Amber Archive Oct 2009 by thread
481 messages
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Starting
Wed Sep 30 2009 - 12:00:02 PDT,
Ending
Sat Oct 31 2009 - 16:00:02 PDT
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[AMBER] xleap problem !
balaji nagarajan
(Wed Sep 30 2009 - 11:40:58 PDT)
Re: [AMBER] trouble using iAPBS
Oliver Kuhn
(Thu Oct 01 2009 - 04:31:51 PDT)
Re: [AMBER] trouble using iAPBS
Robert Konecny
(Thu Oct 01 2009 - 10:27:42 PDT)
[AMBER] decomposing energies
Beroza, Paul
(Thu Oct 01 2009 - 09:15:07 PDT)
[AMBER] Environment Variables in Cygwin Don't Remain
Wallace Kunin
(Thu Oct 01 2009 - 09:54:29 PDT)
Re: [AMBER] Environment Variables in Cygwin Don't Remain
Jack Shultz
(Thu Oct 01 2009 - 10:12:19 PDT)
Re: [AMBER] Environment Variables in Cygwin Don't Remain
Bill Ross
(Thu Oct 01 2009 - 11:57:43 PDT)
[AMBER] method used to determine partial charges?
Paul Brandt
(Thu Oct 01 2009 - 13:25:54 PDT)
Re: [AMBER] method used to determine partial charges?
Jihang Wang
(Thu Oct 01 2009 - 13:36:31 PDT)
Re: [AMBER] method used to determine partial charges?
Bill Ross
(Thu Oct 01 2009 - 14:19:29 PDT)
Re: [AMBER] method used to determine partial charges?
Jihang Wang
(Thu Oct 01 2009 - 14:28:45 PDT)
Re: [AMBER] method used to determine partial charges?
Bill Ross
(Thu Oct 01 2009 - 15:18:01 PDT)
Re: [AMBER] method used to determine partial charges?
Jihang Wang
(Thu Oct 01 2009 - 15:26:24 PDT)
Re: [AMBER] method used to determine partial charges?
Carlos Simmerling
(Thu Oct 01 2009 - 15:30:21 PDT)
Re: [AMBER] method used to determine partial charges?
Jihang Wang
(Thu Oct 01 2009 - 15:42:38 PDT)
Re: [AMBER] method used to determine partial charges?
FyD
(Thu Oct 01 2009 - 21:27:13 PDT)
[AMBER] Dipole moment visualization.
K.R.
(Thu Oct 01 2009 - 14:37:29 PDT)
[AMBER] red problem
James Moore
(Thu Oct 01 2009 - 18:52:46 PDT)
Re: [AMBER] red problem
FyD
(Thu Oct 01 2009 - 21:48:57 PDT)
[AMBER] Protein and charged surface
rrd
(Thu Oct 01 2009 - 20:49:18 PDT)
[AMBER] Different optimized structures with HF and B3LYP
Sanghwa Han
(Fri Oct 02 2009 - 00:50:10 PDT)
Re: [AMBER] Different optimized structures with HF and B3LYP
Karl Kirschner
(Fri Oct 02 2009 - 01:07:08 PDT)
[AMBER] MM_PBSA decomposition pair question
Rubben Torella
(Fri Oct 02 2009 - 04:09:38 PDT)
[AMBER] minimization error
balaji nagarajan
(Fri Oct 02 2009 - 04:42:54 PDT)
Re: [AMBER] minimization error
case
(Fri Oct 02 2009 - 05:00:52 PDT)
Re: [AMBER] Compiling Amber with gfortran-4.5.0 on a mac
case
(Fri Oct 02 2009 - 06:19:11 PDT)
Re: [AMBER] Compiling Amber with gfortran-4.5.0 on a mac
Ben Roberts
(Fri Oct 02 2009 - 07:20:47 PDT)
Re: [AMBER] Compiling Amber with gfortran-4.5.0 on a mac
Mengjuei Hsieh
(Tue Oct 06 2009 - 19:05:54 PDT)
[AMBER] Missing X11 Libraries
Wallace Kunin
(Fri Oct 02 2009 - 09:43:59 PDT)
[AMBER] Re: Missing X11 Libraries
Wallace Kunin
(Fri Oct 02 2009 - 09:55:34 PDT)
Re: [AMBER] Missing X11 Libraries
case
(Fri Oct 02 2009 - 11:56:34 PDT)
Re: [AMBER] Missing X11 Libraries
Wallace Kunin
(Fri Oct 02 2009 - 12:57:49 PDT)
Re: [AMBER] Missing X11 Libraries
Wallace Kunin
(Sat Oct 03 2009 - 10:02:05 PDT)
[AMBER] File format for reading in charges in antechamber
Dean Cuebas
(Sun Oct 04 2009 - 13:20:42 PDT)
Re: [AMBER] Missing X11 Libraries
Wallace Kunin
(Wed Oct 07 2009 - 11:04:39 PDT)
Re: [AMBER] Missing X11 Libraries
Mengjuei Hsieh
(Wed Oct 07 2009 - 13:19:20 PDT)
Re: [AMBER] Missing X11 Libraries
FyD
(Wed Oct 07 2009 - 13:45:34 PDT)
Re: [AMBER] Missing X11 Libraries
Wallace Kunin
(Wed Oct 07 2009 - 14:10:34 PDT)
Re: [AMBER] Missing X11 Libraries
Thomas Patko
(Wed Oct 07 2009 - 14:14:15 PDT)
Re: [AMBER] Missing X11 Libraries
Bill Ross
(Wed Oct 07 2009 - 15:28:34 PDT)
Re: [AMBER] Missing X11 Libraries
Wallace Kunin
(Thu Oct 08 2009 - 10:09:55 PDT)
Re: [AMBER] Missing X11 Libraries
Thomas Patko
(Thu Oct 08 2009 - 10:26:26 PDT)
Re: [AMBER] Missing X11 Libraries
Wallace Kunin
(Fri Oct 09 2009 - 09:59:06 PDT)
Re: [AMBER] Missing X11 Libraries
Wallace Kunin
(Fri Oct 09 2009 - 10:03:51 PDT)
Re: [AMBER] Missing X11 Libraries
Thomas Patko
(Fri Oct 09 2009 - 10:13:22 PDT)
Re: [AMBER] Missing X11 Libraries
Bill Ross
(Thu Oct 08 2009 - 10:25:32 PDT)
Re: [AMBER] Missing X11 Libraries
Bill Ross
(Fri Oct 09 2009 - 10:52:01 PDT)
Re: [AMBER] Missing X11 Libraries
Wallace Kunin
(Fri Oct 09 2009 - 12:20:00 PDT)
Re: [AMBER] Missing X11 Libraries
case
(Fri Oct 09 2009 - 13:02:06 PDT)
Re: [AMBER] Missing X11 Libraries
FyD
(Fri Oct 09 2009 - 13:35:59 PDT)
Re: [AMBER] Missing X11 Libraries
Thomas Patko
(Fri Oct 09 2009 - 13:53:14 PDT)
Re: [AMBER] Missing X11 Libraries
FyD
(Fri Oct 09 2009 - 14:06:20 PDT)
Re: [AMBER] Missing X11 Libraries
Bill Ross
(Fri Oct 09 2009 - 17:24:47 PDT)
[AMBER] RMSD vs time and RMSD vs residues
Olotu Odunayo
(Fri Oct 02 2009 - 10:40:40 PDT)
Re: [AMBER] RMSD vs time and RMSD vs residues
Luis Gracia
(Fri Oct 02 2009 - 11:07:10 PDT)
Re: [AMBER] RMSD vs time and RMSD vs residues
case
(Fri Oct 02 2009 - 12:12:23 PDT)
Re: [AMBER] RMSD vs time and RMSD vs residues
Sally Pias
(Fri Oct 02 2009 - 12:16:33 PDT)
[AMBER] probelm-APBS
Rilei Yu
(Fri Oct 02 2009 - 22:41:07 PDT)
Re: [AMBER] probelm-APBS
Robert Konecny
(Sun Oct 04 2009 - 17:20:18 PDT)
Re: [AMBER] probelm-APBS
Rilei Yu
(Sun Oct 04 2009 - 17:51:10 PDT)
[AMBER] MMPBSA: No radius found for F
Jeff Yeo
(Sun Oct 04 2009 - 17:10:12 PDT)
[AMBER] TiO2 modeling
stefano_elli.libero.it
(Mon Oct 05 2009 - 09:00:59 PDT)
[AMBER] new process_mdout.pl script????
