AMBER Archive (2003) - Sep 2003 By Subject

237 messages sorted by: [ author ] [ date ] [ thread ]
About this archive

Starting: Mon Sep 01 2003 - 14:30:04 CDT
Ending: Tue Sep 30 2003 - 15:15:28 CDT

AMBER: 'high' temp. simulation!!
- Pradipta Bandyopadhyay (Fri Sep 19 2003 - 15:09:05 CDT)
AMBER: 'ho' vDW parameters
- Yong Duan (Mon Sep 08 2003 - 15:27:48 CDT)
- Carlos Simmerling (Mon Sep 08 2003 - 15:10:13 CDT)
- Junmei Wang (Mon Sep 08 2003 - 15:01:25 CDT)
- Lee, Matthew (Fri Sep 05 2003 - 17:33:12 CDT)
AMBER: ?small bugs? - 2nd suggestion
- Chris Moth (Wed Sep 24 2003 - 15:23:41 CDT)
AMBER: A problem about xleap
- John Bushnell (Tue Sep 30 2003 - 12:13:06 CDT)
- Jiang Pengju (Mon Sep 29 2003 - 21:04:14 CDT)
AMBER: about the mopac7 installation.
- Yong Wang (Fri Sep 26 2003 - 02:07:16 CDT)
AMBER: Accuracy of PB solvation energy
- Jiri Sponer (Fri Sep 05 2003 - 12:46:04 CDT)
- Qing Zhang (Fri Sep 05 2003 - 12:15:15 CDT)
AMBER: altering mass in .top file
- Pascal Bonnet (Thu Sep 11 2003 - 05:05:15 CDT)
- hagop demirdjian (Thu Sep 11 2003 - 04:07:02 CDT)
AMBER: Amber 7 - bugfix 42 problem.
- David A. Case (Fri Sep 19 2003 - 13:17:10 CDT)
- Bengt Svensson (Wed Sep 17 2003 - 20:21:08 CDT)
AMBER: AMBER Carnal files
- Yong Duan (Sun Sep 21 2003 - 21:02:40 CDT)
- Frederico.Miranda_at_ibmb.uib.no (Sun Sep 21 2003 - 19:09:01 CDT)
- Yong Duan (Sat Sep 20 2003 - 17:44:44 CDT)
- Frederico.Miranda_at_ibmb.uib.no (Sat Sep 20 2003 - 17:24:12 CDT)
AMBER: AMBER error in CHALANGE
- David A. Case (Mon Sep 15 2003 - 15:06:21 CDT)
- Carlos Simmerling (Mon Sep 15 2003 - 11:04:26 CDT)
- sd233_at_georgetown.edu (Mon Sep 15 2003 - 10:58:31 CDT)
AMBER: AMBER on LINUX ?? (fwd)
- David A. Case (Mon Sep 15 2003 - 15:08:56 CDT)
- Sanjeev B.S. (Mon Sep 15 2003 - 04:17:01 CDT)
- sangeeta_at_bioinfo.ernet.in (Mon Sep 15 2003 - 01:57:20 CDT)
AMBER: AMBER quasih question(s)
- Rachel Ward (Mon Sep 29 2003 - 14:39:17 CDT)
AMBER: Antechamber problem
- David A. Case (Tue Sep 23 2003 - 10:19:54 CDT)
- Shafinaz (Mon Sep 22 2003 - 11:33:58 CDT)
AMBER: atomic clash or structure size?
