Amber Archive Nov 2009 by subject
536 messages
:
Starting
Sat Oct 31 2009 - 13:00:03 PDT,
Ending
Mon Nov 30 2009 - 22:30:02 PST
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[AMBER] -np not 2^x a problem w/ sander???
Ross Walker
(Fri Nov 06 2009 - 17:43:04 PST)
Dean Cuebas
(Fri Nov 06 2009 - 11:27:48 PST)
[AMBER] -np not 2^x a problem w/ sander??? update
Ross Walker
(Sat Nov 07 2009 - 08:31:36 PST)
Dean Cuebas
(Fri Nov 06 2009 - 11:46:39 PST)
[AMBER] 60 giga output file .mdcrd file
case
(Wed Nov 04 2009 - 04:17:47 PST)
Ross Walker
(Tue Nov 03 2009 - 15:10:17 PST)
Silvia Carlotto
(Tue Nov 03 2009 - 08:42:43 PST)
Richard Owczarzy
(Tue Nov 03 2009 - 07:14:44 PST)
Jason Swails
(Tue Nov 03 2009 - 05:49:01 PST)
Fernando Martín García
(Tue Nov 03 2009 - 02:35:41 PST)
Silvia Carlotto
(Tue Nov 03 2009 - 02:24:03 PST)
Ross Walker
(Mon Nov 02 2009 - 15:36:48 PST)
Peter Schmidtke
(Mon Nov 02 2009 - 10:40:48 PST)
Silvia Carlotto
(Mon Nov 02 2009 - 09:41:32 PST)
[AMBER] about divcon
Jason Swails
(Wed Nov 18 2009 - 11:09:43 PST)
Alan
(Wed Nov 18 2009 - 09:07:44 PST)
case
(Wed Nov 18 2009 - 08:53:16 PST)
Alan
(Wed Nov 18 2009 - 08:24:51 PST)
[AMBER] About zinc parameters ?
Sally Pias
(Tue Nov 17 2009 - 09:38:29 PST)
Jason Swails
(Tue Nov 17 2009 - 07:17:23 PST)
steinbrt.rci.rutgers.edu
(Tue Nov 17 2009 - 02:35:24 PST)
xuemeiwang1103
(Tue Nov 17 2009 - 00:52:56 PST)
[AMBER] amber 10 test failures...
peker milas
(Tue Nov 03 2009 - 06:11:01 PST)
Jason Swails
(Mon Nov 02 2009 - 16:19:43 PST)
Mark Williamson
(Mon Nov 02 2009 - 16:11:40 PST)
Ross Walker
(Mon Nov 02 2009 - 15:36:48 PST)
peker milas
(Mon Nov 02 2009 - 06:18:29 PST)
[AMBER] amber 9 compilation
Myunggi Yi
(Fri Nov 06 2009 - 07:13:00 PST)
[AMBER] amber parameter file creation and usage
Donald Keidel
(Wed Nov 04 2009 - 09:53:23 PST)
Jason Swails
(Tue Nov 03 2009 - 21:29:30 PST)
Donald Keidel
(Tue Nov 03 2009 - 20:47:36 PST)
[AMBER] amber9 compilation
David Watson
(Fri Nov 06 2009 - 08:16:58 PST)
Myunggi Yi
(Fri Nov 06 2009 - 07:50:25 PST)
David Watson
(Fri Nov 06 2009 - 07:19:31 PST)
Myunggi Yi
(Fri Nov 06 2009 - 07:10:03 PST)
[AMBER] AMBER: segmentation fault when running parmchk
Junmei Wang
(Wed Nov 04 2009 - 11:22:54 PST)
Bill Ross
(Wed Nov 04 2009 - 10:39:32 PST)
Mark Williamson
(Wed Nov 04 2009 - 09:06:53 PST)
Alexander Boncheff
(Wed Nov 04 2009 - 08:02:50 PST)
Bill Ross
(Tue Nov 03 2009 - 15:15:00 PST)
Alexander Boncheff
(Tue Nov 03 2009 - 14:29:00 PST)
Jason Swails
(Tue Nov 03 2009 - 12:22:10 PST)
Alexander Boncheff
(Tue Nov 03 2009 - 11:41:55 PST)
[AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala
Wallace Kunin
(Thu Nov 12 2009 - 08:05:03 PST)
Ross Walker
(Thu Nov 12 2009 - 02:52:44 PST)
Wallace Kunin
(Thu Nov 12 2009 - 00:15:40 PST)
case
(Wed Nov 11 2009 - 14:36:59 PST)
Jason Swails
(Wed Nov 11 2009 - 14:30:35 PST)
Wallace Kunin
(Wed Nov 11 2009 - 14:04:28 PST)
Bill Ross
(Wed Nov 11 2009 - 09:54:01 PST)
David Watson
(Wed Nov 11 2009 - 08:56:01 PST)
Giorgio Maccari
(Wed Nov 11 2009 - 08:53:04 PST)
Wallace Kunin
(Wed Nov 11 2009 - 06:17:42 PST)
case
(Tue Nov 10 2009 - 08:28:17 PST)
Wallace Kunin
(Tue Nov 10 2009 - 07:41:18 PST)
David Watson
(Mon Nov 09 2009 - 16:25:12 PST)
David Watson
(Mon Nov 09 2009 - 14:35:32 PST)
Wallace Kunin
(Mon Nov 09 2009 - 14:05:32 PST)
case
(Mon Nov 09 2009 - 12:41:59 PST)
Mark Williamson
(Mon Nov 09 2009 - 12:14:03 PST)
case
(Mon Nov 09 2009 - 12:02:42 PST)
David Watson
(Mon Nov 09 2009 - 11:28:31 PST)
Wallace Kunin
(Mon Nov 09 2009 - 11:14:25 PST)
[AMBER] AmberTools 1.3 has a likely release date?