Dean Cuebas
(Mon Oct 05 2009 - 11:11:49 PDT)
RE: [AMBER] new process_mdout.pl script????
Ross Walker
(Mon Oct 05 2009 - 11:38:17 PDT)
[AMBER] R.E.D.-III.3 tools release - q4md-forcefieldtools.org
FyD
(Sun Oct 04 2009 - 07:37:06 PDT)
[AMBER] pucker calculation for six member rings
Ganesh Kamath
(Mon Oct 05 2009 - 11:03:15 PDT)
[AMBER] MM/PBSA: NaN, Infinity and ************* in snapshot_com.all.out
Jeff Yeo
(Mon Oct 05 2009 - 16:22:53 PDT)
Re: [AMBER] MM/PBSA: NaN, Infinity and ************* in snapshot_com.all.out
Rubben Torella
(Tue Oct 06 2009 - 00:56:18 PDT)
[AMBER] MM_PBSA: abnormal VDW interaction energy
LIU Huanxiang
(Mon Oct 05 2009 - 19:43:21 PDT)
Re: [AMBER] MM_PBSA: abnormal VDW interaction energy
steinbrt.rci.rutgers.edu
(Tue Oct 06 2009 - 01:09:27 PDT)
Re: [AMBER] MM_PBSA: abnormal VDW interaction energy
LIU Huanxiang
(Tue Oct 06 2009 - 19:54:49 PDT)
[AMBER] mm_pbsa- Decomposition: bad atom type
Antonija Tomić
(Tue Oct 06 2009 - 06:53:25 PDT)
[AMBER] Problem with memory in nmode analysis
Alireza Shaneh
(Tue Oct 06 2009 - 08:23:55 PDT)
Re: [AMBER] DMF solvent box
Abhishek Banerjee
(Tue Oct 06 2009 - 21:10:22 PDT)
Re: [AMBER] DMF solvent box
FyD
(Wed Oct 07 2009 - 13:34:35 PDT)
Re: [AMBER] DMF solvent box
Abhishek Banerjee
(Thu Oct 08 2009 - 20:41:02 PDT)
Re: [AMBER] DMF solvent box
FyD
(Thu Oct 08 2009 - 21:08:59 PDT)
[AMBER] using RESP program
gunajyoti das
(Wed Oct 07 2009 - 03:30:27 PDT)
Re: [AMBER] using RESP program
Ganesh Kamath
(Wed Oct 07 2009 - 03:36:13 PDT)
Re: [AMBER] using RESP program
FyD
(Wed Oct 07 2009 - 13:04:38 PDT)
[AMBER] Re: Fw: Help required in Amber10 Installation
Sudeep Narayan Banerjee
(Wed Oct 07 2009 - 08:48:02 PDT)
Re: [AMBER] Re: Fw: Help required in Amber10 Installation
David Watson
(Wed Oct 07 2009 - 08:53:26 PDT)
Re: [AMBER] Re: Fw: Help required in Amber10 Installation
Sudeep Narayan Banerjee
(Thu Oct 15 2009 - 06:30:25 PDT)
Re: [AMBER] Re: Fw: Help required in Amber10 Installation
case
(Thu Oct 15 2009 - 06:45:42 PDT)
Re: [AMBER] Re: Fw: Help required in Amber10 Installation
Bill Ross
(Thu Oct 15 2009 - 09:28:26 PDT)
Re: [AMBER] Using idecomp=3 with igb=10 (PB)
Chris Whittleston
(Wed Oct 07 2009 - 09:57:25 PDT)
Re: [AMBER] Using idecomp=3 with igb=10 (PB)
Chris Whittleston
(Thu Oct 08 2009 - 03:47:22 PDT)
Re: [AMBER] Using idecomp=3 with igb=10 (PB)
Hannes Kopitz
(Thu Oct 08 2009 - 13:30:19 PDT)
Re: [AMBER] Using idecomp=3 with igb=10 (PB)
Chris Whittleston
(Fri Oct 09 2009 - 08:16:53 PDT)
Re: [AMBER] Using idecomp=3 with igb=10 (PB)
Hannes Kopitz
(Sun Oct 11 2009 - 14:13:45 PDT)
Re: [AMBER] Using idecomp=3 with igb=10 (PB)
Chris Whittleston
(Mon Oct 12 2009 - 08:56:06 PDT)
Re: [AMBER] Using idecomp=3 with igb=10 (PB)
Hannes Kopitz
(Mon Oct 12 2009 - 12:51:23 PDT)
Re: [AMBER] Using idecomp=3 with igb=10 (PB)
Chris Whittleston
(Tue Oct 13 2009 - 03:02:17 PDT)
Re: [AMBER] Re: Fw: Help required in Amber10 Installation
Bill Ross
(Wed Oct 07 2009 - 09:59:21 PDT)
Re: [AMBER] Re: Fw: Help required in Amber10 Installation
Chris Whittleston
(Wed Oct 07 2009 - 10:48:18 PDT)
Re: [AMBER] Re: Fw: Help required in Amber10 Installation
Sudeep Narayan Banerjee
(Thu Oct 15 2009 - 05:11:01 PDT)
Re: [AMBER] Re: Fw: Help required in Amber10 Installation
Nicolas Sapay
(Thu Oct 15 2009 - 05:34:28 PDT)
Re: [AMBER] Re: Fw: Help required in Amber10 Installation
Sudeep Narayan Banerjee
(Thu Oct 15 2009 - 05:53:42 PDT)
Re: [AMBER] Re: Fw: Help required in Amber10 Installation
Jason Swails
(Thu Oct 15 2009 - 05:55:31 PDT)
Re: [AMBER] Re: Fw: Help required in Amber10 Installation
Jason Swails
(Thu Oct 15 2009 - 06:01:38 PDT)
Re: [AMBER] Re: Fw: Help required in Amber10 Installation
Sudeep Narayan Banerjee
(Thu Oct 15 2009 - 06:13:27 PDT)
Re: [AMBER] Re: Fw: Help required in Amber10 Installation
Abhishek Banerjee
(Thu Oct 15 2009 - 08:51:56 PDT)
[AMBER] Combine and rename group of residues in xleap
Lili Peng
(Wed Oct 07 2009 - 14:49:23 PDT)
Re: [AMBER] Combine and rename group of residues in xleap
case
(Fri Oct 09 2009 - 06:32:57 PDT)
[AMBER] The hydrophobic contribution
Rilei Yu
(Wed Oct 07 2009 - 22:48:32 PDT)
Re: [AMBER] The hydrophobic contribution
case
(Thu Oct 08 2009 - 05:41:28 PDT)
Re: [AMBER] solvent accessible surface area
Siddharth Rastogi
(Thu Oct 08 2009 - 02:54:01 PDT)
Re: [AMBER] solvent accessible surface area
Ray Luo
(Thu Oct 08 2009 - 11:17:09 PDT)
[AMBER] solvent accessible surface area
Siddharth Rastogi
(Thu Oct 08 2009 - 03:02:20 PDT)
[AMBER] Fwd: Group specification
Pavan G
(Thu Oct 08 2009 - 11:30:09 PDT)
Re: [AMBER] Fwd: Group specification
Carlos Simmerling
(Thu Oct 08 2009 - 11:35:43 PDT)
Re: [AMBER] Fwd: Group specification
Bill Ross
(Thu Oct 08 2009 - 13:15:44 PDT)
Re: [AMBER] Fwd: Group specification
Bill Ross
(Thu Oct 08 2009 - 13:22:54 PDT)
[AMBER] RE: VDW and TI for free energy
Ross Walker
(Thu Oct 08 2009 - 17:43:48 PDT)
[AMBER] ff03 parameter for GDP and GTP
mmg8.ualberta.ca
(Thu Oct 08 2009 - 18:05:18 PDT)
Re: [AMBER] ff03 parameter for GDP and GTP
FyD
(Fri Oct 09 2009 - 03:37:40 PDT)
Re: [AMBER] ff03 parameter for GDP and GTP
Carlos Simmerling
(Fri Oct 09 2009 - 05:45:04 PDT)
Re: [AMBER] ff03 parameter for GDP and GTP
case
(Fri Oct 09 2009 - 06:03:02 PDT)
Re: [AMBER] ff03 parameter for GDP and GTP