- David A. Case (Wed Sep 03 2003 - 10:32:42 CDT)
- Qiang Lu (Tue Sep 02 2003 - 16:20:32 CDT)
- atobak_at_eden.rutgers.edu (Tue Sep 02 2003 - 16:08:51 CDT)
AMBER: Benchmark of AMBER on Apple G5 machine
- Mengjuei Hsieh (Mon Sep 15 2003 - 15:56:43 CDT)
AMBER: C-alpha RMS
- Kun Song (Mon Sep 22 2003 - 08:45:20 CDT)
- Do Anh Tuan (Sat Sep 20 2003 - 01:39:42 CDT)
AMBER: Calculating solvation energies for MM-PBSA use
- samantha hughes (Thu Sep 18 2003 - 08:13:04 CDT)
- Thomas Steinbrecher (Thu Sep 18 2003 - 07:43:37 CDT)
AMBER: Carnal Input file
- Ming Lei (Mon Sep 22 2003 - 22:34:05 CDT)
- Bill Ross (Mon Sep 22 2003 - 18:23:27 CDT)
- Frederico.Miranda_at_ibmb.uib.no (Mon Sep 22 2003 - 18:06:55 CDT)
AMBER: cd-c-os and c3-cd-c angle parameters
- Junmei Wang (Wed Sep 24 2003 - 13:16:18 CDT)
- Vikas Varshney (Wed Sep 24 2003 - 10:10:09 CDT)
AMBER: charge definition
- Holger Gohlke (Sat Sep 06 2003 - 14:00:01 CDT)
- Khanh KIm Dao (Sat Sep 06 2003 - 13:40:31 CDT)
AMBER: charge of IRON in HEME!!
- Ming Lei (Fri Sep 05 2003 - 13:15:32 CDT)
- Qiang Lu (Thu Sep 04 2003 - 19:40:48 CDT)
- Pradipta Bandyopadhyay (Thu Sep 04 2003 - 19:28:11 CDT)
AMBER: Compiling 64-bit version on AIX
- Pratul K. Agarwal (Tue Sep 09 2003 - 12:01:13 CDT)
- David A. Case (Tue Sep 09 2003 - 11:36:12 CDT)
- Carlos P. Sosa (Tue Sep 09 2003 - 11:06:39 CDT)
- Pratul K. Agarwal (Tue Sep 09 2003 - 10:45:58 CDT)
- Nicolas Grima (Tue Sep 09 2003 - 02:11:03 CDT)
- Pratul K. Agarwal (Mon Sep 08 2003 - 21:00:55 CDT)
AMBER: Compiling sander with single precision
- Mengjuei Hsieh (Wed Sep 17 2003 - 16:56:34 CDT)
- Scott Brozell (Tue Sep 16 2003 - 20:59:25 CDT)
- rluo_at_uci.edu (Tue Sep 16 2003 - 20:37:01 CDT)
AMBER: density equilibrium & harmonic restrain
- yuann (Mon Sep 29 2003 - 21:59:50 CDT)
AMBER: dielectric constant for blends
- David A. Case (Mon Sep 08 2003 - 10:23:34 CDT)
- Taner E. Dirama (Mon Sep 08 2003 - 09:21:11 CDT)
AMBER: DMSO box
- Jiten (Fri Sep 12 2003 - 20:05:46 CDT)
- Dalmaris, John (Fri Sep 12 2003 - 04:25:21 CDT)
AMBER: DNA helix is not in z-direction
- David A. Case (Fri Sep 05 2003 - 19:37:20 CDT)
- A. Hungie (Fri Sep 05 2003 - 04:35:50 CDT)
AMBER: double bonds in prmtop
- David A. Case (Fri Sep 19 2003 - 17:42:23 CDT)
- Herbert Georg (Fri Sep 19 2003 - 16:27:53 CDT)
- Ioana Cozmuta (Fri Sep 19 2003 - 15:24:18 CDT)
- Herbert Georg (Fri Sep 19 2003 - 15:09:16 CDT)
AMBER: error message is the same after I added a title
- nie beining (Tue Sep 02 2003 - 10:20:11 CDT)
AMBER: EWALD BOMB and solvent density problem
- northrop_at_chem.ucla.edu (Thu Sep 11 2003 - 13:28:51 CDT)
AMBER: FEP problem
- David A. Case (Thu Sep 18 2003 - 10:08:18 CDT)
- Itziar Maestre Asenjo (Thu Sep 18 2003 - 07:35:37 CDT)
AMBER: FF parameters for BOC - group
- Martin Lepsik (Fri Sep 12 2003 - 09:57:24 CDT)
- Balvinder Singh (Fri Sep 12 2003 - 12:38:34 CDT)
AMBER: following salt and waterbridges during a simulation
- Karsten Suhre (Tue Sep 30 2003 - 01:33:31 CDT)
AMBER: gaff parameters
- Junmei Wang (Fri Sep 12 2003 - 16:46:24 CDT)
- Kazuo Koyano (Fri Sep 12 2003 - 05:31:33 CDT)
- astrid.maass (Fri Sep 12 2003 - 04:10:32 CDT)
AMBER: Generalized Born parameters
- Peter VARNAI (Thu Sep 18 2003 - 13:51:24 CDT)
AMBER: GLYCAM/AMBER Configurator
- ayongye_at_sunchem.chem.uga.edu (Tue Sep 02 2003 - 13:36:51 CDT)
AMBER: GROUP
- Atchara Wijitkosoom (Tue Sep 23 2003 - 15:04:20 CDT)
AMBER: How can I set ntx=7, but exclude the velocity?
