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AMBER Archive (2005) - Mar 2005 By Thread
Most recent messages384 messages sorted by: [ author ] [ date ] [ subject ]
About this archive
Starting: Tue Mar 01 2005 - 01:14:51 CST
Ending: Thu Mar 31 2005 - 22:30:40 CST
- AMBER: Re: inconsistent ordering in an improper dihedral of TRP Sanghyun Park (Thu Mar 10 2005 - 21:08:25 CST)
- Re: AMBER: Cu++ and RED Cenk Andac (Sat Mar 12 2005 - 06:28:34 CST)
- Re:Re: AMBER: Cu++ and RED Cenk Andac (Sat Mar 12 2005 - 12:39:10 CST)
- Re: AMBER: Amber Poisson-Boltzmann MD :Equilibration Problem David A. Case (Tue Mar 01 2005 - 10:41:08 CST)
- AMBER: An error during minimization using RED tomjas_at_poczta.onet.pl (Tue Mar 01 2005 - 01:18:55 CST)
- AMBER: Controlling number of water residues... Pavan G (Tue Mar 01 2005 - 01:14:51 CST)
- AMBER: problem with MD simulation Ye Mei (Tue Mar 01 2005 - 02:00:31 CST)
- AMBER: NaNQ ilaria massarelli (Tue Mar 01 2005 - 02:45:10 CST)
- AMBER: Dihedral Energy calculation yen li (Tue Mar 01 2005 - 12:12:56 CST)
- RE: AMBER: Dihedral Energy calculation Junmei Wang (Tue Mar 01 2005 - 12:57:49 CST)
- AMBER: MM-GBSA Alessio Coi (Wed Mar 02 2005 - 04:00:52 CST)
- RE: AMBER: Dihedral Energy calculation yen li (Fri Mar 04 2005 - 15:29:08 CST)
- AMBER: PMEMD on Opterons; building/benchmarks/recommendations Robert Duke (Tue Mar 01 2005 - 13:14:56 CST)
- AMBER: Xleap execution problems on Solaris Joe Nolan (Tue Mar 01 2005 - 14:51:26 CST)
- AMBER: RESP of negatively charged molecule Rhoad, Jonathan S. (Tue Mar 01 2005 - 15:39:05 CST)
- AMBER: Sample more conformational space Bogos Agianian (Wed Mar 02 2005 - 06:52:49 CST)
- AMBER: bond type for a virtual bond in a biomolecular transition state Eric Hu (Wed Mar 02 2005 - 16:54:45 CST)
- AMBER: Installation problem S.Sundar Raman (Thu Mar 03 2005 - 00:28:29 CST)
- AMBER: Amber 8 on cygwin install problem Maciej (Thu Mar 03 2005 - 04:49:17 CST)
- AMBER: phosphorylated DNA not recognized Annette Höglund (Thu Mar 03 2005 - 08:55:18 CST)
- AMBER: bond connectivity among dummy atoms Eric Hu (Thu Mar 03 2005 - 12:56:32 CST)
- AMBER: A problem about Gaussian Yanze Zhang (Thu Mar 03 2005 - 16:38:59 CST)
- Re: AMBER: A problem about Gaussian FyD (Thu Mar 03 2005 - 17:27:23 CST)
- AMBER: Dummy atoms: Changing the source code Ilyas Yildirim (Thu Mar 03 2005 - 18:24:03 CST)
- Re: AMBER: Dummy atoms: Changing the source code Julien Michel (Fri Mar 04 2005 - 03:44:31 CST)
- Re: AMBER: Dummy atoms: Changing the source code Ilyas Yildirim (Fri Mar 04 2005 - 20:56:34 CST)
- Re: AMBER: Dummy atoms: Changing the source code David A. Case (Tue Mar 08 2005 - 13:50:58 CST)
- Re: AMBER: Dummy atoms: Changing the source code Ilyas Yildirim (Tue Mar 08 2005 - 14:56:48 CST)
- AMBER: Dummy atoms: Changing the source code Ilyas Yildirim (Thu Mar 03 2005 - 18:24:03 CST)
- Re: AMBER: A problem about Gaussian David A. Case (Thu Mar 03 2005 - 18:55:35 CST)