Carlos Simmerling
(Fri Oct 09 2009 - 06:09:32 PDT)
Re: [AMBER] ff03 parameter for GDP and GTP
FyD
(Fri Oct 09 2009 - 22:52:27 PDT)
Re: [AMBER] ff03 parameter for GDP and GTP
Carlos Simmerling
(Sat Oct 10 2009 - 04:36:35 PDT)
Re: [AMBER] ff03 parameter for GDP and GTP
FyD
(Sun Oct 11 2009 - 04:42:25 PDT)
Re: [AMBER] ff03 parameter for GDP and GTP
mmg8.ualberta.ca
(Fri Oct 09 2009 - 07:30:46 PDT)
Re: [AMBER] ff03 parameter for GDP and GTP
FyD
(Fri Oct 09 2009 - 13:38:08 PDT)
[AMBER] Some queries about pH simulation
nicholus bhattacharjee
(Thu Oct 08 2009 - 21:36:56 PDT)
Re: [AMBER] Some queries about pH simulation
Jason Swails
(Fri Oct 09 2009 - 11:48:44 PDT)
Re: [AMBER] Some queries about pH simulation
Carlos Simmerling
(Fri Oct 09 2009 - 11:59:17 PDT)
Re: [AMBER] Some queries about pH simulation
nicholus bhattacharjee
(Fri Oct 09 2009 - 22:07:21 PDT)
[AMBER] DG improper torsion problem, two missing parameters
Youn Kyeung Lee
(Fri Oct 09 2009 - 00:02:03 PDT)
Re: [AMBER] DG improper torsion problem, two missing parameters
case
(Fri Oct 09 2009 - 04:46:34 PDT)
[AMBER] Distance Replica Exchange
Steve Seibold
(Fri Oct 09 2009 - 06:18:44 PDT)
Re: [AMBER] Distance Replica Exchange
Carlos Simmerling
(Fri Oct 09 2009 - 06:40:17 PDT)
RE: [AMBER] Distance Replica Exchange
Steve Seibold
(Fri Oct 09 2009 - 07:21:13 PDT)
Re: [AMBER] DG improper torsion problem, two missing parameters
Bill Ross
(Fri Oct 09 2009 - 10:25:30 PDT)
[AMBER] The -c option in Sander
phani ghanakota
(Fri Oct 09 2009 - 17:47:18 PDT)
Re: [AMBER] The -c option in Sander
case
(Fri Oct 09 2009 - 18:54:05 PDT)
[AMBER] RE: VDW and TI for free energy
Qicun Shi
(Fri Oct 09 2009 - 19:00:08 PDT)
Re: [AMBER] RE: VDW and TI for free energy
steinbrt.rci.rutgers.edu
(Sat Oct 10 2009 - 01:44:31 PDT)
Re: [AMBER] RE: VDW and TI for free energy
Qicun Shi
(Sat Oct 10 2009 - 21:05:20 PDT)
[AMBER] decomposition and calculation of entropy
Qinghua Liao
(Fri Oct 09 2009 - 23:13:49 PDT)
[AMBER] xleap-does not work
Rilei Yu
(Sat Oct 10 2009 - 01:30:06 PDT)
Re: [AMBER] xleap-does not work
case
(Sat Oct 10 2009 - 05:27:01 PDT)
Re: [AMBER] xleap-does not work
Rilei Yu
(Sat Oct 10 2009 - 06:35:53 PDT)
Re: [AMBER] xleap-does not work
case
(Sat Oct 10 2009 - 06:53:57 PDT)
Re: [AMBER] xleap-does not work(Being solved!)
Rilei Yu
(Sat Oct 10 2009 - 07:13:28 PDT)
Re: [AMBER] xleap-does not work
Jason Swails
(Sat Oct 10 2009 - 10:08:08 PDT)
Re: [AMBER] xleap-does not work
Rilei Yu
(Sun Oct 11 2009 - 04:01:07 PDT)
[AMBER] A bug in LEaP ?
FyD
(Sun Oct 11 2009 - 05:08:37 PDT)
[AMBER] Energy-from-MM/PBSA-VS-experiment
Rilei Yu
(Sun Oct 11 2009 - 05:53:00 PDT)
Re: [AMBER] Energy-from-MM/PBSA-VS-experiment
Jason Swails
(Sun Oct 11 2009 - 07:54:08 PDT)
Re: [AMBER] Energy-from-MM/PBSA-VS-experiment
Rilei Yu
(Sun Oct 11 2009 - 15:51:26 PDT)
[AMBER] S-S problem-in protein
Rilei Yu
(Sun Oct 11 2009 - 18:53:24 PDT)
Re: [AMBER] S-S problem-in protein
Jason Swails
(Sun Oct 11 2009 - 19:15:10 PDT)
Re: [AMBER] S-S problem-in protein
Jason Swails
(Sun Oct 11 2009 - 21:24:51 PDT)
Re: [AMBER] S-S problem-in protein
Rilei Yu
(Sun Oct 11 2009 - 23:28:14 PDT)
Re: [AMBER] S-S problem-in protein
Rilei Yu
(Mon Oct 12 2009 - 02:16:15 PDT)
Re: [AMBER] S-S problem-in protein
Jason Swails
(Mon Oct 12 2009 - 04:23:25 PDT)
Re: [AMBER] S-S problem-in protein
Rilei Yu
(Mon Oct 12 2009 - 15:14:02 PDT)
[AMBER] unit converter for force constants
GÜL ALTINBAŞ
(Mon Oct 12 2009 - 05:22:00 PDT)
[AMBER] unit convertion for force constants
GÜL ALTINBAŞ
(Mon Oct 12 2009 - 05:47:42 PDT)
Re: [AMBER] unit convertion for force constants
vhakkim boy
(Mon Oct 12 2009 - 06:26:05 PDT)
[AMBER] OpenMP
Ben Roberts
(Mon Oct 12 2009 - 10:35:35 PDT)
RE: [AMBER] OpenMP
Ross Walker
(Mon Oct 12 2009 - 11:29:45 PDT)
Re: [AMBER] OpenMP
michael
(Tue Oct 13 2009 - 07:43:09 PDT)
[AMBER] Simulating transmembrane protein.
Jayalakshmi Sridhar
(Mon Oct 12 2009 - 11:42:11 PDT)
Re: [AMBER] Simulating transmembrane protein.
case
(Mon Oct 12 2009 - 14:55:42 PDT)
[AMBER] Is iwrap mapping water molecules to my protein cavity?
ben rodriguez
(Mon Oct 12 2009 - 11:55:23 PDT)
Re: [AMBER] Is iwrap mapping water molecules to my protein cavity?
Carlos Simmerling
(Mon Oct 12 2009 - 12:28:12 PDT)
Re: [AMBER] Simulating transmembrane protein.
Bill Ross
(Mon Oct 12 2009 - 12:04:36 PDT)
Re: [AMBER] Simulating transmembrane protein.
Jayalakshmi Sridhar
(Mon Oct 12 2009 - 12:57:02 PDT)
Re: [AMBER] Simulating transmembrane protein.
Bill Ross
(Mon Oct 12 2009 - 15:37:50 PDT)
Re: [AMBER] Is iwrap mapping water molecules to my protein cavity?
Bill Ross
(Mon Oct 12 2009 - 12:12:19 PDT)
Re: [AMBER] nasty memory bug in calculatePrincipalAxis
Scott Brozell
(Mon Oct 12 2009 - 14:38:06 PDT)
[AMBER] Computing an Hessian matrix using NAB
Brut Marie
(Mon Oct 12 2009 - 15:12:44 PDT)
Re: [AMBER] Computing an Hessian matrix using NAB
case
(Tue Oct 13 2009 - 05:13:42 PDT)
Re: [AMBER] Computing an Hessian matrix using NAB
Brut Marie
(Tue Oct 13 2009 - 11:56:19 PDT)
Re: [AMBER] Computing an Hessian matrix using NAB
Brut Marie
(Tue Oct 13 2009 - 12:00:53 PDT)
[AMBER] How to prepare the acetate ion file in leap?
xuemeiwang1103
(Tue Oct 13 2009 - 00:05:57 PDT)
Re: [AMBER] How to prepare the acetate ion file in leap?
