT)
Re: AMBER: A script file for measuring the distance between 2 atoms during MD
Carlos Simmerling
(Wed Sep 27 2006 - 11:33:01 PDT)
Re: AMBER: A script file for measuring the distance between 2 atoms during MD
Fenghui Fan
(Wed Sep 27 2006 - 12:44:08 PDT)
AMBER: Restart problem on PMEMD with position restraint.
Chunhu Tan
(Mon Sep 18 2006 - 10:46:35 PDT)
Re: AMBER: Restart problem on PMEMD with position restraint.
Robert Duke
(Mon Sep 18 2006 - 11:20:27 PDT)
RE: AMBER: Restart problem on PMEMD with position restraint.
Ross Walker
(Mon Sep 18 2006 - 11:32:05 PDT)
Re: AMBER: Restart problem on PMEMD with position restraint.
David A. Case
(Mon Sep 18 2006 - 12:09:46 PDT)
RE: AMBER: Restart problem on PMEMD with position restraint.
Chunhu Tan
(Mon Sep 18 2006 - 14:10:44 PDT)
RE: AMBER: Restart problem on PMEMD with position restraint.
Ross Walker
(Mon Sep 18 2006 - 14:57:58 PDT)
AMBER: Questions
Joseph Fernandez
(Mon Sep 18 2006 - 11:48:25 PDT)
AMBER: coordinate files
Ed Pate
(Tue Sep 19 2006 - 13:17:26 PDT)
AMBER: the sequence command in leap
Shuting Wei
(Wed Sep 20 2006 - 08:32:17 PDT)
Re: AMBER: coordinate files
David A. Case
(Wed Sep 20 2006 - 18:22:47 PDT)
AMBER: ptraj RMSD vs. RMSF
Steve Seibold
(Mon Sep 18 2006 - 12:54:02 PDT)
AMBER: Question about Streptavidin/Biotin Tutorial.
Qingning Shu
(Mon Sep 18 2006 - 13:39:38 PDT)
RE: AMBER: Question about Streptavidin/Biotin Tutorial.
Ross Walker
(Mon Sep 18 2006 - 15:10:39 PDT)
AMBER: A question about Dynamics.
Qingning Shu
(Mon Sep 18 2006 - 13:40:21 PDT)
Re: AMBER: A question about Dynamics.
David A. Case
(Mon Sep 18 2006 - 13:55:47 PDT)
Re: AMBER: A question about Dynamics.
Chunhu Tan
(Mon Sep 18 2006 - 14:24:22 PDT)
Re: Re: AMBER: A question about Dynamics.
Qingning Shu
(Thu Sep 21 2006 - 07:38:47 PDT)
RE: Re: AMBER: A question about Dynamics.
Ross Walker
(Thu Sep 21 2006 - 08:58:08 PDT)
Re: RE: Re: AMBER: A question about Dynamics.
Qingning Shu
(Fri Sep 22 2006 - 15:28:54 PDT)
Re: RE: Re: AMBER: A question about Dynamics.
David A. Case
(Fri Sep 22 2006 - 17:57:46 PDT)
AMBER: A question about Dynamics.
Qingning Shu
(Mon Sep 18 2006 - 13:57:17 PDT)
AMBER: Can salt effect be determined in GB medel?
Xioling Chuang
(Mon Sep 18 2006 - 21:04:03 PDT)
Re: AMBER: Can salt effect be determined in GB medel?
linfu
(Mon Sep 18 2006 - 23:32:16 PDT)
AMBER: implicit solovent model by adjusting the parameter EXTDIEL ?
linfu
(Mon Sep 18 2006 - 23:40:52 PDT)
Re: AMBER: implicit solovent model by adjusting the parameter EXTDIEL ?