case
(Fri Nov 20 2009 - 06:50:23 PST)
Alan
(Thu Nov 19 2009 - 10:15:30 PST)
[AMBER] analyzeMatrix: cannot find a match in the matrixInfoStack
Naser Alijabbari
(Sun Nov 08 2009 - 17:43:56 PST)
[AMBER] Antechamber and Parmchk problems
Junmei Wang
(Thu Nov 05 2009 - 13:16:51 PST)
cyk5056
(Thu Nov 05 2009 - 10:59:28 PST)
Junmei Wang
(Wed Nov 04 2009 - 13:07:35 PST)
cyk5056
(Wed Nov 04 2009 - 12:37:55 PST)
cyk5056
(Wed Nov 04 2009 - 11:56:32 PST)
Junmei Wang
(Wed Nov 04 2009 - 11:21:25 PST)
case
(Wed Nov 04 2009 - 07:26:03 PST)
cyk5056
(Tue Nov 03 2009 - 18:22:38 PST)
[AMBER] Asking help for parallel installation of Amber9
David Watson
(Wed Nov 18 2009 - 10:04:38 PST)
Bill Ross
(Wed Nov 18 2009 - 09:48:51 PST)
David Watson
(Wed Nov 18 2009 - 05:23:17 PST)
nicholus bhattacharjee
(Wed Nov 18 2009 - 05:00:36 PST)
David Watson
(Wed Nov 18 2009 - 04:36:03 PST)
nicholus bhattacharjee
(Wed Nov 18 2009 - 04:27:03 PST)
[AMBER] Atomic radii assignment for WAT molecules
Ray Luo
(Sat Nov 28 2009 - 10:13:42 PST)
DIMAS SUAREZ RODRIGUEZ
(Thu Nov 26 2009 - 08:43:33 PST)
[AMBER] build up solvate box
Huikuan Chao
(Sat Nov 07 2009 - 12:29:50 PST)
[AMBER] Calculaiton stop ?
xuemeiwang1103
(Thu Nov 05 2009 - 05:11:31 PST)
[AMBER] Can I get an average trajectory?
cyk5056
(Wed Nov 18 2009 - 08:02:38 PST)
Carlos Simmerling
(Wed Nov 18 2009 - 04:08:59 PST)
cyk5056
(Tue Nov 17 2009 - 20:46:25 PST)
[AMBER] check MAXPR in locmem.f error on minimization
Robert Duke
(Fri Nov 27 2009 - 06:44:36 PST)
Jason Swails
(Wed Nov 25 2009 - 10:50:43 PST)
Jodi Hadden
(Wed Nov 25 2009 - 10:29:51 PST)
case
(Wed Nov 25 2009 - 05:29:41 PST)
Jodi Hadden
(Tue Nov 24 2009 - 15:46:03 PST)
[AMBER] coarse-grained MD
Francesco Pietra
(Wed Nov 11 2009 - 00:27:27 PST)
[AMBER] combining parameter files of ligand and enzyme
FyD
(Tue Nov 17 2009 - 23:49:23 PST)
Amire-Brahimi Benjamin
(Tue Nov 17 2009 - 14:31:32 PST)
[AMBER] compilation problem of amber
Jason Swails
(Tue Nov 17 2009 - 06:51:42 PST)
sculiujl
(Mon Nov 16 2009 - 23:33:52 PST)
[AMBER] compilation problem of amber9
Jason Swails
(Tue Nov 17 2009 - 06:55:46 PST)
sculiujl
(Mon Nov 16 2009 - 23:03:22 PST)
[AMBER] conversion of kelvin to kcal/mol
aneesh cna
(Sun Nov 08 2009 - 22:56:36 PST)
manoj singh
(Sun Nov 08 2009 - 21:17:03 PST)
aneesh cna
(Sun Nov 08 2009 - 21:08:33 PST)
[AMBER] Creating new residue with tleap.
case
(Wed Nov 11 2009 - 04:37:47 PST)
rrd
(Wed Nov 11 2009 - 03:02:23 PST)
[AMBER] difference between two inputs
case
(Fri Nov 27 2009 - 06:59:01 PST)
Jio M
(Wed Nov 25 2009 - 22:32:12 PST)
[AMBER] Different results for different computers
cyk5056
(Sat Oct 31 2009 - 12:39:59 PDT)
[AMBER] distance-dependent dielectric constant minimization
case
(Mon Nov 30 2009 - 05:02:11 PST)
Rilei Yu
(Sun Nov 29 2009 - 23:02:32 PST)
[AMBER] enquiry regarding parameter file to be used
Carlos Simmerling
(Fri Nov 20 2009 - 03:20:05 PST)
bharat lakhani
(Thu Nov 19 2009 - 21:35:14 PST)
Carlos Simmerling
(Mon Nov 16 2009 - 03:40:49 PST)
bharat lakhani
(Fri Nov 13 2009 - 21:52:58 PST)
Carlos Simmerling
(Fri Nov 13 2009 - 05:41:50 PST)
bharat lakhani
(Fri Nov 13 2009 - 05:35:30 PST)
[AMBER] error in kclust of MMTB_tool set
kureeckal ramesh
(Tue Nov 10 2009 - 04:41:31 PST)
kureeckal ramesh
(Sun Nov 08 2009 - 16:10:58 PST)
kureeckal ramesh
(Thu Nov 05 2009 - 23:33:01 PST)
[AMBER] error in reading namelist cntrl
Ross Walker
(Tue Nov 03 2009 - 14:57:58 PST)
Giuseppe De Marco
(Tue Nov 03 2009 - 11:44:01 PST)
[AMBER] error reading namelist cntrl
Jason Swails
(Wed Nov 11 2009 - 06:01:42 PST)
Shaikh Abdul R S Ramaju
(Tue Nov 10 2009 - 22:51:45 PST)
[AMBER] errors on leap for a RNA + Non-Standard molecule pdb structure
Yunjie Zhao
(Thu Nov 19 2009 - 20:37:34 PST)
[AMBER] errors on leap for a RNA+Adenine pdb structure
FyD
(Wed Nov 04 2009 - 05:39:02 PST)
zgong.hust
(Wed Nov 04 2009 - 04:59:20 PST)
case
(Wed Nov 04 2009 - 04:17:53 PST)
zgong.hust
(Tue Nov 03 2009 - 22:18:41 PST)
[AMBER] errors on leap for a RNA+Adenine pdb structure with antechamber
FyD
(Wed Nov 04 2009 - 07:28:04 PST)
zgong.hust
(Wed Nov 04 2009 - 07:07:23 PST)
[AMBER] errors on leap for a RNA+Adenine pdb structure withantechamber
FyD
(Wed Nov 04 2009 - 21:42:43 PST)
zgong.hust
(Wed Nov 04 2009 - 18:18:52 PST)
[AMBER] Etot positive
Ross Walker
(Mon Nov 16 2009 - 18:50:02 PST)
Carlos Simmerling
(Mon Nov 16 2009 - 03:13:55 PST)
Jio M
(Sun Nov 15 2009 - 21:06:22 PST)
[AMBER] ff fitting ?