Balazs Jojart
(Tue Oct 13 2009 - 00:36:03 PDT)
[AMBER] "Cannot open file ATOMTYPE.INF, exit" when using antechamber
haifeng yuan
(Tue Oct 13 2009 - 00:44:55 PDT)
Re: [AMBER] "Cannot open file ATOMTYPE.INF, exit" when using antechamber
case
(Wed Oct 14 2009 - 04:37:35 PDT)
[AMBER] iAPBS - how to set the right grid dimensions
Oliver Kuhn
(Tue Oct 13 2009 - 01:36:27 PDT)
Re: [AMBER] iAPBS - how to set the right grid dimensions
Robert Konecny
(Tue Oct 13 2009 - 07:42:12 PDT)
Re: [AMBER] iAPBS - how to set the right grid dimensions
Oliver Kuhn
(Tue Oct 13 2009 - 08:17:06 PDT)
Re: [AMBER] iAPBS - how to set the right grid dimensions
Robert Konecny
(Tue Oct 13 2009 - 10:12:04 PDT)
Re: [AMBER] iAPBS - how to set the right grid dimensions
Oliver Kuhn
(Wed Oct 14 2009 - 06:16:28 PDT)
Re: [AMBER] iAPBS - how to set the right grid dimensions
Robert Konecny
(Wed Oct 14 2009 - 06:21:07 PDT)
[AMBER] LES and NEB problem
Rima Chaudhuri
(Tue Oct 13 2009 - 12:35:37 PDT)
Re: [AMBER] LES and NEB problem
Carlos Simmerling
(Wed Oct 14 2009 - 07:14:04 PDT)
Re: [AMBER] LES and NEB problem
Rima Chaudhuri
(Thu Oct 15 2009 - 09:50:08 PDT)
Re: [AMBER] LES and NEB problem
Carlos Simmerling
(Thu Oct 15 2009 - 09:54:18 PDT)
Re: [AMBER] LES and NEB problem
Rima Chaudhuri
(Thu Oct 15 2009 - 10:53:41 PDT)
Re: [AMBER] LES and NEB problem
Jason Swails
(Thu Oct 15 2009 - 11:09:14 PDT)
Re: [AMBER] LES and NEB problem
Carlos Simmerling
(Thu Oct 15 2009 - 11:09:34 PDT)
[AMBER] mean square displacment
Nancy
(Tue Oct 13 2009 - 16:59:15 PDT)
Re: [AMBER] mean square displacment
Bill Ross
(Tue Oct 13 2009 - 17:09:49 PDT)
[Amber]AMBER: MM_PBSA problems in AMBER10
He Hongqing
(Tue Oct 13 2009 - 20:43:57 PDT)
回复： [Amber]AMBER: MM_PBSA problems in AMBER10
Rilei Yu
(Tue Oct 13 2009 - 22:47:02 PDT)
Re: 回复： [Amber]AMBER: MM_PBSA problems in AMBER10
He Hongqing
(Wed Oct 14 2009 - 00:32:25 PDT)
Re: 回复： [Amber]AMBER: MM_PBSA problems in AMBER10
Rilei Yu
(Wed Oct 14 2009 - 01:18:34 PDT)
Re: [Amber]AMBER: MM_PBSA problems in AMBER10
Ray Luo
(Wed Oct 14 2009 - 09:48:48 PDT)
[AMBER] How to add a hydrogen to the residue?
xuemeiwang1103
(Tue Oct 13 2009 - 20:57:53 PDT)
Re: [AMBER] How to add a hydrogen to the residue?
case
(Wed Oct 14 2009 - 04:51:08 PDT)
Re: Re: 回复： [Amber]AMBER: MM_PBSA problemsin AMBER10
He Hongqing
(Wed Oct 14 2009 - 01:39:33 PDT)
Re: Re: 回复： [Amber]AMBER: MM_PBSA problemsin AMBER10
Qinghua Liao
(Wed Oct 14 2009 - 02:22:41 PDT)
Re: Re: Re: 回复： [Amber]AMBER: MM_PBSA problemsin AMBER10
Bill Ross
(Wed Oct 14 2009 - 09:56:41 PDT)
[AMBER] Add the hydrogen to the carboxyl of the GLU residue?
xuemeiwang1103
(Wed Oct 14 2009 - 05:05:48 PDT)
Re: [AMBER] Add the hydrogen to the carboxyl of the GLU residue?
Andrew Purkiss-Trew
(Wed Oct 14 2009 - 05:19:43 PDT)
Re: [AMBER] Add the hydrogen to the carboxyl of the GLU residue?
FyD
(Wed Oct 14 2009 - 06:40:09 PDT)
Re: [AMBER] Add the hydrogen to the carboxyl of the GLU residue?
Carlos Simmerling
(Wed Oct 14 2009 - 06:49:00 PDT)
[AMBER] ptraj and prmtop
Beale, John
(Wed Oct 14 2009 - 05:46:11 PDT)
Re: [AMBER] ptraj and prmtop
Carlos Simmerling
(Wed Oct 14 2009 - 06:41:04 PDT)
[AMBER] six member pucker calculation
Ganesh Kamath
(Wed Oct 14 2009 - 07:27:24 PDT)
[AMBER] nab normal mode analysis has imaginary frequencies
Junmei Wang
(Wed Oct 14 2009 - 09:05:06 PDT)
Re: [AMBER] nab normal mode analysis has imaginary frequencies
case
(Wed Oct 14 2009 - 11:34:05 PDT)
[AMBER] installation of Amber on OSX
Ramgopal Mettu
(Wed Oct 14 2009 - 14:46:59 PDT)
Re: [AMBER] installation of Amber on OSX
David Watson
(Wed Oct 14 2009 - 15:03:51 PDT)
Re: [AMBER] installation of Amber on OSX
case
(Wed Oct 14 2009 - 15:10:04 PDT)
Re: [AMBER] installation of Amber on OSX
Jason Swails
(Wed Oct 14 2009 - 15:41:31 PDT)
[AMBER] Simulated annealing
waleed zalloum
(Thu Oct 15 2009 - 03:59:29 PDT)
Re: [AMBER] Simulated annealing
Carlos Simmerling
(Thu Oct 15 2009 - 04:43:56 PDT)
[AMBER] part of the protein escaped from the water box
qiaoyan
(Thu Oct 15 2009 - 04:33:00 PDT)
Re: [AMBER] part of the protein escaped from the water box
Carlos Simmerling
(Thu Oct 15 2009 - 04:39:40 PDT)
Re: [AMBER] part of the protein escaped from the water box
case
(Thu Oct 15 2009 - 04:40:53 PDT)
Re: [AMBER] part of the protein escaped from the water box
Jason Swails
(Thu Oct 15 2009 - 04:43:00 PDT)
[AMBER] Large File Support
Beale, John
(Thu Oct 15 2009 - 05:40:27 PDT)
RE: [AMBER] Large File Support
Ross Walker
(Thu Oct 15 2009 - 11:14:01 PDT)
[AMBER] AMBER 11.
Peter Winn
(Thu Oct 15 2009 - 09:27:39 PDT)
Re: [AMBER] AMBER 11.
case
(Thu Oct 15 2009 - 09:52:51 PDT)
[AMBER] B-factor
Cristina Sisu
(Thu Oct 15 2009 - 10:04:25 PDT)
Re: [AMBER] B-factor
Thomas Cheatham III
(Fri Oct 16 2009 - 15:16:35 PDT)
Re: [AMBER] B-factor
Cristina Sisu
(Sat Oct 17 2009 - 03:58:34 PDT)
[AMBER] Time scale of the Protein domain motion ?
Chih-Ying Lin
(Sat Oct 17 2009 - 12:18:34 PDT)
Re: [AMBER] Time scale of the Protein domain motion ?
Carlos Simmerling
(Sat Oct 17 2009 - 12:23:34 PDT)
Re: [AMBER] Time scale of the Protein domain motion ?
Chih-Ying Lin
(Sat Oct 17 2009 - 12:36:18 PDT)
Re: [AMBER] Time scale of the Protein domain motion ?
Carlos Simmerling
(Sat Oct 17 2009 - 12:42:01 PDT)
Re: [AMBER] Time scale of the Protein domain motion ?