- Re: AMBER: A problem about Gaussian FyD (Thu Mar 03 2005 - 17:27:23 CST)
- AMBER: Antechamber/Divcon assigned charges Marc Christensen (Thu Mar 03 2005 - 21:38:10 CST)
- AMBER: atom type designation Lihua Wang (Fri Mar 04 2005 - 18:05:10 CST)
- AMBER: R.E.D Wai Keat Yam (Sat Mar 05 2005 - 23:14:49 CST)
- Re: AMBER: R.E.D Piotr Cieplak (Sun Mar 06 2005 - 18:20:42 CST)
- AMBER: Citing Generalized Born Implicit solvent Model (igb=5) Cenk Andac (Sun Mar 06 2005 - 18:57:21 CST)
- AMBER: AMBER8 Compile Error on Dual Opteron Thomas Patko (Sun Mar 06 2005 - 19:53:46 CST)
- AMBER: amber with mpich-G2 putra abdullah (Sun Mar 06 2005 - 20:55:44 CST)
- AMBER: A problem about removing waters and counterions by ptraj scopio (Mon Mar 07 2005 - 06:28:19 CST)
- AMBER: New pmemd build utility; pathscale vs. pgi vs. ifort em64 opteron benchmarks Robert Duke (Mon Mar 07 2005 - 10:47:02 CST)
- AMBER: What PRESS is? hj zou (Mon Mar 07 2005 - 21:08:39 CST)
- AMBER: global pH variation in AMBER. Osman Gani (Tue Mar 08 2005 - 04:56:06 CST)
- AMBER: Error limits of TI and MM_PBSA methods Nelson Fonseca (Tue Mar 08 2005 - 10:54:42 CST)
- AMBER: Energy fluctuations David.LeBard_at_asu.edu (Tue Mar 08 2005 - 11:40:46 CST)
- AMBER: radii "leap" from which file xhu1_at_memphis.edu (Tue Mar 08 2005 - 13:34:48 CST)
- AMBER: Sander questions on dual-processor Sun with MPICH Joe Nolan (Tue Mar 08 2005 - 14:37:50 CST)
- RE: AMBER: Sander questions on dual-processor Sun with MPICH Ross Walker (Tue Mar 08 2005 - 19:50:55 CST)
- Re: AMBER: Sander questions on dual-processor Sun with MPICH Robert Duke (Wed Mar 09 2005 - 07:41:08 CST)
- Re: AMBER: Sander questions on dual-processor Sun with MPICH Joe Nolan (Thu Mar 10 2005 - 10:46:23 CST)
- AMBER: X Windows for LEaP on SGI Akshay Patny (Tue Mar 08 2005 - 15:07:44 CST)
- AMBER: capping? Hui-Hsu Tsai (Tue Mar 08 2005 - 15:34:59 CST)
- Re: AMBER: radii "leap" from which file Bill Ross (Tue Mar 08 2005 - 15:43:18 CST)
- AMBER: heating Gustavo Pierdominici Sottile (Tue Mar 08 2005 - 16:20:34 CST)
- Re: AMBER: heating Bill Ross (Tue Mar 08 2005 - 16:55:47 CST)
- AMBER: The pressure bybaker_at_itsa.ucsf.edu (Tue Mar 08 2005 - 19:54:44 CST)
- AMBER: how can I deal with the puzzle? hj zou (Tue Mar 08 2005 - 21:36:39 CST)
- AMBER: Problems Binding Protein to DNA Pieter Smith (Tue Mar 08 2005 - 23:21:30 CST)
- AMBER: amber on sgi mathew k varghese (Wed Mar 09 2005 - 05:23:12 CST)
- AMBER: For further question about Targeted MD ZhangJian (Wed Mar 09 2005 - 06:48:44 CST)
- AMBER: vlimit in heating Gustavo Pierdominici Sottile (Wed Mar 09 2005 - 08:13:20 CST)
- Re: AMBER: vlimit in heating Bill Ross (Wed Mar 09 2005 - 09:44:06 CST)
- AMBER: solvatebox problem in the antechamber tutorial Heiko Meyer (Wed Mar 09 2005 - 10:29:00 CST)
- AMBER: vlimit heat Gustavo Pierdominici Sottile (Wed Mar 09 2005 - 11:36:30 CST)