Marek Maly
(Mon Nov 09 2009 - 04:38:35 PST)
case
(Sun Nov 08 2009 - 09:42:42 PST)
Marek Maly
(Thu Nov 05 2009 - 13:38:38 PST)
[AMBER] fillratio
Qinghua Liao
(Mon Nov 30 2009 - 21:59:05 PST)
Ray Luo
(Mon Nov 30 2009 - 19:30:50 PST)
Qinghua Liao
(Mon Nov 30 2009 - 18:38:34 PST)
[AMBER] Fortran error in standard simulation
Ross Walker
(Tue Nov 24 2009 - 08:21:33 PST)
Oliver Kuhn
(Mon Nov 23 2009 - 01:26:30 PST)
[AMBER] Fortran error in standard simulation 2
Oliver Kuhn
(Mon Nov 23 2009 - 01:34:21 PST)
[AMBER] Fortran error in standard simulation 3
Oliver Kuhn
(Mon Nov 23 2009 - 01:47:44 PST)
[AMBER] Gaussian log file error
Junmei Wang
(Mon Nov 02 2009 - 07:58:10 PST)
Ben Roberts
(Mon Nov 02 2009 - 07:16:23 PST)
[AMBER] GB and Atom Type
Sally Pias
(Wed Nov 18 2009 - 21:11:27 PST)
Alexander Seifert
(Wed Nov 18 2009 - 00:58:32 PST)
[AMBER] Getting minimized .pdb file without non-polar hydrogens
Francesco Pietra
(Mon Nov 09 2009 - 11:31:40 PST)
[AMBER] Gly -> Ala mutation
manoj singh
(Mon Nov 09 2009 - 08:26:00 PST)
Adrian Roitberg
(Mon Nov 09 2009 - 08:13:11 PST)
manoj singh
(Mon Nov 09 2009 - 08:10:40 PST)
Carlos Simmerling
(Mon Nov 09 2009 - 07:13:08 PST)
manoj singh
(Sun Nov 08 2009 - 13:18:37 PST)
Jason Swails
(Sun Nov 08 2009 - 12:16:42 PST)
manoj singh
(Sun Nov 08 2009 - 11:14:23 PST)
Jason Swails
(Sun Nov 08 2009 - 09:53:29 PST)
manoj singh
(Sun Nov 08 2009 - 09:25:46 PST)
[AMBER] have a question
Bill Ross
(Tue Nov 17 2009 - 18:02:45 PST)
jacky zhao
(Tue Nov 17 2009 - 17:54:36 PST)
[AMBER] HB for each snapshot
Nicolas Sapay
(Thu Nov 05 2009 - 00:30:51 PST)
Jason Swails
(Wed Nov 04 2009 - 11:35:07 PST)
Marcin Krol
(Wed Nov 04 2009 - 11:14:41 PST)
[AMBER] hbond analysis by ptraj- segmentation fault
Jayalakshmi Sridhar
(Mon Nov 23 2009 - 10:36:25 PST)
Daniel Roe
(Mon Nov 23 2009 - 09:49:23 PST)
Daniel Roe
(Mon Nov 23 2009 - 09:42:49 PST)
Jayalakshmi Sridhar
(Mon Nov 23 2009 - 07:51:00 PST)
[AMBER] Hbond analysis output giving no hbonds
Jayalakshmi Sridhar
(Tue Nov 24 2009 - 09:52:47 PST)
Thomas Cheatham
(Tue Nov 24 2009 - 08:58:27 PST)
Jayalakshmi Sridhar
(Tue Nov 24 2009 - 08:32:41 PST)
[AMBER] heme (united-atom)
case
(Mon Nov 30 2009 - 05:28:05 PST)
Simon Becker
(Thu Nov 26 2009 - 06:34:59 PST)
case
(Wed Nov 25 2009 - 08:39:10 PST)
Simon Becker
(Wed Nov 25 2009 - 08:30:51 PST)
[AMBER] High-temperature simulation ?
Carlos Simmerling
(Wed Nov 11 2009 - 09:26:15 PST)
Chih-Ying Lin
(Wed Nov 11 2009 - 07:36:16 PST)
[AMBER] How to change the input matrix for "analyze matrix" instruction?
陈一侃
(Wed Nov 18 2009 - 08:18:51 PST)
cyk5056
(Tue Nov 17 2009 - 20:37:43 PST)
[AMBER] How to compile and recompile ptraj?
cyk5056
(Sun Nov 29 2009 - 14:06:55 PST)
[AMBER] How to get total energy of asystem
case
(Tue Nov 24 2009 - 04:36:30 PST)
steinbrt.rci.rutgers.edu
(Tue Nov 24 2009 - 01:43:06 PST)
gunajyoti das
(Tue Nov 24 2009 - 01:14:06 PST)
[AMBER] How to split mdcrd files
Thomas Cheatham
(Sun Nov 15 2009 - 13:06:34 PST)
Carlos Simmerling
(Sun Nov 15 2009 - 09:56:48 PST)
Jason Swails
(Sun Nov 15 2009 - 09:35:24 PST)
Carlos Simmerling
(Sun Nov 15 2009 - 09:28:06 PST)
shamoon siddiqui
(Sun Nov 15 2009 - 09:22:52 PST)
[AMBER] how to use amber to verify the reason for difference in affinity
case
(Sun Nov 29 2009 - 18:55:38 PST)
Josmar R. da Rocha
(Tue Nov 24 2009 - 14:01:34 PST)
[AMBER] how to use GLYCAM04 for carbonhydrate in amber9?