David A. Case
(Tue Sep 19 2006 - 10:29:51 PDT)
AMBER: resolving a bad initial model
wang.cbs.cnrs.fr
(Tue Sep 19 2006 - 07:42:11 PDT)
Re: AMBER: resolving a bad initial model
Andy Purkiss-Trew
(Tue Sep 19 2006 - 07:51:01 PDT)
Re: AMBER: resolving a bad initial model
Carlos Simmerling
(Tue Sep 19 2006 - 07:53:47 PDT)
Re: AMBER: resolving a bad initial model
Stefano Pieraccini
(Tue Sep 19 2006 - 08:25:46 PDT)
AMBER: ACML and MASS/MASSV for sander and pmemd
Nicolas Lux Fawzi
(Tue Sep 19 2006 - 12:36:21 PDT)
Re: AMBER: ACML and MASS/MASSV for sander and pmemd
Robert Duke
(Tue Sep 19 2006 - 13:03:00 PDT)
RE: AMBER: ACML and MASS/MASSV for sander and pmemd
Ross Walker
(Tue Sep 19 2006 - 13:24:02 PDT)
Re: AMBER: ACML and MASS/MASSV for sander and pmemd
Robert Duke
(Tue Sep 19 2006 - 13:42:05 PDT)
AMBER: installation error for pmemd in Amber 9/Opteron
Sergio Aragon
(Tue Sep 19 2006 - 14:25:53 PDT)
RE: AMBER: installation error for pmemd in Amber 9/Opteron
Ross Walker
(Tue Sep 19 2006 - 14:41:11 PDT)
AMBER: zzfft issue resolved -thanks!
Sergio Aragon
(Tue Sep 19 2006 - 16:09:25 PDT)
AMBER: zzfft error for pmemd in Amber 9/Opteron
Sergio Aragon
(Tue Sep 19 2006 - 15:53:10 PDT)
AMBER:
Steve Seibold
(Wed Sep 20 2006 - 09:56:00 PDT)
AMBER: GPCR-membrane issue
Akshay Patny
(Wed Sep 20 2006 - 10:30:24 PDT)
AMBER: Problems using rst distance constraints in Amber 8
Whitney Allen
(Wed Sep 20 2006 - 11:30:05 PDT)
Re: AMBER: Problems using rst distance constraints in Amber 8
David A. Case
(Wed Sep 20 2006 - 12:12:20 PDT)
AMBER: Which POPC Bilayer to start?
Akshay Patny
(Wed Sep 20 2006 - 14:48:42 PDT)
AMBER: mm-pbsa output
Stefano Pieraccini
(Thu Sep 21 2006 - 01:51:28 PDT)
Re: AMBER: mm-pbsa output
alfredoq.fcq.unc.edu.ar
(Thu Sep 21 2006 - 04:29:51 PDT)
AMBER: bad atom type: Li
jitrayut jitonnom
(Thu Sep 21 2006 - 03:30:24 PDT)
Re: AMBER: bad atom type: Li
David A. Case
(Tue Sep 26 2006 - 23:03:56 PDT)
AMBER: proposed patch for ptraj/evec.c (Amber 9.0)
Cameron Abrams
(Thu Sep 21 2006 - 10:26:35 PDT)
AMBER: Temperature fluctuation BIG with ntt=3
Mingfeng Yang
(Thu Sep 21 2006 - 16:14:24 PDT)
Re: AMBER: Temperature fluctuation BIG with ntt=3
Carlos Simmerling
(Thu Sep 21 2006 - 17:48:07 PDT)
Re: AMBER: Temperature fluctuation BIG with ntt=3
David A. Case
(Thu Sep 21 2006 - 18:39:46 PDT)
Re: AMBER: Temperature fluctuation BIG with ntt=3
Mingfeng Yang
(Thu Sep 21 2006 - 21:59:54 PDT)
AMBER: Amber8: problem related to antechamber
priya priya
(Thu Sep 21 2006 - 21:11:23 PDT)
Re: AMBER: Amber8: problem related to antechamber
David A. Case