- AMBER: Re: Amber 8 dual-Xeon compile problem keiodai_at_shohoku.ac.jp (Wed Mar 09 2005 - 22:14:33 CST)
- AMBER: how to excite a single residue ? Priti Hansia (Wed Mar 09 2005 - 22:28:24 CST)
- AMBER: PTRAJ $ Antechamber Andrew Box (Thu Mar 10 2005 - 00:47:29 CST)
- AMBER: Sander error Vojtěch Klusák (Thu Mar 10 2005 - 06:03:21 CST)
- Re: AMBER: PTRAJ $ Antechamber Bill Ross (Thu Mar 10 2005 - 11:22:39 CST)
- AMBER: expected error in mean (Amber 8 TI tutorial) Eric Hu (Thu Mar 10 2005 - 17:38:13 CST)
- AMBER: IDIEL in sander sebnem (Fri Mar 11 2005 - 01:14:50 CST)
- AMBER: vlimit Gustavo Pierdominici Sottile (Fri Mar 11 2005 - 06:33:36 CST)
- AMBER: Holes in water Lukasz Bielecki (Fri Mar 11 2005 - 08:13:40 CST)
- AMBER: problem with nmode using ntrun=5 Phineus Markwick (Fri Mar 11 2005 - 08:38:34 CST)
- Re: AMBER: Re: inconsistent ordering in an improper dihedral of TRP Bill Ross (Fri Mar 11 2005 - 09:46:40 CST)
- Re: Re :AMBER: Holes in water Bill Ross (Fri Mar 11 2005 - 09:59:03 CST)
- AMBER: problem with nmode using ntrun=5 (2) Phineus Markwick (Fri Mar 11 2005 - 10:39:43 CST)
- AMBER: ptraj xueping (Fri Mar 11 2005 - 22:56:29 CST)
- AMBER: Amber PBMD:Energy fluctuation Praveena Gopal (Sat Mar 12 2005 - 03:48:03 CST)
- AMBER: spherical boundary condition Hui-Hsu Tsai (Sat Mar 12 2005 - 13:05:52 CST)
- AMBER: mesure dihedral angle during MD julien (Sun Mar 13 2005 - 10:52:01 CST)
- AMBER: gyration radius julien (Sun Mar 13 2005 - 10:49:50 CST)
- Re: AMBER: gyration radius Bill Ross (Sun Mar 13 2005 - 13:36:15 CST)
- AMBER: leap warnings mathew k varghese (Mon Mar 14 2005 - 00:34:32 CST)
- AMBER: surfen and surfoff Giulio Rastelli (Mon Mar 14 2005 - 10:21:22 CST)
- AMBER: RDF input preparation problem Maciej (Sun Mar 13 2005 - 22:12:22 CST)
- AMBER: Xserve and amber Markus W. Germann (Mon Mar 14 2005 - 10:55:53 CST)
- AMBER: Geometrical distortion because of charge? peng79_at_email.unc.edu (Mon Mar 14 2005 - 12:21:28 CST)
- AMBER: Question about radial command in ptraj opitz_at_che.udel.edu (Mon Mar 14 2005 - 13:19:11 CST)
- Re: AMBER: Question about radial command in ptraj Bill Ross (Mon Mar 14 2005 - 13:48:17 CST)
- AMBER: antechamber and multiplicity Cenk Andac (Mon Mar 14 2005 - 13:57:27 CST)
- AMBER: determining solvent/ion densities Joseph W.Toporowski (Mon Mar 14 2005 - 17:35:25 CST)
- AMBER: Hydrogen bonding question opitz_at_che.udel.edu (Tue Mar 15 2005 - 08:57:45 CST)
- AMBER: Problem saving file in xleap aanzellotti_at_mail2.vcu.edu (Tue Mar 15 2005 - 11:03:12 CST)
- AMBER: Sander: idecomp lei jia (Tue Mar 15 2005 - 13:45:47 CST)
- AMBER: frcmod.mod_phipsi.2 bybaker_at_itsa.ucsf.edu (Tue Mar 15 2005 - 14:04:31 CST)
- AMBER: in vacuo parameters Stern, Julie (Tue Mar 15 2005 - 17:14:44 CST)
- AMBER: Bio-Image summer school in Paris this year Marc Baaden (Wed Mar 16 2005 - 05:44:47 CST)
- AMBER: restraintmask dimension Piero Altoč (Wed Mar 16 2005 - 05:42:12 CST)