Karl Kirschner
(Mon Nov 30 2009 - 00:53:27 PST)
sculiujl
(Sun Nov 29 2009 - 19:39:08 PST)
[AMBER] Hydrogen bond analysis for protein dna complex using ptraj
Thomas Cheatham
(Sat Nov 14 2009 - 09:06:15 PST)
shamoon siddiqui
(Sat Nov 14 2009 - 08:19:04 PST)
Carlos Simmerling
(Sat Nov 14 2009 - 08:00:39 PST)
shamoon siddiqui
(Sat Nov 14 2009 - 07:56:04 PST)
[AMBER] i-APBS and apbs
Rilei Yu
(Wed Nov 25 2009 - 03:14:15 PST)
Jason Swails
(Tue Nov 24 2009 - 21:33:31 PST)
Robert Konecny
(Tue Nov 24 2009 - 21:33:37 PST)
Rilei Yu
(Tue Nov 24 2009 - 21:14:18 PST)
[AMBER] implicit_run_error
case
(Fri Nov 20 2009 - 06:53:31 PST)
balaji nagarajan
(Thu Nov 19 2009 - 10:37:21 PST)
[AMBER] Increase Temperature to 550 K
Carlos Simmerling
(Fri Nov 13 2009 - 05:35:28 PST)
FyD
(Fri Nov 13 2009 - 03:43:48 PST)
Chih-Ying Lin
(Thu Nov 12 2009 - 20:36:07 PST)
Carlos Simmerling
(Thu Nov 12 2009 - 14:29:13 PST)
Chih-Ying Lin
(Thu Nov 12 2009 - 13:59:11 PST)
Carlos Simmerling
(Thu Nov 12 2009 - 06:22:08 PST)
case
(Thu Nov 12 2009 - 04:55:18 PST)
FyD
(Wed Nov 11 2009 - 23:51:24 PST)
Carlos Simmerling
(Wed Nov 11 2009 - 13:14:24 PST)
Chih-Ying Lin
(Wed Nov 11 2009 - 13:08:12 PST)
Carlos Simmerling
(Wed Nov 11 2009 - 09:52:55 PST)
Chih-Ying Lin
(Wed Nov 11 2009 - 07:27:41 PST)
[AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala
Jason Swails
(Wed Nov 18 2009 - 11:00:09 PST)
Wallace Kunin
(Wed Nov 18 2009 - 06:21:57 PST)
case
(Tue Nov 17 2009 - 09:29:42 PST)
Wallace Kunin
(Tue Nov 17 2009 - 07:20:13 PST)
Mark Williamson
(Mon Nov 16 2009 - 11:49:58 PST)
Wallace Kunin
(Mon Nov 16 2009 - 11:07:20 PST)
Mark Williamson
(Mon Nov 16 2009 - 09:37:18 PST)
Wallace Kunin
(Mon Nov 16 2009 - 08:43:18 PST)
[AMBER] Is it possible to simulate transmembrane protein with GB model ?
cgji
(Mon Nov 02 2009 - 12:52:44 PST)
[AMBER] Is it taking too much time
Nicolas Sapay
(Tue Nov 03 2009 - 00:57:55 PST)
nicholus bhattacharjee
(Mon Nov 02 2009 - 21:35:04 PST)
nicholus bhattacharjee
(Mon Nov 02 2009 - 21:14:26 PST)
Ross Walker
(Mon Nov 02 2009 - 15:36:48 PST)
Nicolas SAPAY
(Mon Nov 02 2009 - 07:00:58 PST)
nicholus bhattacharjee
(Mon Nov 02 2009 - 06:40:25 PST)
Nicolas SAPAY
(Mon Nov 02 2009 - 06:19:17 PST)
manoj singh
(Mon Nov 02 2009 - 05:50:21 PST)
nicholus bhattacharjee
(Mon Nov 02 2009 - 00:37:28 PST)
manoj singh
(Sun Nov 01 2009 - 23:31:07 PST)
nicholus bhattacharjee
(Sun Nov 01 2009 - 22:08:46 PST)
[AMBER] is rst file the last structure?
case
(Sun Nov 15 2009 - 06:33:16 PST)
Jason Swails
(Sat Nov 14 2009 - 09:18:22 PST)
qiaoyan
(Fri Nov 13 2009 - 20:52:40 PST)
[AMBER] Is the integral value from RDF the same as average number of atoms?
Gustaf Olsson (go22bi.student.hik.se)
(Wed Nov 18 2009 - 13:56:31 PST)
[AMBER] ligand parameterization
Ilyas Yildirim
(Thu Nov 26 2009 - 16:13:09 PST)
Jason Swails
(Thu Nov 26 2009 - 14:12:34 PST)
Nahoum Anthony
(Thu Nov 26 2009 - 09:19:47 PST)
Jason Swails
(Thu Nov 26 2009 - 07:47:58 PST)
case
(Thu Nov 26 2009 - 07:09:05 PST)
Nahoum Anthony
(Thu Nov 26 2009 - 02:49:51 PST)
[AMBER] linux version for Amber10
liangchen88.ucla.edu
(Sat Nov 07 2009 - 19:59:53 PST)
Jason Swails
(Sat Nov 07 2009 - 19:38:41 PST)
Sudeep Narayan Banerjee
(Sat Nov 07 2009 - 18:56:19 PST)
Peter Schmidtke
(Sat Nov 07 2009 - 07:58:18 PST)
liangchen88.ucla.edu
(Sat Nov 07 2009 - 07:28:05 PST)
[AMBER] Lisp library for amber analysis?
Eric Shamay
(Wed Nov 11 2009 - 13:54:12 PST)
[AMBER] LJ parameters for HO and HW
Bill Ross
(Mon Nov 09 2009 - 09:29:40 PST)
steinbrt.rci.rutgers.edu
(Mon Nov 09 2009 - 00:23:20 PST)
Jason Swails
(Sun Nov 08 2009 - 07:14:45 PST)
manoj singh
(Sat Nov 07 2009 - 22:09:13 PST)
Jason Swails
(Sat Nov 07 2009 - 21:50:03 PST)
manoj singh
(Sat Nov 07 2009 - 21:21:22 PST)
[AMBER] looking for parameters for DHFR substrates and inhibitors...