(Fri Sep 22 2006 - 07:52:35 PDT)
RE: AMBER: Amber8: problem related to antechamber
Junmei Wang
(Tue Sep 26 2006 - 14:15:07 PDT)
AMBER: RE: Amber8: problem related to antechamber
priya priya
(Tue Sep 26 2006 - 20:49:34 PDT)
AMBER: RMSd vs RMSf
Steve Seibold
(Fri Sep 22 2006 - 06:42:28 PDT)
AMBER: TI-FEP : strange result for different clambda values
Biswa Ranjan Meher
(Fri Sep 22 2006 - 08:26:30 PDT)
Re: AMBER: TI-FEP : strange result for different clambda values
Thomas Steinbrecher
(Fri Sep 22 2006 - 08:38:10 PDT)
Re: AMBER: TI-FEP : strange result for different clambda values
David Mobley
(Fri Sep 22 2006 - 09:38:19 PDT)
AMBER: center of mass dihedral restraints
Lauren O'Neil
(Fri Sep 22 2006 - 12:03:32 PDT)
Re: AMBER: center of mass dihedral restraints
Carlos Simmerling
(Mon Sep 25 2006 - 04:43:49 PDT)
Re: AMBER: center of mass dihedral restraints
Lauren O'Neil
(Mon Sep 25 2006 - 08:39:19 PDT)
Re: AMBER: center of mass dihedral restraints
venditti2.unisi.it
(Mon Sep 25 2006 - 10:44:01 PDT)
AMBER: build a polymer with sequence command
Shuting Wei
(Fri Sep 22 2006 - 13:41:43 PDT)
Re: AMBER: build a polymer with sequence command
David A. Case
(Fri Sep 22 2006 - 14:01:27 PDT)
Re: AMBER: build a polymer with sequence command
Shuting Wei
(Fri Sep 22 2006 - 14:42:04 PDT)
Re: AMBER: build a polymer with sequence command
David A. Case
(Fri Sep 22 2006 - 17:03:35 PDT)
Re: AMBER: build a polymer with sequence command
Shuting Wei
(Mon Sep 25 2006 - 10:15:10 PDT)
Re: AMBER: build a polymer with sequence command
David A. Case
(Mon Sep 25 2006 - 14:37:54 PDT)
AMBER: leap can't assign CALA
Myunggi Yi
(Fri Sep 22 2006 - 15:09:06 PDT)
Re: AMBER: leap can't assign CALA
David A. Case
(Fri Sep 22 2006 - 17:53:29 PDT)
Re: AMBER: leap can't assign CALA
Myunggi Yi
(Sat Sep 23 2006 - 08:36:12 PDT)
AMBER: pbsa segmentation faults
Thomas Steinbrecher
(Fri Sep 22 2006 - 16:46:11 PDT)
Re: AMBER: pbsa segmentation faults
Ray Luo
(Sat Sep 23 2006 - 23:40:58 PDT)
AMBER: mm_pbsa segmentation faults
Thomas Steinbrecher
(Mon Sep 25 2006 - 11:24:17 PDT)
Re: AMBER: mm_pbsa segmentation faults
linfu
(Mon Sep 25 2006 - 17:56:08 PDT)
Re: AMBER: mm_pbsa segmentation faults
Ray Luo
(Mon Sep 25 2006 - 18:17:54 PDT)
Re: AMBER: mm_pbsa segmentation faults
Ray Luo
(Tue Sep 26 2006 - 09:29:26 PDT)
Re: AMBER: mm_pbsa segmentation faults
Thomas Steinbrecher
(Tue Sep 26 2006 - 10:31:34 PDT)
Re: AMBER: mm_pbsa segmentation faults
Mark Williamson
(Tue Sep 26 2006 - 14:41:06 PDT)
AMBER: Picking up water molecules around one molecule
Atsutoshi Okabe
(Sat Sep 23 2006 - 01:26:12 PDT)