Chih-Ying Lin
(Sat Oct 17 2009 - 12:46:37 PDT)
[AMBER] cross correlation analysis with ptraj
Junmei Wang
(Thu Oct 15 2009 - 09:49:29 PDT)
[AMBER] question with pucker in six member ring
Ganesh Kamath
(Thu Oct 15 2009 - 12:55:45 PDT)
Re: [AMBER] question with pucker in six member ring
Nicolas Sapay
(Fri Oct 16 2009 - 08:04:24 PDT)
Re: [AMBER] question with pucker in six member ring
Thomas Cheatham III
(Fri Oct 16 2009 - 11:23:05 PDT)
Re: [AMBER] question with pucker in six member ring
Ganesh Kamath
(Fri Oct 16 2009 - 11:36:41 PDT)
Re: [AMBER] question with pucker in six member ring
Bill Ross
(Fri Oct 16 2009 - 11:43:56 PDT)
Re: [AMBER] question with pucker in six member ring
Ganesh Kamath
(Fri Oct 16 2009 - 12:31:31 PDT)
Re: [AMBER] question with pucker in six member ring
Bill Ross
(Fri Oct 16 2009 - 12:48:04 PDT)
Re: [AMBER] question with pucker in six member ring
Ganesh Kamath
(Mon Oct 19 2009 - 10:42:17 PDT)
Re: [AMBER] question with pucker in six member ring
Bill Ross
(Mon Oct 19 2009 - 10:54:03 PDT)
[AMBER] why is TAUTP scaled by "e" ?
Jose Borreguero
(Thu Oct 15 2009 - 13:49:18 PDT)
RE: [AMBER] why is TAUTP scaled by "e" ?
Ross Walker
(Thu Oct 15 2009 - 15:08:52 PDT)
Re: [AMBER] why is TAUTP scaled by "e" ?
case
(Fri Oct 16 2009 - 06:30:53 PDT)
Re: [AMBER] why is TAUTP scaled by "e" ?
Jose Borreguero
(Fri Oct 16 2009 - 12:13:42 PDT)
[AMBER] eigenvalues add up to more than trace of matrix
Yaw Sing TAN
(Thu Oct 15 2009 - 20:14:59 PDT)
Re: [AMBER] eigenvalues add up to more than trace of matrix
Jason Swails
(Fri Oct 16 2009 - 06:29:13 PDT)
Re: [AMBER] eigenvalues add up to more than trace of matrix
Hannes Loeffler
(Fri Oct 16 2009 - 06:50:50 PDT)
[AMBER] How to introduce the second protein molecule into simulation box?
Siddharth Rastogi
(Fri Oct 16 2009 - 00:00:03 PDT)
Re: [AMBER] How to introduce the second protein molecule into simulation box?
Jason Swails
(Fri Oct 16 2009 - 06:15:57 PDT)
[AMBER] Re: AMBER: periodic bondary condition
Markus Kaukonen
(Fri Oct 16 2009 - 00:38:03 PDT)
Re: [AMBER] Re: AMBER: periodic bondary condition
case
(Fri Oct 16 2009 - 06:13:49 PDT)
Re: [AMBER] Re: AMBER: periodic bondary condition
Markus Kaukonen
(Mon Oct 26 2009 - 01:14:48 PDT)
[AMBER] binding energy
Simon Becker
(Fri Oct 16 2009 - 02:28:39 PDT)
Re: [AMBER] binding energy
steinbrt.rci.rutgers.edu
(Fri Oct 16 2009 - 04:27:24 PDT)
[AMBER] MMTSB cluster analysis versus ptraj cluster analysis
Cenk \(Jenk\) Andac
(Fri Oct 16 2009 - 05:19:24 PDT)
Re: [AMBER] MMTSB cluster analysis versus ptraj cluster analysis
Thomas Cheatham III
(Fri Oct 16 2009 - 08:33:22 PDT)
Re: [AMBER] MMTSB cluster analysis versus ptraj cluster analysis
Cenk \(Jenk\) Andac
(Sat Oct 17 2009 - 00:02:20 PDT)
Re: [AMBER] MMTSB cluster analysis versus ptraj cluster analysis
Jianyin Shao
(Mon Oct 19 2009 - 11:16:47 PDT)
Re: [AMBER] MMTSB cluster analysis versus ptraj cluster analysis
Cenk \(Jenk\) Andac
(Mon Oct 19 2009 - 14:44:42 PDT)
[AMBER] AMBER FF and NAMD
stefano_elli\.libero\.it
(Fri Oct 16 2009 - 07:26:14 PDT)
Re: [AMBER] AMBER FF and NAMD
Hannes Loeffler
(Fri Oct 16 2009 - 07:45:25 PDT)
Re: [AMBER] AMBER FF and NAMD
Nicolas Sapay
(Fri Oct 16 2009 - 07:59:53 PDT)
Re: [AMBER] AMBER FF and NAMD
FyD
(Fri Oct 16 2009 - 12:19:13 PDT)
[AMBER] Dihedral energy profile in a single molecule
Frank X. Vázquez
(Fri Oct 16 2009 - 07:55:53 PDT)
Re: [AMBER] Dihedral energy profile in a single molecule
Jason Swails
(Fri Oct 16 2009 - 08:02:35 PDT)
Re: [AMBER] Any tutorial on the proper way to merge a ligand and protein?
Scott Brozell
(Fri Oct 16 2009 - 12:40:56 PDT)
[AMBER] RDC and alignment tensor
Eliana Asciutto
(Fri Oct 16 2009 - 13:21:34 PDT)
Re: [AMBER] RDC and alignment tensor
Thomas Cheatham III
(Fri Oct 16 2009 - 13:45:25 PDT)
Re: [AMBER] RDC and alignment tensor
Eliana Asciutto
(Mon Oct 19 2009 - 09:50:31 PDT)
Re: [AMBER] RDC and alignment tensor
case
(Mon Oct 19 2009 - 10:36:16 PDT)
Re: [AMBER] RDC and alignment tensor
Eliana Asciutto
(Mon Oct 19 2009 - 12:03:43 PDT)
Re: [AMBER] RDC and alignment tensor
case
(Tue Oct 20 2009 - 05:24:45 PDT)
Re: [AMBER] RDC and alignment tensor
Eliana Asciutto
(Fri Oct 23 2009 - 12:19:00 PDT)
[AMBER] (no subject)
Prakash Patodia
(Sat Oct 17 2009 - 00:12:39 PDT)
[AMBER] How create PRMTOP and INCPRD for surface?
rrd
(Sat Oct 17 2009 - 19:40:02 PDT)
[AMBER] how to get hold of older versions of MKL ?
Nahoum Anthony
(Mon Oct 19 2009 - 01:59:57 PDT)
Re: [AMBER] how to get hold of older versions of MKL ?
Jason Swails
(Mon Oct 19 2009 - 03:54:45 PDT)
RE: [AMBER] how to get hold of older versions of MKL ?
Ross Walker
(Mon Oct 19 2009 - 09:58:54 PDT)
AW: [AMBER] Add the hydrogen to the carboxyl of the GLU residue?
Aust, Susanne
(Mon Oct 19 2009 - 02:01:27 PDT)
[AMBER] error message from iAPBS
Oliver Kuhn
(Mon Oct 19 2009 - 04:47:32 PDT)
[AMBER] Re: RDC and alignment tensor
Eliana Asciutto
(Mon Oct 19 2009 - 10:51:50 PDT)
Re: [AMBER] Re: RDC and alignment tensor
case
(Mon Oct 19 2009 - 11:22:47 PDT)
[AMBER] Centering and reimaging with ptraj- stop rotating.
ben rodriguez
(Mon Oct 19 2009 - 20:00:26 PDT)
Re: [AMBER] Centering and reimaging with ptraj- stop rotating.
Thomas Cheatham
(Mon Oct 19 2009 - 20:47:07 PDT)
Re: [AMBER] Centering and reimaging with ptraj- stop rotating.
Bill Ross
(Mon Oct 19 2009 - 22:14:10 PDT)
[AMBER] Error: unable to find mopac charges in mopac.out
Rilei Yu
(Mon Oct 19 2009 - 22:34:34 PDT)
RE: [AMBER] Error: unable to find mopac charges in mopac.out
Ross Walker
(Mon Oct 19 2009 - 22:50:17 PDT)
RE: [AMBER] Error: unable to find mopac charges in mopac.out
Rilei Yu
(Tue Oct 20 2009 - 00:12:19 PDT)
Re: [AMBER] Error: unable to find mopac charges in mopac.out
case
(Tue Oct 20 2009 - 04:45:59 PDT)
[AMBER] How to create FF for diamond.
rrd
(Mon Oct 19 2009 - 23:16:07 PDT)
[AMBER] GAFF parameter
stefano_elli\.libero\.it
(Tue Oct 20 2009 - 06:26:26 PDT)
Re: [AMBER] GAFF parameter
Jason Swails
(Tue Oct 20 2009 - 07:57:09 PDT)
RE: [AMBER] GAFF parameter
Ross Walker
(Tue Oct 20 2009 - 11:50:18 PDT)
[AMBER] question with hbond in carnal
Ganesh Kamath
(Tue Oct 20 2009 - 06:58:36 PDT)
[AMBER] HBOND analysis
Marcin Krol
(Tue Oct 20 2009 - 08:42:35 PDT)
Re: [AMBER] question with hbond in carnal
Bill Ross
(Tue Oct 20 2009 - 09:32:56 PDT)
[AMBER] can I run EVB in other ensemble than NVE?