- AMBER: Velocity Info Vineet Pande (Wed Mar 16 2005 - 08:08:42 CST)
- AMBER: "personality" of Amber force field Hui-Hsu Tsai (Wed Mar 16 2005 - 10:01:00 CST)
- AMBER: question about amber parameter file format etc. jz7_at_duke.edu (Wed Mar 16 2005 - 11:37:29 CST)
- AMBER: periodicity problem Stern, Julie (Wed Mar 16 2005 - 15:02:28 CST)
- AMBER: Zn complex parametrization question Ashutosh Suhas Jogalekar (Wed Mar 16 2005 - 15:27:38 CST)
- Re: AMBER: periodicity problem Bill Ross (Wed Mar 16 2005 - 16:23:03 CST)
- AMBER: sander.QMMM and fcap Claudio Morgado (Thu Mar 17 2005 - 07:56:34 CST)
- AMBER: van der Waals interactions (PTRAJ) Vineet Pande (Thu Mar 17 2005 - 08:07:12 CST)
- AMBER: Minimization of avg structure-SANDER Bomb Vineet Pande (Thu Mar 17 2005 - 08:50:03 CST)
- AMBER: Bus error - ambpdb David C. Chan (Thu Mar 17 2005 - 08:54:17 CST)
- AMBER: compiler for amber8 on opteron Marc Petitmermet (Thu Mar 17 2005 - 09:56:37 CST)
- AMBER: Making topology files of big moleucles in antechamber Hwankyu Lee (Thu Mar 17 2005 - 10:09:06 CST)
- AMBER: add waters to a system + leap problem with solvateOct command Fabien Cailliez (Thu Mar 17 2005 - 12:30:24 CST)
- AMBER: Trajectory problems Steve Seibold (Thu Mar 17 2005 - 13:21:37 CST)
- AMBER: building helix bundle Yanze Zhang (Thu Mar 17 2005 - 15:30:54 CST)
- AMBER: Trajectory problems Steve Seibold (Thu Mar 17 2005 - 15:44:23 CST)
- AMBER: Separating solvent and solute energy in the microcanonical mode Mey Khalili (Thu Mar 17 2005 - 16:50:09 CST)
- AMBER: ptraj: determining solvent/ion densities Joseph W.Toporowski (Thu Mar 17 2005 - 19:40:38 CST)
- AMBER: re Updating Tutorials Vidana.Epa_at_csiro.au (Thu Mar 17 2005 - 21:17:50 CST)
- AMBER: Replica Exchange crashing Hayden Eastwood (Fri Mar 18 2005 - 06:39:48 CST)
- AMBER: layer Gustavo Pierdominici Sottile (Fri Mar 18 2005 - 08:42:53 CST)
- AMBER: lmanal input file problem Phineus Markwick (Fri Mar 18 2005 - 10:00:18 CST)
- AMBER: parameter meaning Wei Wang (Fri Mar 18 2005 - 12:33:15 CST)
- AMBER: Problems with Iodine David.Maxwell_at_di.mdacc.tmc.edu (Fri Mar 18 2005 - 15:03:38 CST)
- AMBER: question about periodicity of torsion parameter jz7_at_duke.edu (Fri Mar 18 2005 - 16:08:50 CST)
- AMBER: PMEMD with big systems Florian Barth (Fri Mar 18 2005 - 17:25:41 CST)
- AMBER: substrate exit from protein in Amber 8.0 TI vdw simulation Eric Hu (Fri Mar 18 2005 - 17:35:39 CST)
- AMBER: igb=10 some vdW terms disappear? Wells, David H (Mon Mar 21 2005 - 01:54:23 CST)
- AMBER: Making prepin file for individual residues of huge molecule. Hwankyu Lee (Mon Mar 21 2005 - 09:00:11 CST)
- AMBER: mm-pbsa with multiple-processors Eric Hu (Mon Mar 21 2005 - 16:21:16 CST)
- AMBER: Dual Xeon EM64T Intel Fortran Compile Problem Shekter, Lee (Mon Mar 21 2005 - 18:12:26 CST)