- Carlos Simmerling (Tue Sep 23 2003 - 10:35:28 CDT)
- Margaret S. Cheung (Tue Sep 23 2003 - 10:30:28 CDT)
AMBER: iam a newbie !!!
- Vlad Cojocaru (Tue Sep 30 2003 - 04:12:43 CDT)
- Karthikeyan Pasupathy (Mon Sep 29 2003 - 23:25:05 CDT)
AMBER: IG value
- David A. Case (Fri Sep 05 2003 - 09:46:58 CDT)
- Carlos Simmerling (Fri Sep 05 2003 - 06:57:07 CDT)
- SEKIJIMA Masakazu (Fri Sep 05 2003 - 06:50:05 CDT)
AMBER: improper
- Bill Ross (Tue Sep 30 2003 - 15:15:28 CDT)
- Li Ying (Tue Sep 30 2003 - 15:08:11 CDT)
AMBER: increase size of NATOM or NRES for "ambpdb"
- David A. Case (Mon Sep 22 2003 - 14:24:12 CDT)
- Wen Li (Mon Sep 22 2003 - 14:14:36 CDT)
AMBER: leap/frcmod problem
- David A. Case (Wed Sep 17 2003 - 15:57:18 CDT)
- Joseph Nachman (Wed Sep 17 2003 - 15:08:37 CDT)
AMBER: MD problem!
- darden (Wed Sep 17 2003 - 10:29:50 CDT)
- Pradipta Bandyopadhyay (Tue Sep 16 2003 - 19:33:17 CDT)
AMBER: MD problem!!
- yduan_at_udel.edu (Thu Sep 18 2003 - 16:21:22 CDT)
- Pradipta Bandyopadhyay (Thu Sep 18 2003 - 15:35:36 CDT)
AMBER: MD simulations on small molecules immersed in sparse water shell
- Carlos Simmerling (Tue Sep 16 2003 - 14:21:18 CDT)
- rluo_at_uci.edu (Tue Sep 16 2003 - 14:07:03 CDT)
- Carlos Simmerling (Tue Sep 16 2003 - 13:23:53 CDT)
- rluo_at_uci.edu (Tue Sep 16 2003 - 13:16:41 CDT)
- Alfonso Garcia Sosa (Tue Sep 16 2003 - 12:08:24 CDT)
- Junmei Wang (Tue Sep 16 2003 - 11:42:56 CDT)
AMBER: MeCNBOX
- Pascal Bonnet (Fri Sep 26 2003 - 03:38:03 CDT)
- James W. Caldwell (Thu Sep 25 2003 - 16:04:03 CDT)
- northrop_at_chem.ucla.edu (Thu Sep 25 2003 - 15:47:03 CDT)
- northrop_at_chem.ucla.edu (Thu Sep 25 2003 - 15:40:37 CDT)
- David A. Case (Thu Sep 25 2003 - 15:25:23 CDT)
- northrop_at_chem.ucla.edu (Thu Sep 25 2003 - 14:35:03 CDT)
AMBER: mfef90 - installation problem
- Joseph Maxwell (Wed Sep 17 2003 - 13:11:58 CDT)
- Michael Crowley (Wed Sep 17 2003 - 12:28:19 CDT)
- Joseph Maxwell (Wed Sep 17 2003 - 11:34:18 CDT)
AMBER: minimization error
- David A. Case (Fri Sep 12 2003 - 16:19:48 CDT)
- Scott Brozell (Fri Sep 12 2003 - 14:24:37 CDT)
- Venkata S Koppuravuri (Fri Sep 12 2003 - 14:00:05 CDT)
AMBER: MIPS R14000 and Machine-file
- David A. Case (Tue Sep 02 2003 - 09:56:26 CDT)
- Sanjeev B.S. (Tue Sep 02 2003 - 07:48:33 CDT)
- Antonio J.Díaz Quintana (Tue Sep 02 2003 - 06:49:37 CDT)
- Antonio J.Díaz Quintana (Tue Sep 02 2003 - 03:14:33 CDT)
AMBER: mm_pbsa - ?small bugs?