Jose Borreguero
(Tue Oct 20 2009 - 09:57:04 PDT)
Re: [AMBER] can I run EVB in other ensemble than NVE?
case
(Tue Oct 20 2009 - 10:08:58 PDT)
[AMBER] man pages?
Louis-Frédéric Feuillette
(Tue Oct 20 2009 - 10:09:09 PDT)
Re: [AMBER] man pages?
Ben Roberts
(Tue Oct 20 2009 - 10:33:16 PDT)
Re: [AMBER] man pages?
Louis-Frédéric Feuillette
(Tue Oct 20 2009 - 13:17:52 PDT)
Re: [AMBER] man pages?
Jason Swails
(Tue Oct 20 2009 - 14:28:56 PDT)
[AMBER] amber8 pmemd trajectory coordinates problem
wong105.llnl.gov
(Tue Oct 20 2009 - 17:32:24 PDT)
Re: [AMBER] amber8 pmemd trajectory coordinates problem
Thomas Cheatham
(Tue Oct 20 2009 - 17:39:22 PDT)
Re: [AMBER] amber8 pmemd trajectory coordinates problem
Sergio Wong
(Tue Oct 20 2009 - 17:49:11 PDT)
Re: [AMBER] amber8 pmemd trajectory coordinates problem
Robert Duke
(Tue Oct 20 2009 - 18:03:37 PDT)
Re: [AMBER] amber8 pmemd trajectory coordinates problem
Robert Duke
(Tue Oct 20 2009 - 18:15:56 PDT)
[AMBER] simulation blown up
moitrayee.mbu.iisc.ernet.in
(Tue Oct 20 2009 - 10:41:29 PDT)
Re: [AMBER] simulation blown up
Jason Swails
(Tue Oct 20 2009 - 19:58:47 PDT)
Re: [AMBER] simulation blown up
Robert Duke
(Tue Oct 20 2009 - 20:55:39 PDT)
[AMBER] Problem with running anal module in amber
moitrayee.mbu.iisc.ernet.in
(Tue Oct 20 2009 - 23:47:17 PDT)
[AMBER] "extra points" incompatibility with pmemd
mousumi
(Wed Oct 21 2009 - 00:57:51 PDT)
Re: [AMBER] "extra points" incompatibility with pmemd
Robert Duke
(Wed Oct 21 2009 - 05:02:54 PDT)
Re: [AMBER] "extra points" incompatibility with pmemd
Brent Krueger
(Wed Oct 21 2009 - 05:28:58 PDT)
Re: [AMBER] "extra points" incompatibility with pmemd
mousumi
(Wed Oct 21 2009 - 22:20:48 PDT)
Re: [AMBER] "extra points" incompatibility with pmemd
case
(Wed Oct 21 2009 - 05:22:28 PDT)
[AMBER] Can I use other ntb options in constant pH simulation
nicholus bhattacharjee
(Wed Oct 21 2009 - 02:26:43 PDT)
Re: [AMBER] Can I use other ntb options in constant pH simulation
Jason Swails
(Wed Oct 21 2009 - 04:42:42 PDT)
[AMBER] Why the calculation ofen stop with the calculation process not end?
xuemeiwang1103
(Wed Oct 21 2009 - 07:04:57 PDT)
[AMBER] xleap editing window icons inactive
Jayalakshmi Sridhar
(Wed Oct 21 2009 - 11:20:01 PDT)
RE: [AMBER] xleap editing window icons inactive
Niel Henriksen
(Wed Oct 21 2009 - 11:21:54 PDT)
RE: [AMBER] xleap editing window icons inactive
Jayalakshmi Sridhar
(Wed Oct 21 2009 - 11:32:46 PDT)
[AMBER] Circular RNA topology file
Kasprzak, Wojciech (NIH/NCI) [C]
(Wed Oct 21 2009 - 11:26:04 PDT)
Re: [AMBER] Circular RNA topology file
case
(Wed Oct 21 2009 - 12:06:17 PDT)
[AMBER] translate multiple residues
Taufik Al-Sarraj
(Wed Oct 21 2009 - 13:33:12 PDT)
Re: [AMBER] translate multiple residues
Bill Ross
(Wed Oct 21 2009 - 15:40:51 PDT)
Re: [AMBER] Circular RNA topology file
Filip Lankas
(Mon Oct 26 2009 - 03:13:46 PDT)
Re: [AMBER] translate multiple residues
Bill Ross
(Wed Oct 21 2009 - 13:53:20 PDT)
Re: [AMBER] translate multiple residues
Taufik Al-Sarraj
(Wed Oct 21 2009 - 14:32:30 PDT)
[AMBER] Ptraj Segmentation Fault
Katrina Hill
(Wed Oct 21 2009 - 19:15:31 PDT)
[AMBER] too many undefined parameters in frcmod
xueqin pang
(Thu Oct 22 2009 - 01:52:57 PDT)
Re: [AMBER] too many undefined parameters in frcmod
FyD
(Thu Oct 22 2009 - 02:37:46 PDT)
Re: [AMBER] too many undefined parameters in frcmod
Jason Swails
(Thu Oct 22 2009 - 04:59:55 PDT)
Re: [AMBER] too many undefined parameters in frcmod
Junmei Wang
(Mon Oct 26 2009 - 07:45:04 PDT)
Re: [AMBER] too many undefined parameters in frcmod
xueqin pang
(Thu Oct 29 2009 - 06:06:24 PDT)
[AMBER] Salt bridge time scale
Mannan
(Sun Oct 25 2009 - 18:57:20 PDT)
[AMBER] units of measures
lorenzo
(Thu Oct 22 2009 - 04:20:26 PDT)
Re: [AMBER] units of measures
case
(Thu Oct 22 2009 - 05:42:11 PDT)
[AMBER] problem with minimization
moitrayee.mbu.iisc.ernet.in
(Thu Oct 22 2009 - 04:01:14 PDT)
[AMBER] [Fwd: problem with minimization]
moitrayee.mbu.iisc.ernet.in
(Thu Oct 22 2009 - 05:46:32 PDT)
[AMBER] parameters for O2 molecule
Jeffrey
(Thu Oct 22 2009 - 06:32:07 PDT)
Re: [AMBER] parameters for O2 molecule
Jason Swails
(Thu Oct 22 2009 - 07:19:51 PDT)
Re: [AMBER] parameters for O2 molecule
Jeffrey
(Thu Oct 29 2009 - 06:01:44 PDT)
[AMBER] charges for heme-cys in p450
Jayalakshmi Sridhar
(Thu Oct 22 2009 - 09:03:08 PDT)
Re: [AMBER] charges for heme-cys in p450
FyD
(Fri Oct 23 2009 - 03:57:43 PDT)
[AMBER] Unable to correctly identify element when running QM/MM in amber10
Jifeng Wang
(Thu Oct 22 2009 - 09:20:30 PDT)
RE: [AMBER] Unable to correctly identify element when running QM/MM in amber10
Ross Walker
(Thu Oct 22 2009 - 12:03:40 PDT)
Re: [AMBER] [Fwd: problem with minimization]
Bill Ross
(Thu Oct 22 2009 - 09:49:45 PDT)
Re: [AMBER] [Fwd: problem with minimization]
moitrayee.mbu.iisc.ernet.in
(Thu Oct 22 2009 - 11:53:11 PDT)
Re: [AMBER] [Fwd: problem with minimization]
Bill Ross
(Fri Oct 23 2009 - 10:40:57 PDT)
[AMBER] XServe cluster
Abdul Rehman Gani
(Thu Oct 22 2009 - 12:14:36 PDT)
Re: [AMBER] XServe cluster
Jim Paugh
(Thu Oct 22 2009 - 12:24:37 PDT)
Re: [AMBER] XServe cluster
Abdul Rehman Gani
(Thu Oct 22 2009 - 12:40:11 PDT)
Re: [AMBER] XServe cluster
Jim Paugh
(Thu Oct 22 2009 - 14:10:49 PDT)
RE: [AMBER] XServe cluster
Richard Owczarzy
(Thu Oct 22 2009 - 13:02:24 PDT)
[AMBER] Question about distance restraint ?
xuemeiwang1103
(Fri Oct 23 2009 - 03:07:47 PDT)
Re: [AMBER] Question about distance restraint ?