Sidney Elmer
(Sat Nov 21 2009 - 20:47:50 PST)
[AMBER] Low frequency Raman spectra
case
(Sat Nov 07 2009 - 07:02:02 PST)
babak minoofar
(Sat Nov 07 2009 - 04:53:37 PST)
[AMBER] LYS-ASP
case
(Fri Nov 27 2009 - 19:08:58 PST)
Jason Swails
(Fri Nov 27 2009 - 17:25:33 PST)
s. Bill
(Fri Nov 27 2009 - 13:47:28 PST)
[AMBER] matrixInfoStack
Naser Alijabbari
(Mon Nov 23 2009 - 06:42:43 PST)
Naser Alijabbari
(Fri Nov 13 2009 - 06:52:52 PST)
Naser Alijabbari
(Tue Nov 10 2009 - 06:45:12 PST)
[AMBER] MD snapshots of most probable protein conformations in Amber
Andrew Voronkov
(Mon Nov 30 2009 - 04:56:42 PST)
Carlos Simmerling
(Wed Nov 18 2009 - 09:14:50 PST)
Andrew Voronkov
(Wed Nov 18 2009 - 07:33:54 PST)
Andrew Voronkov
(Wed Nov 18 2009 - 07:32:11 PST)
Carlos Simmerling
(Wed Nov 18 2009 - 05:53:14 PST)
Renata KWIECIEN
(Wed Nov 18 2009 - 05:39:52 PST)
Andrew Voronkov
(Wed Nov 18 2009 - 05:09:52 PST)
Adrian Roitberg
(Thu Nov 12 2009 - 05:30:53 PST)
Andrew Voronkov
(Thu Nov 12 2009 - 05:23:22 PST)
[AMBER] MM-PB/GBSA NMODE
Zhongjie Liang
(Tue Nov 24 2009 - 22:50:50 PST)
[AMBER] MM-PBSA NMODE
case
(Wed Nov 25 2009 - 05:31:28 PST)
Zhongjie Liang
(Tue Nov 24 2009 - 19:12:38 PST)
[AMBER] MM_PBSA energy per residue
Hemant Kumar
(Thu Nov 12 2009 - 06:27:22 PST)
[AMBER] MM_PBSA enquiries
manoj singh
(Sun Nov 08 2009 - 07:21:12 PST)
s. Bill
(Sun Nov 08 2009 - 06:53:04 PST)
[AMBER] MM_PBSA error
Jagdeesh C
(Thu Nov 26 2009 - 20:28:44 PST)
[AMBER] MMTSB tool set PDF
kureeckal ramesh
(Tue Nov 10 2009 - 06:02:39 PST)
[AMBER] MPI process terminated unexpectedly after cluster upgrade
Ross Walker
(Thu Nov 05 2009 - 08:22:19 PST)
Dmitri Nilov
(Thu Nov 05 2009 - 06:55:16 PST)
Dmitri Nilov
(Thu Nov 05 2009 - 06:38:32 PST)
Jason Swails
(Thu Nov 05 2009 - 06:12:39 PST)
Dmitri Nilov
(Thu Nov 05 2009 - 05:39:59 PST)
Ross Walker
(Tue Nov 03 2009 - 15:13:45 PST)
Jason Swails
(Tue Nov 03 2009 - 06:11:48 PST)
Dmitri Nilov
(Tue Nov 03 2009 - 06:06:11 PST)
Dmitri Nilov
(Tue Nov 03 2009 - 05:20:17 PST)
Ross Walker
(Mon Nov 02 2009 - 15:36:48 PST)
Jason Swails
(Mon Nov 02 2009 - 09:04:14 PST)
Dmitri Nilov
(Mon Nov 02 2009 - 05:11:15 PST)
Jason Swails
(Mon Nov 02 2009 - 04:15:19 PST)
Dmitri Nilov
(Mon Nov 02 2009 - 01:17:19 PST)
[AMBER] MSD of ligand??
Chih-Ying Lin
(Tue Nov 17 2009 - 11:07:12 PST)
[AMBER] NAD - mmpbsa
Urszula Uciechowska
(Sun Nov 22 2009 - 03:02:22 PST)
[AMBER] non standart residue library creation with tleap (Zn atom)
Bill Ross
(Tue Nov 24 2009 - 10:09:45 PST)
Ross Walker
(Tue Nov 24 2009 - 08:29:42 PST)
Ross Walker
(Tue Nov 24 2009 - 08:28:21 PST)
Andrew Voronkov
(Tue Nov 24 2009 - 06:57:30 PST)
FyD
(Tue Nov 24 2009 - 06:16:54 PST)
Andrew Voronkov
(Tue Nov 24 2009 - 02:12:53 PST)
FyD
(Tue Nov 24 2009 - 01:26:37 PST)
Andrew Voronkov
(Tue Nov 24 2009 - 00:40:42 PST)
FyD
(Mon Nov 23 2009 - 11:50:42 PST)
FyD
(Mon Nov 23 2009 - 09:49:05 PST)
Andrew Voronkov
(Mon Nov 23 2009 - 09:38:28 PST)
FyD
(Mon Nov 23 2009 - 09:31:31 PST)
FyD
(Mon Nov 23 2009 - 09:22:23 PST)
Andrew Voronkov
(Mon Nov 23 2009 - 08:35:51 PST)
FyD
(Mon Nov 23 2009 - 08:06:01 PST)
Andrew Voronkov
(Mon Nov 23 2009 - 07:44:45 PST)
FyD
(Mon Nov 23 2009 - 05:25:15 PST)
Andrew Voronkov
(Mon Nov 23 2009 - 04:35:55 PST)
FyD
(Fri Nov 20 2009 - 09:47:00 PST)
Andrew Voronkov
(Fri Nov 20 2009 - 08:02:57 PST)
FyD
(Fri Nov 20 2009 - 07:40:50 PST)
Andrew Voronkov
(Fri Nov 20 2009 - 07:25:30 PST)
FyD
(Fri Nov 20 2009 - 05:42:58 PST)
case
(Fri Nov 20 2009 - 05:30:54 PST)
Andrew Voronkov
(Fri Nov 20 2009 - 03:35:31 PST)
FyD
(Wed Nov 18 2009 - 06:29:14 PST)
Andrew Voronkov
(Wed Nov 18 2009 - 05:19:58 PST)
FyD
(Tue Nov 17 2009 - 12:10:03 PST)
Jason Swails
(Tue Nov 17 2009 - 10:05:05 PST)
Andrew Voronkov
(Tue Nov 17 2009 - 08:34:33 PST)
intra\\sa175950
(Tue Nov 17 2009 - 08:18:38 PST)
Jason Swails
(Tue Nov 17 2009 - 07:57:41 PST)
Andrew Voronkov
(Tue Nov 17 2009 - 07:47:12 PST)
[AMBER] Not able to compile pmemd with openmpi in Amber9
Robert Duke
(Wed Nov 25 2009 - 14:48:21 PST)
case
(Wed Nov 25 2009 - 13:06:53 PST)