- RE: AMBER: Dual Xeon EM64T Intel Fortran Compile Problem Ross Walker (Mon Mar 21 2005 - 18:54:52 CST)
- RE: AMBER: Dual Xeon EM64T Intel Fortran Compile Problem Shekter, Lee (Mon Mar 21 2005 - 21:39:42 CST)
- RE: AMBER: Dual Xeon EM64T Intel Fortran Compile Problem Shekter, Lee (Wed Mar 23 2005 - 10:29:57 CST)
- AMBER: TMD force constant Phineus Markwick (Tue Mar 22 2005 - 07:14:53 CST)
- Re: AMBER: MD: Water network analysis + visualization sanjeev_at_mbu.iisc.ernet.in (Tue Mar 22 2005 - 07:58:24 CST)
- AMBER: nonbonded interaction Svetlana Kirillova (Tue Mar 22 2005 - 10:37:54 CST)
- Re: AMBER: nonbonded interaction David A. Case (Tue Mar 22 2005 - 23:38:08 CST)
- AMBER: align snapshots to a reference Wen Li (Tue Mar 29 2005 - 15:38:36 CST)
- Re: AMBER: align snapshots to a reference Carlos Simmerling (Tue Mar 29 2005 - 16:15:29 CST)
- Re: AMBER: align snapshots to a reference Wen Li (Wed Mar 30 2005 - 09:43:21 CST)
- Re: AMBER: align snapshots to a reference Carlos Simmerling (Wed Mar 30 2005 - 10:08:01 CST)
- Re: AMBER: align snapshots to a reference Wen Li (Wed Mar 30 2005 - 10:14:44 CST)
- Re: AMBER: align snapshots to a reference Thomas E. Cheatham, III (Wed Mar 30 2005 - 10:23:21 CST)
- Re: AMBER: align snapshots to a reference Wen Li (Wed Mar 30 2005 - 13:52:34 CST)
- Re: AMBER: align snapshots to a reference Carlos Simmerling (Wed Mar 30 2005 - 10:28:13 CST)
- AMBER: align snapshots to a reference Wen Li (Tue Mar 29 2005 - 15:38:36 CST)
- Re: AMBER: nonbonded interaction David A. Case (Tue Mar 22 2005 - 23:38:08 CST)
- AMBER: ANAL module/AMBER8 Vineet Pande (Tue Mar 22 2005 - 11:32:06 CST)
- AMBER: Amber8 Parallel installation troubles Joe Nolan (Tue Mar 22 2005 - 13:03:05 CST)
- AMBER: wierd behavior of addions jz7_at_duke.edu (Tue Mar 22 2005 - 13:22:54 CST)
- AMBER: Methionine with both C-ter and N-ter jz7_at_duke.edu (Tue Mar 22 2005 - 16:17:18 CST)
- AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' luckyang_at_gmail.com (Tue Mar 22 2005 - 17:34:05 CST)
- Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' Wei Zhang (Tue Mar 22 2005 - 18:29:26 CST)
- Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' luckyang_at_gmail.com (Tue Mar 22 2005 - 18:46:26 CST)
- Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' Wei Zhang (Tue Mar 22 2005 - 19:34:26 CST)
- Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' luckyang_at_gmail.com (Wed Mar 23 2005 - 16:18:45 CST)
- Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' luckyang_at_gmail.com (Wed Mar 23 2005 - 17:01:49 CST)
- Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' Wei Zhang (Wed Mar 23 2005 - 18:49:14 CST)
- Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' luckyang_at_gmail.com (Tue Mar 22 2005 - 18:46:26 CST)
- Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' Wei Zhang (Tue Mar 22 2005 - 18:29:26 CST)
- AMBER: "ERROR TERMINATION DUE TO SHAKE OR TORCON" in Gibbs tanc_at_uci.edu (Tue Mar 22 2005 - 23:11:41 CST)