Carlos Simmerling
(Fri Oct 23 2009 - 03:56:24 PDT)
[AMBER] amber parallel test fail
Nahoum Anthony
(Fri Oct 23 2009 - 03:20:45 PDT)
Re: [AMBER] amber parallel test fail
Jason Swails
(Fri Oct 23 2009 - 04:58:19 PDT)
RE: [AMBER] amber parallel test fail
Nahoum Anthony
(Fri Oct 23 2009 - 08:12:40 PDT)
[AMBER] software to hydrate protein pockets
Vlad Cojocaru
(Fri Oct 23 2009 - 05:23:54 PDT)
Re: [AMBER] software to hydrate protein pockets
Alessandro Nascimento
(Fri Oct 23 2009 - 05:50:05 PDT)
Re: [AMBER] software to hydrate protein pockets
Hannes Kopitz
(Fri Oct 23 2009 - 06:11:26 PDT)
[AMBER] pmemd ifort problem
Sel Ercan
(Fri Oct 23 2009 - 07:57:59 PDT)
Re: [AMBER] pmemd ifort problem
Robert Duke
(Fri Oct 23 2009 - 08:33:27 PDT)
[AMBER] inhibitor prepin not recognized in xleap
Jayalakshmi Sridhar
(Fri Oct 23 2009 - 08:56:40 PDT)
[AMBER] inhibitor prepin not recognized in xleap
Jayalakshmi Sridhar
(Fri Oct 23 2009 - 09:05:46 PDT)
[AMBER] xleap not reconizing inhibitor prepin
Jayalakshmi Sridhar
(Fri Oct 23 2009 - 09:21:07 PDT)
Re: [AMBER] xleap not reconizing inhibitor prepin
Junmei Wang
(Mon Oct 26 2009 - 07:51:41 PDT)
Re: [AMBER] inhibitor prepin not recognized in xleap
Bill Ross
(Fri Oct 23 2009 - 11:32:03 PDT)
Re: [AMBER] xleap not reconizing inhibitor prepin
Bill Ross
(Fri Oct 23 2009 - 11:33:44 PDT)
[AMBER] the criterion of equilibrium
qiaoyan
(Fri Oct 23 2009 - 19:19:58 PDT)
[AMBER] resp_problem
vhakkim boy
(Sat Oct 24 2009 - 03:16:22 PDT)
RE: [AMBER] resp_problem
Ross Walker
(Sat Oct 24 2009 - 15:39:01 PDT)
Re: [AMBER] resp_problem
FyD
(Sat Oct 24 2009 - 23:12:31 PDT)
Re: [AMBER] the criterion of equilibrium
Bill Ross
(Sat Oct 24 2009 - 10:19:09 PDT)
Re: [AMBER] the criterion of equilibrium
Adrian Roitberg
(Sat Oct 24 2009 - 11:22:25 PDT)
[AMBER] A bug in LEaP II ?
FyD
(Sun Oct 25 2009 - 05:58:36 PDT)
[AMBER] error in AMBer distance constraint
xuemeiwang1103
(Sun Oct 25 2009 - 19:24:09 PDT)
Re: [AMBER] error in AMBer distance constraint
Carlos Simmerling
(Sun Oct 25 2009 - 19:38:23 PDT)
Re:Re: [AMBER] error in AMBer distance constraint
xuemeiwang1103
(Mon Oct 26 2009 - 00:35:08 PDT)
Re: Re: [AMBER] error in AMBer distance constraint
Carlos Simmerling
(Tue Oct 27 2009 - 04:28:22 PDT)
Re: [AMBER] error in AMBer distance constraint
Bill Ross
(Sun Oct 25 2009 - 20:03:19 PDT)
[AMBER] Preparing distance restraints
Yunjie Zhao
(Mon Oct 26 2009 - 01:44:58 PDT)
Re: [AMBER] Preparing distance restraints
case
(Mon Oct 26 2009 - 14:26:26 PDT)
[AMBER] contradictive hydrogen bonds using ptraj
Binbin Liu
(Mon Oct 26 2009 - 09:42:20 PDT)
[AMBER] [amber10] atom groups used in torsion constrain
Han Zheng
(Mon Oct 26 2009 - 11:09:07 PDT)
[AMBER] PEMD
Cristina Sisu
(Mon Oct 26 2009 - 14:44:42 PDT)
Re: [AMBER] PEMD
Tom Joseph
(Mon Oct 26 2009 - 16:03:26 PDT)
[AMBER] Possible bug in "com" group torsion angle constrain? Thanks!
Han Zheng
(Tue Oct 27 2009 - 10:28:16 PDT)
RE: [AMBER] Possible bug in "com" group torsion angle constrain? Thanks!
Seetin, Matthew
(Tue Oct 27 2009 - 14:17:41 PDT)
Re: [AMBER] Possible bug in "com" group torsion angle constrain? Thanks!
Han Zheng
(Tue Oct 27 2009 - 15:47:20 PDT)
Re: [AMBER] Possible bug in "com" group torsion angle constrain? Thanks!
Carlos Simmerling
(Tue Oct 27 2009 - 16:22:43 PDT)
Re: [AMBER] building quadruplex with NAB
Peter Varnai
(Tue Oct 27 2009 - 13:00:09 PDT)
Re: [AMBER] building quadruplex with NAB
case
(Tue Oct 27 2009 - 19:23:29 PDT)
[AMBER] NMR restraint
xuemeiwang1103
(Tue Oct 27 2009 - 19:31:39 PDT)
Re: [AMBER] NMR restraint
Sally Pias
(Tue Oct 27 2009 - 21:32:33 PDT)
[AMBER] Simulated annealing
Shaikh Abdul R S Ramaju
(Tue Oct 27 2009 - 22:44:33 PDT)
Re: [AMBER] Simulated annealing
Carlos Simmerling
(Wed Oct 28 2009 - 03:51:41 PDT)
[AMBER] Conversion of Gaussian output file to mol2
megha bajaj
(Wed Oct 28 2009 - 00:49:51 PDT)
[AMBER] Conversion of Gaussian output file into mol2
megha bajaj
(Wed Oct 28 2009 - 01:00:35 PDT)
Re: [AMBER] Conversion of Gaussian output file into mol2
Junmei Wang
(Thu Oct 29 2009 - 08:45:27 PDT)
[AMBER] error in distance restraint
xuemeiwang1103
(Wed Oct 28 2009 - 06:56:48 PDT)
Re: [AMBER] error in distance restraint
Adrian Roitberg
(Wed Oct 28 2009 - 07:01:07 PDT)
[AMBER] vlimit
Taufik Al-Sarraj
(Wed Oct 28 2009 - 14:16:32 PDT)
RE: [AMBER] vlimit
Ross Walker
(Wed Oct 28 2009 - 14:29:21 PDT)
Re: [AMBER] vlimit
Taufik Al-Sarraj
(Wed Oct 28 2009 - 15:02:43 PDT)
RE: [AMBER] vlimit
Ross Walker
(Wed Oct 28 2009 - 15:35:15 PDT)
RE: [AMBER] vlimit
Bill Ross
(Wed Oct 28 2009 - 14:55:55 PDT)
Re: [AMBER] error in distance restraint
Carlos Simmerling
(Wed Oct 28 2009 - 13:48:13 PDT)
Re:Re: [AMBER] error in distance restraint
xuemeiwang1103
(Wed Oct 28 2009 - 20:43:55 PDT)
Re: Re: [AMBER] error in distance restraint
Carlos Simmerling
(Thu Oct 29 2009 - 03:20:13 PDT)
[AMBER] pairwise per-residue decomposition
manoj singh
(Wed Oct 28 2009 - 21:34:32 PDT)
Re: [AMBER] pairwise per-residue decomposition
Carlos Simmerling
(Thu Oct 29 2009 - 03:20:55 PDT)
Re: [AMBER] pairwise per-residue decomposition
manoj singh
(Thu Oct 29 2009 - 10:32:38 PDT)
Re: [AMBER] pairwise per-residue decomposition
Tom Joseph
(Thu Oct 29 2009 - 17:30:51 PDT)
Re: [AMBER] pairwise per-residue decomposition
Tom Joseph
(Thu Oct 29 2009 - 22:15:40 PDT)
Re: [AMBER] pairwise per-residue decomposition
manoj singh
(Thu Oct 29 2009 - 22:46:22 PDT)
Re: [AMBER] pairwise per-residue decomposition
Tom Joseph
(Fri Oct 30 2009 - 11:18:52 PDT)
Re: [AMBER] pairwise per-residue decomposition
manoj singh
(Fri Oct 30 2009 - 11:26:14 PDT)
[AMBER] Thermodynamic Integration calculation on an artificial anion receptor