- Chris Moth (Wed Sep 24 2003 - 12:37:37 CDT)
AMBER: MM_PBSA(GBSA) Examples
- Kazuo Koyano (Fri Sep 26 2003 - 05:37:40 CDT)
- Chris Moth (Thu Sep 25 2003 - 10:56:23 CDT)
- Kazuo Koyano (Thu Sep 25 2003 - 05:35:50 CDT)
AMBER: NaCl ion pairs in TIP3P water box
- Pascal Auffinger (Thu Sep 25 2003 - 08:30:08 CDT)
- Jiri Sponer (Thu Sep 25 2003 - 06:59:51 CDT)
- Nathan A. Baker (Wed Sep 24 2003 - 20:14:47 CDT)
- M. L. Dodson (Wed Sep 24 2003 - 18:53:22 CDT)
- Ioana Cozmuta (Wed Sep 24 2003 - 17:30:26 CDT)
- Bill Ross (Wed Sep 24 2003 - 17:13:47 CDT)
- Jiri Sponer (Wed Sep 24 2003 - 16:41:27 CDT)
- David A. Case (Wed Sep 24 2003 - 16:09:06 CDT)
- Bill Ross (Wed Sep 24 2003 - 15:53:39 CDT)
- Nathan A. Baker (Wed Sep 24 2003 - 15:13:11 CDT)
AMBER: no defined type for atom N atom
- David A. Case (Fri Sep 19 2003 - 12:01:29 CDT)
- Wu Yingliang (Fri Sep 19 2003 - 08:02:31 CDT)
- Wu Yingliang (Fri Sep 19 2003 - 07:57:12 CDT)
AMBER: non-bonded cutoffs
- Michael Dolan (Fri Sep 26 2003 - 10:39:34 CDT)
- David A. Case (Fri Sep 26 2003 - 10:32:09 CDT)
- Michael Dolan (Fri Sep 26 2003 - 10:17:16 CDT)
AMBER: nstlim
- Robert Duke (Mon Sep 29 2003 - 20:40:24 CDT)
- Amber Administration (Mon Sep 29 2003 - 18:55:42 CDT)
AMBER: Online model of 2C9
- Peter Gannett (Thu Sep 25 2003 - 14:23:22 CDT)
AMBER: pair-cutoff
- David A. Case (Tue Sep 23 2003 - 10:59:01 CDT)
- nie beining (Tue Sep 23 2003 - 10:40:32 CDT)
AMBER: parm. and top. for sugars, charmm?
- Itziar Maestre Asenjo (Tue Sep 09 2003 - 00:57:27 CDT)
- Endres, Robert G. (Mon Sep 08 2003 - 11:05:00 CDT)
AMBER: performance vs number of processors
- David A. Case (Mon Sep 15 2003 - 14:53:32 CDT)
- zhaoxc_at_puccini.che.pitt.edu (Mon Sep 15 2003 - 14:41:20 CDT)
- GUILLERMINA L ESTIU (Mon Sep 15 2003 - 13:58:37 CDT)
AMBER: Phase for torsion angle different of 0 or 180 ?
- David A. Case (Fri Sep 26 2003 - 15:41:35 CDT)
- Teletchéa Stéphane (Fri Sep 26 2003 - 11:27:34 CDT)
AMBER: plane angle.
- Bill Ross (Mon Sep 22 2003 - 13:42:40 CDT)
- Pascal Bonnet (Mon Sep 22 2003 - 10:14:44 CDT)
AMBER: PMEMD 3.03 Update available
- Robert Duke (Tue Sep 23 2003 - 21:13:57 CDT)
AMBER: PMEMD: dual XEON vs SGI cluster
- Chris Moth (Mon Sep 15 2003 - 20:55:46 CDT)
- Johannes Zuegg (Mon Sep 15 2003 - 18:45:27 CDT)
- Robert Duke (Mon Sep 15 2003 - 17:55:28 CDT)
- Chris Moth (Tue Sep 16 2003 - 16:46:45 CDT)
AMBER: PMF calculations
- Sébastien Canneaux (Tue Sep 09 2003 - 07:29:36 CDT)
AMBER: PMF ethane example: Can someone correct the INPUT? Thanks.