- Re: AMBER: nonbonded interactions Svetlana Kirillova (Wed Mar 23 2005 - 03:23:47 CST)
- AMBER: warning in PBSA Fabien Cailliez (Wed Mar 23 2005 - 07:39:00 CST)
- AMBER: Could not open file (trajin) with mode (r) Maciej (Wed Mar 23 2005 - 07:52:20 CST)
- AMBER: antechamber availability dmitri.mikhailov_at_novartis.com (Wed Mar 23 2005 - 14:40:47 CST)
- AMBER: A few question about RDF input preparation Maciej (Thu Mar 24 2005 - 05:13:10 CST)
- AMBER: Make test error Amber (Thu Mar 24 2005 - 15:10:53 CST)
- AMBER: question about placing a substrate in a protein pocket Kara Di Giorgio (Thu Mar 24 2005 - 22:33:26 CST)
- AMBER: Re: ask for your help: parallel on mm_pbsa FyD (Sat Mar 26 2005 - 11:09:23 CST)
- AMBER: PTRAJ:"hbond" doubts Vineet Pande (Sun Mar 27 2005 - 07:55:24 CST)
- AMBER: missing residue xueping (Mon Mar 28 2005 - 01:34:17 CST)
- AMBER: ptraj analysis Tatyana B Mamonova (Mon Mar 28 2005 - 11:24:55 CST)
- AMBER: Parameter files for general lipids Nitin Bhardwaj (Mon Mar 28 2005 - 18:57:46 CST)
- AMBER: REM mdinfo file Sergio E. Wong (Mon Mar 28 2005 - 19:51:45 CST)
- AMBER: vlimit exceeded in thermalization Holly Freedman (Mon Mar 28 2005 - 22:16:12 CST)
- AMBER: Are the constant pH simulations with explicit water possible? Kateryna Miroshnychenko (Tue Mar 29 2005 - 07:54:14 CST)
- AMBER: protonated aspartic acid Adrian E. Roitberg (Tue Mar 29 2005 - 14:14:35 CST)
- AMBER: tleap,xleap bond order for triple bonds Stern, Julie (Tue Mar 29 2005 - 16:49:38 CST)
- AMBER: Minimization failure S.Sundar Raman (Tue Mar 29 2005 - 22:47:22 CST)
- AMBER: how to cap regions S.Sundar Raman (Tue Mar 29 2005 - 23:00:12 CST)
- AMBER: Amber Performance in Parallel on Itanium Robert J. Woods (Wed Mar 30 2005 - 09:32:10 CST)
- AMBER: PTRAJ:"hbond" analysis Vineet Pande (Wed Mar 30 2005 - 11:15:30 CST)
- AMBER: OH- dynamics Eric Hu (Wed Mar 30 2005 - 11:55:19 CST)
- AMBER: igb10 vlimit exceeded Wells, David H (Thu Mar 31 2005 - 03:08:55 CST)
- AMBER: All the tests passed except prmtop and prepin... mmv_at_whu.edu.cn (Thu Mar 31 2005 - 03:59:26 CST)
- AMBER: AMBER under MOSIX? Atro Tossavainen (Thu Mar 31 2005 - 05:47:47 CST)
- AMBER: Compiling on dual-opteron with pathscale 2.1 on RHEL 4 AS Marc Petitmermet (Thu Mar 31 2005 - 09:32:31 CST)
- AMBER: What does this mean .. ? Pavan Ghatty (Thu Mar 31 2005 - 13:14:53 CST)
- AMBER: leap bond error Stern, Julie (Thu Mar 31 2005 - 19:11:29 CST)
- AMBER: Target MD and nmode test hang Mingfeng Yang (Thu Mar 31 2005 - 20:08:13 CST)
- AMBER: GB dynamics mathew k varghese (Thu Mar 31 2005 - 22:01:30 CST)
- AMBER: solvateoct mymolecule CHCL3BOX 10 PROBLEM!!! chaiann ng (Thu Mar 31 2005 - 22:30:40 CST)
Last message date: Sat Dec 31 2005 - 12:51:27 CST
Archived on: Sat Dec 31 2005 - 12:51:45 CST
384 messages sorted by: [ author ] [ date ] [ subject ]
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