Huifang
(Wed Oct 28 2009 - 21:38:05 PDT)
Re: [AMBER] Thermodynamic Integration calculation on an artificial anion receptor
steinbrt.rci.rutgers.edu
(Thu Oct 29 2009 - 03:35:24 PDT)
[AMBER] ligand exiting a protein cavity
moitrayee.mbu.iisc.ernet.in
(Thu Oct 29 2009 - 05:27:58 PDT)
[AMBER] [Fwd: ligand exiting a protein cavity]
moitrayee.mbu.iisc.ernet.in
(Thu Oct 29 2009 - 05:36:13 PDT)
Re: [AMBER] [Fwd: ligand exiting a protein cavity]
Kshatresh Dutta Dubey
(Thu Oct 29 2009 - 07:44:28 PDT)
Re: [AMBER] [Fwd: ligand exiting a protein cavity]
Jason Swails
(Thu Oct 29 2009 - 08:17:40 PDT)
Re: [AMBER] [Fwd: ligand exiting a protein cavity]
moitrayee.mbu.iisc.ernet.in
(Thu Oct 29 2009 - 22:43:22 PDT)
Re: [AMBER] [Fwd: ligand exiting a protein cavity]
Jason Swails
(Fri Oct 30 2009 - 06:07:17 PDT)
Re: [AMBER] [Fwd: ligand exiting a protein cavity]
moitrayee.mbu.iisc.ernet.in
(Fri Oct 30 2009 - 06:42:57 PDT)
Re: [AMBER] [Fwd: ligand exiting a protein cavity]
Jason Swails
(Fri Oct 30 2009 - 09:23:29 PDT)
[AMBER] rms fit of mutant with respect to wild type structure
Siddharth Rastogi
(Thu Oct 29 2009 - 06:55:12 PDT)
Re: [AMBER] rms fit of mutant with respect to wild type structure
Carlos Simmerling
(Thu Oct 29 2009 - 07:03:35 PDT)
[AMBER] Parallel sander & polarisability
Thomas Taylor
(Thu Oct 29 2009 - 09:19:14 PDT)
RE: [AMBER] Parallel sander & polarisability
Ross Walker
(Thu Oct 29 2009 - 10:00:13 PDT)
Re: [AMBER] Parallel sander & polarisability
case
(Thu Oct 29 2009 - 10:02:28 PDT)
[AMBER] Analyzing per-residue decomposition data
manoj singh
(Thu Oct 29 2009 - 13:18:45 PDT)
[AMBER] stacking clusters
Shaikh Abdul R S Ramaju
(Thu Oct 29 2009 - 19:44:59 PDT)
[AMBER] some queries on -states flag in constant pH simulation
nicholus bhattacharjee
(Thu Oct 29 2009 - 21:21:27 PDT)
Re: [AMBER] some queries on -states flag in constant pH simulation
Jason Swails
(Fri Oct 30 2009 - 06:00:37 PDT)
Re: [AMBER] some queries on -states flag in constant pH simulation
nicholus bhattacharjee
(Fri Oct 30 2009 - 23:31:31 PDT)
Re: [AMBER] some queries on -states flag in constant pH simulation
Jason Swails
(Sat Oct 31 2009 - 05:28:22 PDT)
[AMBER] Ligand covalent bonds appear to be broken
moitrayee.mbu.iisc.ernet.in
(Thu Oct 29 2009 - 23:32:39 PDT)
Re: [AMBER] Ligand covalent bonds appear to be broken
Tom Joseph
(Fri Oct 30 2009 - 04:53:44 PDT)
Re: [AMBER] Ligand covalent bonds appear to be broken
Jason Swails
(Fri Oct 30 2009 - 06:11:03 PDT)
Re: [AMBER] Ligand covalent bonds appear to be broken
moitrayee.mbu.iisc.ernet.in
(Fri Oct 30 2009 - 06:43:25 PDT)
Re: [AMBER] Ligand covalent bonds appear to be broken
Thomas Cheatham
(Fri Oct 30 2009 - 08:48:07 PDT)
[AMBER] Is it the way to do simulation in vacuum
nicholus bhattacharjee
(Fri Oct 30 2009 - 03:18:45 PDT)
Re: [AMBER] Is it the way to do simulation in vacuum
Carlos Simmerling
(Fri Oct 30 2009 - 03:21:49 PDT)
Re: [AMBER] Is it the way to do simulation in vacuum
nicholus bhattacharjee
(Fri Oct 30 2009 - 04:11:03 PDT)
Re: [AMBER] Is it the way to do simulation in vacuum
case
(Fri Oct 30 2009 - 05:49:46 PDT)
Re: [AMBER] Is it the way to do simulation in vacuum
Carlos Simmerling
(Fri Oct 30 2009 - 06:26:20 PDT)
Re: [AMBER] Is it the way to do simulation in vacuum
Jason Swails
(Fri Oct 30 2009 - 09:06:14 PDT)
Re: [AMBER] Is it the way to do simulation in vacuum
Carlos Simmerling
(Fri Oct 30 2009 - 09:10:22 PDT)
RE: [AMBER] Is it the way to do simulation in vacuum
Ross Walker
(Fri Oct 30 2009 - 12:15:01 PDT)
[AMBER] SPC/E HOH angle
Hemant Kumar
(Fri Oct 30 2009 - 03:36:55 PDT)
Re: [AMBER] SPC/E HOH angle
case
(Fri Oct 30 2009 - 05:51:41 PDT)
Re: [AMBER] SPC/E HOH angle
Carlos Simmerling
(Fri Oct 30 2009 - 06:47:18 PDT)
[AMBER] RESP charges with -a and without -a flag
Jio M
(Fri Oct 30 2009 - 06:36:43 PDT)
Re: [AMBER] RESP charges with -a and without -a flag
Junmei Wang
(Fri Oct 30 2009 - 09:49:00 PDT)
Re: [AMBER] RESP charges with -a and without -a flag
Jio M
(Fri Oct 30 2009 - 22:13:03 PDT)
[AMBER] Lennard Jones Potential A and B coefficients in Topology file
Peter Schmidtke
(Fri Oct 30 2009 - 11:32:32 PDT)
Re: [AMBER] Lennard Jones Potential A and B coefficients in Topology file
Tom Joseph
(Fri Oct 30 2009 - 15:04:43 PDT)
Re: [AMBER] Lennard Jones Potential A and B coefficients in Topology file
Peter Schmidtke
(Fri Oct 30 2009 - 17:09:46 PDT)
Re: [AMBER] Lennard Jones Potential A and B coefficients in Topology file
Tom Joseph
(Fri Oct 30 2009 - 22:23:03 PDT)
Re: [AMBER] Lennard Jones Potential A and B coefficients in Topology file
Tom Joseph
(Sat Oct 31 2009 - 07:59:14 PDT)
Re: [AMBER] Lennard Jones Potential A and B coefficients in Topology file
Peter Schmidtke
(Sat Oct 31 2009 - 08:10:12 PDT)
Re: [AMBER] Lennard Jones Potential A and B coefficients in Topology file
Crowley, Michael
(Sat Oct 31 2009 - 10:32:12 PDT)
[AMBER] Re: (files attached) RESP with -a and witout -a flag
Jio M
(Fri Oct 30 2009 - 22:17:55 PDT)
[AMBER] surface binding protein
sadaf iqbal
(Fri Oct 30 2009 - 22:28:22 PDT)
Re: [AMBER] surface binding protein
Jason Swails
(Sat Oct 31 2009 - 05:35:44 PDT)
[AMBER] Gaussian log file error
megha bajaj
(Sat Oct 31 2009 - 06:10:22 PDT)
Re: [AMBER] Different results for different computers
manoj singh
(Sat Oct 31 2009 - 12:47:36 PDT)
Re: [AMBER] Different results for different computers
Jason Swails
(Sat Oct 31 2009 - 12:57:34 PDT)
Re: [AMBER] Different results for different computers
Robert Duke
(Sat Oct 31 2009 - 15:56:28 PDT)
Last message date
:
Sat Oct 31 2009 - 16:00:02 PDT
Archived on
: Fri Nov 22 2024 - 05:53:53 PST
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