AMBER: one question on MD
Fenghui Fan
(Sat Sep 23 2006 - 18:03:11 PDT)
Re: AMBER: one question on MD
Carlos Simmerling
(Sat Sep 23 2006 - 18:32:46 PDT)
AMBER: the RMSD of MD
Fenghui Fan
(Sun Sep 24 2006 - 10:07:56 PDT)
Re: AMBER: the RMSD of MD
Adrian Roitberg
(Sun Sep 24 2006 - 10:49:52 PDT)
AMBER: strange values of the energy of "1-4 EEL" , "EAMBER" and the RMS
Zhihong Yu
(Sun Sep 24 2006 - 20:03:28 PDT)
Re: AMBER: strange values of the energy of "1-4 EEL" , "EAMBER" and the RMS
Carlos Simmerling
(Mon Sep 25 2006 - 04:30:57 PDT)
Re: AMBER: strange values of the energy of "1-4 EEL" , "EAMBER" and the RMS
JunJun Liu
(Mon Sep 25 2006 - 12:28:55 PDT)
AMBER: polarizable ff for ligand
bala
(Mon Sep 25 2006 - 06:53:02 PDT)
AMBER: question on Lennard-Jones fitting in FF94 and 96
David Mobley
(Mon Sep 25 2006 - 10:07:45 PDT)
Re: AMBER: strange values of the energy of "1-4 EEL" , "EAMBER" andthe RMS
Zhihong Yu
(Mon Sep 25 2006 - 18:20:14 PDT)
AMBER: from ADP-small protein complex to GTP-protein complex
Fenghui Fan
(Mon Sep 25 2006 - 21:00:53 PDT)
AMBER: lifetime and maxocc
Sergey Samsonov
(Tue Sep 26 2006 - 08:56:26 PDT)
AMBER: structure from MD
Fenghui Fan
(Tue Sep 26 2006 - 09:42:14 PDT)
Re: AMBER: structure from MD
Carlos Simmerling
(Tue Sep 26 2006 - 09:43:58 PDT)
AMBER: chemical shift restrains
Emilia Sikorska
(Tue Sep 26 2006 - 11:22:05 PDT)
AMBER: missing benchmark files
Mark H. Schofield
(Tue Sep 26 2006 - 15:32:38 PDT)
Re: AMBER: missing benchmark files
David A. Case
(Tue Sep 26 2006 - 23:50:49 PDT)
AMBER: job crashes
Xiaowei (David) Li
(Tue Sep 26 2006 - 20:09:04 PDT)
Re: AMBER: job crashes
JunJun Liu
(Tue Sep 26 2006 - 20:39:52 PDT)
Re: AMBER: job crashes
Xiaowei (David) Li
(Tue Sep 26 2006 - 20:57:18 PDT)
AMBER: RE: Amber8: problem related to antechamber
priya priya
(Wed Sep 27 2006 - 00:29:01 PDT)
AMBER: kclust
Fabiana Caporuscio
(Wed Sep 27 2006 - 01:32:51 PDT)
AMBER: Error in compiling Amber 8 parallel
Jianhui Tian
(Wed Sep 27 2006 - 13:28:48 PDT)
AMBER: Multiple Timestep MD
David LeBard
(Wed Sep 27 2006 - 18:03:35 PDT)
RE: AMBER: Error in compiling Amber 8 parallel
Ross Walker
(Thu Sep 28 2006 - 08:36:25 PDT)
AMBER: running sander on several nodes
Fenghui Fan
(Thu Sep 28 2006 - 09:45:34 PDT)
Re: AMBER: running sander on several nodes
Fenghui Fan
(Thu Sep 28 2006 - 10:21:26 PDT)
RE: AMBER: running sander on several nodes
Ross Walker
(Thu Sep 28 2006 - 10:37:28 PDT)
AMBER: Questions/observations about Nudged Elastic Band (NEB)
Pietro Amodeo
(Thu Sep 28 2006 - 03:56:36 PDT)