- David A. Case (Wed Sep 03 2003 - 10:38:56 CDT)
- Christophe L M J Verlinde (Tue Sep 02 2003 - 12:57:52 CDT)
AMBER: polarizability and PME
- David A. Case (Sat Sep 27 2003 - 11:17:46 CDT)
- Martin Mucha (Sat Sep 27 2003 - 09:46:08 CDT)
AMBER: problem with file format
- Junmei Wang (Wed Sep 24 2003 - 15:34:14 CDT)
- Shafinaz (Wed Sep 24 2003 - 15:29:10 CDT)
- David A. Case (Wed Sep 24 2003 - 14:28:22 CDT)
- Shafinaz (Wed Sep 24 2003 - 14:05:23 CDT)
AMBER: problems with periodic boundary conditions
- David A. Case (Fri Sep 05 2003 - 09:43:29 CDT)
- Michael Crowley (Fri Sep 05 2003 - 09:32:29 CDT)
- Monika Fuxreiter (Fri Sep 05 2003 - 04:17:40 CDT)
AMBER: processors
- Scott Brozell (Thu Sep 04 2003 - 11:50:10 CDT)
- Herbert Georg (Mon Sep 01 2003 - 14:30:04 CDT)
AMBER: ptraj question
- Lishan Yao (Thu Sep 11 2003 - 14:48:08 CDT)
AMBER: radial distribution-function by Ptraj
- Petrodler_at_aol.com (Tue Sep 09 2003 - 04:15:10 CDT)
AMBER: reporting atoms clashed during simple energy minimization
- David A. Case (Tue Sep 09 2003 - 10:36:29 CDT)
- Dr. Yong Duan (Tue Sep 09 2003 - 07:18:44 CDT)
- jackie_at_ibms.sinica.edu.tw (Tue Sep 09 2003 - 05:19:36 CDT)
AMBER: residues and molecules
- Robert Duke (Wed Sep 24 2003 - 14:53:20 CDT)
- David A. Case (Wed Sep 24 2003 - 13:45:40 CDT)
- GUILLERMINA L ESTIU (Tue Sep 23 2003 - 16:56:01 CDT)
AMBER: sander on cygwin
- David E. Konerding DSD Staff (Mon Sep 15 2003 - 16:21:57 CDT)
- David A. Case (Mon Sep 15 2003 - 15:03:23 CDT)
- David E. Konerding DSD Staff (Mon Sep 15 2003 - 13:24:29 CDT)
- Lee, Matthew (Mon Sep 15 2003 - 13:14:40 CDT)
AMBER: Scyld cluster amber 7 compile problems
- Scott Brozell (Thu Sep 18 2003 - 12:50:08 CDT)
- Bengt Svensson (Wed Sep 17 2003 - 20:11:04 CDT)
AMBER: SHAKE poblem with dummy atoms
- David A. Case (Tue Sep 09 2003 - 10:38:49 CDT)
- Itziar Maestre Asenjo (Tue Sep 09 2003 - 05:06:57 CDT)
AMBER: slow simulation
- David A. Case (Mon Sep 22 2003 - 09:54:46 CDT)
- nie beining (Mon Sep 22 2003 - 01:46:21 CDT)
AMBER: slower simulation
- Carlos Simmerling (Mon Sep 22 2003 - 10:59:02 CDT)
- nie beining (Mon Sep 22 2003 - 10:43:24 CDT)
AMBER: Slower simulation and pair-range cutoff?
- nie beining (Mon Sep 22 2003 - 12:11:11 CDT)
AMBER: solvatebox-solvateshell
- Xavier Periole (Mon Sep 08 2003 - 16:46:00 CDT)
- Thomas E. Cheatham, III (Sat Sep 06 2003 - 15:16:38 CDT)
- David A. Case (Sat Sep 06 2003 - 14:56:39 CDT)
- Majid moghaddam (Sat Sep 06 2003 - 06:42:55 CDT)
AMBER: Suggestion regarding long simulation.