Ross Walker
(Wed Nov 25 2009 - 12:24:23 PST)
Jason Swails
(Wed Nov 25 2009 - 08:50:41 PST)
Kito
(Wed Nov 25 2009 - 00:12:51 PST)
Kito
(Tue Nov 24 2009 - 23:50:25 PST)
Kito
(Tue Nov 24 2009 - 23:11:00 PST)
Jason Swails
(Tue Nov 24 2009 - 23:06:14 PST)
Kito
(Tue Nov 24 2009 - 22:39:42 PST)
[AMBER] Output Does Not Match in Tutorial B1
case
(Mon Nov 30 2009 - 11:50:34 PST)
Wallace Kunin
(Mon Nov 30 2009 - 11:11:02 PST)
Bill Ross
(Mon Nov 30 2009 - 11:03:19 PST)
case
(Mon Nov 30 2009 - 11:01:20 PST)
Wallace Kunin
(Mon Nov 30 2009 - 10:38:07 PST)
[AMBER] pairwise per-residue decomposition
manoj singh
(Sat Oct 31 2009 - 21:59:38 PDT)
[AMBER] PCA analysis with ptraj
Alessandro Contini
(Tue Nov 10 2009 - 04:03:48 PST)
hannes.loeffler.stfc.ac.uk
(Tue Nov 10 2009 - 00:13:29 PST)
Alessandro Contini
(Mon Nov 09 2009 - 09:00:19 PST)
[AMBER] Phosphorylated Threonine
FyD
(Tue Nov 03 2009 - 11:41:49 PST)
Beale, John
(Tue Nov 03 2009 - 08:31:09 PST)
[AMBER] Phosphothreonine
Anselm Horn
(Thu Nov 05 2009 - 05:17:59 PST)
Beale, John
(Thu Nov 05 2009 - 05:03:58 PST)
[AMBER] pmemd failure
Francesco Pietra
(Sun Nov 08 2009 - 11:08:53 PST)
Robert Duke
(Sun Nov 08 2009 - 09:00:52 PST)
Francesco Pietra
(Sun Nov 08 2009 - 08:52:28 PST)
[AMBER] pmemd vs sander.MPI
Marek Maly
(Thu Nov 05 2009 - 15:58:50 PST)
Ross Walker
(Thu Nov 05 2009 - 14:58:37 PST)
Marek Maly
(Thu Nov 05 2009 - 10:47:06 PST)
Marek Maly
(Thu Nov 05 2009 - 10:34:31 PST)
Ross Walker
(Thu Nov 05 2009 - 10:27:19 PST)
Robert Duke
(Thu Nov 05 2009 - 10:06:24 PST)
Marek Maly
(Thu Nov 05 2009 - 10:03:08 PST)
Robert Duke
(Thu Nov 05 2009 - 05:35:41 PST)
Marek Maly
(Thu Nov 05 2009 - 05:36:39 PST)
Ross Walker
(Wed Nov 04 2009 - 10:33:23 PST)
Taufik Al-Sarraj
(Wed Nov 04 2009 - 09:32:05 PST)
[AMBER] Polarizable simulation of the slab
Robert Duke
(Fri Nov 27 2009 - 08:48:07 PST)
Jan Heyda
(Fri Nov 27 2009 - 08:27:13 PST)
case
(Fri Nov 27 2009 - 08:10:38 PST)
Jan Heyda
(Fri Nov 27 2009 - 06:53:57 PST)
case
(Fri Nov 27 2009 - 06:24:41 PST)
Jan Heyda
(Thu Nov 26 2009 - 10:20:52 PST)
Jan Heyda
(Sun Nov 22 2009 - 05:13:16 PST)
[AMBER] problem with FAD in tleap
FyD
(Mon Nov 30 2009 - 11:25:15 PST)
FyD
(Mon Nov 30 2009 - 11:15:56 PST)
M. Shahid
(Mon Nov 30 2009 - 10:33:35 PST)
case
(Mon Nov 30 2009 - 09:15:19 PST)
M. Shahid
(Mon Nov 30 2009 - 07:54:26 PST)
case
(Mon Nov 30 2009 - 05:26:37 PST)
FyD
(Mon Nov 30 2009 - 05:02:59 PST)
M. Shahid
(Mon Nov 30 2009 - 04:17:09 PST)
[AMBER] ptraj script for H bond for protein (explicit )
kureeckal ramesh
(Fri Nov 06 2009 - 23:38:29 PST)
[AMBER] R.E.D. resp error
FyD
(Thu Nov 12 2009 - 21:36:44 PST)
s. Bill
(Thu Nov 12 2009 - 12:23:31 PST)
[AMBER] R.E.D. too small charges
FyD
(Fri Nov 13 2009 - 05:06:51 PST)
Andrei Neamtu
(Fri Nov 13 2009 - 00:57:04 PST)
[AMBER] read substrate into leap
Bill Ross
(Wed Nov 18 2009 - 17:59:33 PST)
Jason Swails
(Wed Nov 18 2009 - 17:35:37 PST)
sculiujl
(Wed Nov 18 2009 - 17:12:13 PST)
Jason Swails
(Wed Nov 18 2009 - 10:53:30 PST)
sculiujl
(Wed Nov 18 2009 - 05:37:19 PST)
[AMBER] reagarding Dihedral PCA
jani sahil
(Sun Nov 29 2009 - 22:24:28 PST)
[AMBER] rectangular box with PME problem
Ivan Gladich
(Mon Nov 09 2009 - 14:18:16 PST)
[AMBER] reg. GBA
case
(Thu Nov 12 2009 - 05:02:43 PST)
balaji nagarajan
(Thu Nov 12 2009 - 04:06:30 PST)
[AMBER] regarding Dihedral PCA
jani sahil
(Sun Nov 29 2009 - 22:25:08 PST)
[AMBER] Regarding rigid bond
Carlos Simmerling
(Fri Nov 27 2009 - 10:24:35 PST)
aneesh cna
(Fri Nov 27 2009 - 09:29:15 PST)
[AMBER] Regarding Urey-Bradley term in amber calculation
Ross Walker
(Tue Nov 24 2009 - 08:36:49 PST)
Jason Swails
(Tue Nov 24 2009 - 04:48:31 PST)
aneesh cna
(Mon Nov 23 2009 - 22:48:04 PST)
[AMBER] request
sculiujl
(Fri Nov 13 2009 - 18:59:22 PST)
[AMBER] RESP using antechamber with Se atom
Eric Pettersen
(Fri Nov 06 2009 - 08:49:16 PST)
subarna thakur
(Thu Nov 05 2009 - 21:21:46 PST)
Junmei Wang
(Thu Nov 05 2009 - 13:39:46 PST)
Donald Keidel
(Thu Nov 05 2009 - 11:21:37 PST)
[AMBER] retinal lib file, params?