RE: AMBER: Questions/observations about Nudged Elastic Band (NEB)
Ross Walker
(Thu Sep 28 2006 - 08:29:29 PDT)
AMBER: Machine File for Intel Core 2 Duo E6400
Osmar Norberto de Souza
(Thu Sep 28 2006 - 11:47:06 PDT)
RE: AMBER: Machine File for Intel Core 2 Duo E6400
Ross Walker
(Thu Sep 28 2006 - 12:05:02 PDT)
Re: AMBER: Machine File for Intel Core 2 Duo E6400
Osmar Norberto de Souza
(Thu Sep 28 2006 - 12:22:15 PDT)
RE: AMBER: Questions/observations about Nudged Elastic Band (NEB)
Pietro Amodeo
(Fri Sep 29 2006 - 02:21:43 PDT)
AMBER: NAD parameters
Uni-Halle
(Thu Sep 28 2006 - 06:06:06 PDT)
Re: AMBER: NAD parameters
cristian obiol
(Thu Sep 28 2006 - 06:56:43 PDT)
RE: AMBER: NAD parameters
Ross Walker
(Thu Sep 28 2006 - 08:32:48 PDT)
AMBER: Problem about installing amber9 on Mac OS X
gtg549i.mail.gatech.edu
(Thu Sep 28 2006 - 09:28:51 PDT)
RE: AMBER: Problem about installing amber9 on Mac OS X
Ross Walker
(Thu Sep 28 2006 - 10:40:26 PDT)
RE: AMBER: Problem about installing amber9 on Mac OS X
gtg549i.mail.gatech.edu
(Thu Sep 28 2006 - 11:32:18 PDT)
RE: AMBER: Problem about installing amber9 on Mac OS X
Ross Walker
(Thu Sep 28 2006 - 11:52:30 PDT)
RE: AMBER: Problem about installing amber9 on Mac OS X
Shuting Wei
(Fri Sep 29 2006 - 14:08:42 PDT)
AMBER: parm*.dat
Ivelin Georgiev
(Thu Sep 28 2006 - 09:39:23 PDT)
Re: AMBER: parm*.dat
Jianhui
(Thu Sep 28 2006 - 14:24:49 PDT)
AMBER: Parameterization of ethidium - phenyl ring
sethl.gatech.edu
(Thu Sep 28 2006 - 13:02:08 PDT)
AMBER: WHAT IF CHeck after MD
Fenghui Fan
(Thu Sep 28 2006 - 15:06:04 PDT)
Re: AMBER: WHAT IF CHeck after MD
David Mobley
(Thu Sep 28 2006 - 15:58:32 PDT)
AMBER: problem to center solvateshell
Bonnet, Pascal [PRDBE]
(Fri Sep 29 2006 - 02:30:49 PDT)
AMBER: Problem using antechamber
Gustavo Seabra
(Fri Sep 29 2006 - 09:19:12 PDT)
RE: AMBER: Problem using antechamber
Junmei Wang
(Fri Sep 29 2006 - 11:17:37 PDT)
Re: AMBER: Problem using antechamber
Gustavo Seabra
(Fri Sep 29 2006 - 12:06:34 PDT)
AMBER: Electrostatic Energy Constant
Ivelin Georgiev
(Fri Sep 29 2006 - 10:50:03 PDT)
Re: AMBER: Electrostatic Energy Constant
Thomas Cheatham
(Fri Sep 29 2006 - 11:19:00 PDT)
Re: AMBER: Electrostatic Energy Constant
Fenghui Fan
(Fri Sep 29 2006 - 12:23:03 PDT)
Re: AMBER: Electrostatic Energy Constant
Thomas Cheatham
(Fri Sep 29 2006 - 12:44:25 PDT)
Re: AMBER: Electrostatic Energy Constant
Carlos Simmerling
(Fri Sep 29 2006 - 13:20:24 PDT)
Last message date
:
Sun Oct 01 2006 - 06:07:20 PDT
Archived on
: Mon Nov 18 2024 - 05:53:28 PST
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