- Carlos Simmerling (Fri Sep 19 2003 - 07:05:58 CDT)
- Carlos Simmerling (Thu Sep 18 2003 - 21:12:20 CDT)
- Yong Duan (Thu Sep 18 2003 - 19:33:30 CDT)
- Johannes Zuegg (Thu Sep 18 2003 - 17:56:39 CDT)
- uddhavesh bhaskar sonavane (Thu Sep 18 2003 - 01:50:37 CDT)
AMBER: surften value in mm_gbsa/mm_pbsa calculations
- Holger Gohlke (Tue Sep 02 2003 - 15:30:15 CDT)
- Sergio E. Wong (Tue Sep 02 2003 - 14:34:22 CDT)
AMBER: TIP5P
- David A. Case (Wed Sep 10 2003 - 10:14:18 CDT)
- Ulf Johansson (Wed Sep 10 2003 - 02:37:36 CDT)
- David A. Case (Tue Sep 09 2003 - 10:32:58 CDT)
- Ulf Johansson (Tue Sep 09 2003 - 08:27:27 CDT)
AMBER: TTF parameters
- northrop_at_chem.ucla.edu (Tue Sep 30 2003 - 01:49:20 CDT)
AMBER: update to answer about solvateShell
- David A. Case (Sat Sep 06 2003 - 15:00:50 CDT)
AMBER: Using NWCHEM for esp?
- FyD (Sun Sep 07 2003 - 16:19:33 CDT)
- Peter Oelschlaeger (Fri Sep 05 2003 - 23:03:29 CDT)
- David E. Konerding DSD Staff (Fri Sep 05 2003 - 12:59:45 CDT)
AMBER: what can't I use ibelly?
- David A. Case (Mon Sep 01 2003 - 23:18:12 CDT)
- nie beining (Mon Sep 01 2003 - 21:39:06 CDT)
AMBER: xLEAP Problem
- Donald Thomas (Sun Sep 21 2003 - 21:37:23 CDT)
- Kazuo Koyano (Sun Sep 21 2003 - 21:18:49 CDT)
- Niko Jukarainen (Fri Sep 19 2003 - 16:18:30 CDT)
- Stephen P. Molnar, Ph.D. (Fri Sep 19 2003 - 15:07:14 CDT)
AMBER: Zn in antechamber
- Lishan Yao (Mon Sep 29 2003 - 15:15:04 CDT)
- Junmei Wang (Mon Sep 29 2003 - 11:38:09 CDT)
- Lishan Yao (Mon Sep 29 2003 - 10:59:09 CDT)
- Junmei Wang (Mon Sep 29 2003 - 10:32:52 CDT)
- Lishan Yao (Mon Sep 29 2003 - 10:13:42 CDT)
- Junmei Wang (Fri Sep 26 2003 - 15:24:46 CDT)
- Lishan Yao (Fri Sep 26 2003 - 14:15:21 CDT)
- Rhonda Torres (Fri Sep 26 2003 - 12:24:16 CDT)
- Junmei Wang (Fri Sep 26 2003 - 12:00:11 CDT)
- Lishan Yao (Fri Sep 26 2003 - 10:01:41 CDT)
- Junmei Wang (Fri Sep 26 2003 - 09:47:45 CDT)
- Lishan Yao (Fri Sep 26 2003 - 08:48:44 CDT)
MD problem!!
- Yong Duan (Thu Sep 18 2003 - 14:32:49 CDT)
- Pradipta Bandyopadhyay (Thu Sep 18 2003 - 12:36:59 CDT)
MeCNBOX
- Pradipta Bandyopadhyay (Thu Sep 25 2003 - 16:23:09 CDT)
Residual dipolar couplings
- David A. Case (Fri Sep 26 2003 - 15:36:25 CDT)
- McAteer, Kathleen (Fri Sep 26 2003 - 14:44:57 CDT)
torsional energy
- David A. Case (Wed Sep 10 2003 - 17:15:34 CDT)
xLEAP Problem
- Stephen P. Molnar, Ph.D. (Mon Sep 22 2003 - 11:36:48 CDT)

Last message date: Fri Feb 06 2004 - 10:15:04 CST
Archived on: Thu May 05 2005 - 14:17:44 CDT

237 messages sorted by: [ author ] [ date ] [ thread ]
About this archive