Simon Becker
(Mon Nov 02 2009 - 00:34:14 PST)
Mark M Huntress
(Sun Nov 01 2009 - 09:59:34 PST)
[AMBER] rings getting planar
case
(Thu Nov 26 2009 - 07:07:43 PST)
Jio M
(Thu Nov 26 2009 - 06:40:34 PST)
Jio M
(Thu Nov 26 2009 - 01:33:09 PST)
[AMBER] rmsd
Taufik Al-Sarraj
(Mon Nov 23 2009 - 11:24:49 PST)
Thomas Cheatham
(Sat Nov 21 2009 - 13:44:41 PST)
Taufik Al-Sarraj
(Fri Nov 20 2009 - 08:32:24 PST)
[AMBER] sander.APBS install problem
Robert Konecny
(Mon Nov 02 2009 - 20:52:09 PST)
Rilei Yu
(Mon Nov 02 2009 - 17:58:30 PST)
[AMBER] sander.mpi. mdfil: Error unknown flag: sander
case
(Mon Nov 09 2009 - 05:17:23 PST)
Andrew Voronkov
(Mon Nov 09 2009 - 04:24:17 PST)
[AMBER] Scripting tleap
Jack Shultz
(Sat Nov 28 2009 - 19:54:25 PST)
Tom Joseph
(Sat Nov 28 2009 - 19:45:40 PST)
Jack Shultz
(Sat Nov 28 2009 - 19:42:00 PST)
[AMBER] Segmentation Fault
Ross Walker
(Thu Nov 05 2009 - 10:29:20 PST)
Beale, John
(Thu Nov 05 2009 - 10:04:52 PST)
[AMBER] Segmentation fault in antechamber
albert albert
(Mon Nov 23 2009 - 07:23:00 PST)
case
(Tue Nov 17 2009 - 20:28:14 PST)
albert albert
(Tue Nov 17 2009 - 09:04:46 PST)
Mark Williamson
(Mon Nov 16 2009 - 09:48:32 PST)
albert albert
(Mon Nov 16 2009 - 08:23:02 PST)
case
(Mon Nov 16 2009 - 07:53:30 PST)
albert albert
(Mon Nov 16 2009 - 07:28:20 PST)
[AMBER] sleap fastbld error
Oliver Kuhn
(Sat Nov 07 2009 - 12:39:29 PST)
[AMBER] sleap fastbld error is not an error
Oliver Kuhn
(Sat Nov 07 2009 - 13:07:35 PST)
[AMBER] slope
Carlos Simmerling
(Tue Nov 17 2009 - 03:10:35 PST)
Jio M
(Mon Nov 16 2009 - 20:07:07 PST)
Carlos Simmerling
(Mon Nov 16 2009 - 03:11:46 PST)
Jio M
(Sun Nov 15 2009 - 20:42:52 PST)
Jio M
(Thu Nov 12 2009 - 11:28:02 PST)
[AMBER] slope {no reply}
Sally Pias
(Sat Nov 21 2009 - 22:53:39 PST)
Jio M
(Thu Nov 19 2009 - 09:15:25 PST)
Sally Pias
(Wed Nov 18 2009 - 21:39:53 PST)
Jio M
(Tue Nov 17 2009 - 21:09:34 PST)
Bill Ross
(Tue Nov 17 2009 - 17:04:48 PST)
Carlos Simmerling
(Tue Nov 17 2009 - 15:49:39 PST)
Jio M
(Tue Nov 17 2009 - 11:13:06 PST)
Bill Ross
(Tue Nov 17 2009 - 09:51:08 PST)
Carlos Simmerling
(Tue Nov 17 2009 - 03:11:23 PST)
Jio M
(Mon Nov 16 2009 - 21:13:44 PST)
Bill Ross
(Mon Nov 16 2009 - 09:48:22 PST)
Carlos Simmerling
(Sun Nov 15 2009 - 11:07:02 PST)
Jio M
(Sun Nov 15 2009 - 11:03:17 PST)
[AMBER] solvent
Jio M
(Sun Nov 08 2009 - 06:12:34 PST)
[AMBER] Some queries about pH simulation
case
(Tue Nov 03 2009 - 03:30:07 PST)
nicholus bhattacharjee
(Mon Nov 02 2009 - 23:34:02 PST)
[AMBER] standard way to upload a lipid bilayer
David Watson
(Sat Nov 21 2009 - 05:06:29 PST)
Syed Kashif Zafar
(Sat Nov 21 2009 - 03:40:08 PST)
[AMBER] Task is running on supercomputer without any output
Andrew Voronkov
(Thu Nov 12 2009 - 05:24:56 PST)
michael bane
(Mon Nov 09 2009 - 04:51:17 PST)
Andrew Voronkov
(Mon Nov 09 2009 - 04:39:36 PST)
[AMBER] The decreasing MSD of ligand??
Chih-Ying Lin
(Wed Nov 18 2009 - 13:19:35 PST)
[AMBER] the different RMSD?
qiaoyan
(Tue Nov 17 2009 - 18:47:42 PST)
qiaoyan
(Sat Nov 14 2009 - 18:02:53 PST)
Thomas Cheatham
(Sat Nov 14 2009 - 08:25:43 PST)
qiaoyan
(Fri Nov 13 2009 - 20:16:27 PST)
Thomas Cheatham
(Fri Nov 13 2009 - 19:40:56 PST)
qiaoyan
(Fri Nov 13 2009 - 19:37:36 PST)
[AMBER] The MSD and periodic boundary condition
Jason Swails
(Thu Nov 19 2009 - 16:00:30 PST)
Chih-Ying Lin
(Thu Nov 19 2009 - 15:30:46 PST)
[AMBER] the problem of nucgen.dat
case
(Sun Nov 08 2009 - 08:19:03 PST)
liangchen88.ucla.edu
(Sat Nov 07 2009 - 19:48:54 PST)
case
(Sat Nov 07 2009 - 06:51:57 PST)
liangchen88.ucla.edu
(Sat Nov 07 2009 - 06:41:49 PST)
[AMBER] three trials to create topologies with sleap and tleap
Oliver Kuhn
(Tue Nov 10 2009 - 01:34:36 PST)
[AMBER] tleap maximum coordination exceeded
case
(Tue Nov 17 2009 - 20:45:55 PST)
Jack Shultz
(Tue Nov 17 2009 - 19:05:41 PST)
Jack Shultz
(Tue Nov 17 2009 - 17:51:38 PST)
case
(Tue Nov 17 2009 - 12:24:09 PST)
FyD
(Tue Nov 17 2009 - 12:18:20 PST)
Jack Shultz
(Tue Nov 17 2009 - 08:52:20 PST)
[AMBER] total number of hydrogen bonds of the system as a function of time
Jason Swails
(Wed Nov 04 2009 - 06:08:21 PST)
Markus Kaukonen
(Wed Nov 04 2009 - 05:59:17 PST)
[AMBER] trajout problem
Sally Pias
(Mon Nov 30 2009 - 11:01:52 PST)
Carlos Simmerling
(Mon Nov 30 2009 - 05:56:43 PST)
Anna Reymer
(Mon Nov 30 2009 - 04:58:39 PST)
Carlos Simmerling
(Mon Nov 30 2009 - 04:09:05 PST)
Anna Reymer
(Mon Nov 30 2009 - 04:03:38 PST)
[AMBER] trouble with antechamber
case
(Mon Nov 30 2009 - 06:57:26 PST)
Jennifer L. Muzyka
(Mon Nov 30 2009 - 06:39:15 PST)
case
(Tue Nov 24 2009 - 12:41:24 PST)
Jennifer L. Muzyka
(Tue Nov 24 2009 - 12:13:46 PST)
[AMBER] unable to find mopac charges in mopac.out
Richard Tseng
(Mon Nov 09 2009 - 11:25:11 PST)
case
(Mon Nov 09 2009 - 08:47:01 PST)
Richard Tseng
(Mon Nov 09 2009 - 08:39:51 PST)
case
(Sat Nov 07 2009 - 05:59:43 PST)
Bill Ross
(Fri Nov 06 2009 - 17:22:22 PST)
Richard Tseng
(Fri Nov 06 2009 - 17:14:20 PST)
[AMBER] varying positional restraints with PMEMD
case
(Sun Nov 08 2009 - 09:37:53 PST)
Julian Garrec
(Thu Nov 05 2009 - 16:43:35 PST)
[AMBER] Verlet update time in explicit water Replica Exchange MD
Ross Walker
(Wed Nov 25 2009 - 12:29:03 PST)
Da-Wei Li
(Wed Nov 25 2009 - 11:43:58 PST)
Robert Duke
(Wed Nov 25 2009 - 09:38:24 PST)
Da-Wei Li
(Wed Nov 25 2009 - 09:28:27 PST)
Da-Wei Li
(Wed Nov 25 2009 - 09:14:17 PST)
Carlos Simmerling
(Wed Nov 25 2009 - 09:10:56 PST)
Da-Wei Li
(Wed Nov 25 2009 - 09:05:55 PST)
[AMBER] where to get leaprc.ff99sb?
Jason Swails
(Sat Nov 28 2009 - 19:51:39 PST)
Jack Shultz
(Sat Nov 28 2009 - 19:19:33 PST)
Jason Swails
(Sat Nov 28 2009 - 17:39:20 PST)
Jack Shultz
(Sat Nov 28 2009 - 16:20:03 PST)
[AMBER] which is the best intel complier for amber 10?
jacky zhao
(Tue Nov 17 2009 - 00:24:30 PST)
[AMBER] zeros in excluded atom list in topology file
Bill Ross
(Fri Nov 06 2009 - 16:09:39 PST)
Peter Schmidtke
(Fri Nov 06 2009 - 16:07:44 PST)
case
(Fri Nov 06 2009 - 14:44:04 PST)
Peter Schmidtke
(Fri Nov 06 2009 - 00:54:57 PST)
Carlos Simmerling
(Thu Nov 05 2009 - 16:39:56 PST)
Peter Schmidtke
(Thu Nov 05 2009 - 09:06:41 PST)
[AMBER]Amber10 + g95
jacky zhao
(Tue Nov 17 2009 - 00:26:56 PST)
Abhishek Banerjee
(Sat Nov 07 2009 - 19:41:54 PST)
Sudeep Narayan Banerjee
(Sat Nov 07 2009 - 18:56:39 PST)
Etot positive
Jio M
(Mon Nov 16 2009 - 20:59:26 PST)
How to compile and recompile ptraj?
case
(Sun Nov 29 2009 - 17:41:24 PST)
cyk5056
(Sun Nov 29 2009 - 14:53:37 PST)
MM_PBSA error
Ray Luo
(Sat Nov 28 2009 - 10:07:26 PST)
Jagdeesh C
(Fri Nov 27 2009 - 02:13:36 PST)
Mengjuei Hsieh
(Fri Nov 27 2009 - 01:39:54 PST)
Jagdeesh C
(Fri Nov 27 2009 - 01:20:27 PST)
question
rrd
(Thu Nov 05 2009 - 16:09:11 PST)
Marek Maly
(Thu Nov 05 2009 - 05:28:03 PST)
steinbrt.rci.rutgers.edu
(Thu Nov 05 2009 - 00:12:47 PST)
rrd
(Wed Nov 04 2009 - 18:52:04 PST)
Marek Maly
(Tue Nov 03 2009 - 12:22:16 PST)
Ross Walker
(Mon Nov 02 2009 - 15:36:48 PST)
RESP with -a and witout -a flag
Jio M
(Tue Nov 03 2009 - 22:47:55 PST)
Junmei Wang
(Mon Nov 02 2009 - 08:48:48 PST)
Jio M
(Sun Nov 01 2009 - 21:58:58 PST)
Verlet update time in explicit water Replica Exchange MD
Da-Wei Li
(Wed Nov 25 2009 - 09:12:23 PST)
回复： [AMBER] the different RMSD?
Rilei Yu
(Tue Nov 17 2009 - 21:25:17 PST)
Last message date
:
Mon Nov 30 2009 - 22:30:02 PST
Archived on
: Fri Apr 19 2024 - 05:53:42 PDT
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