AMBER Archive (2005) - Jun 2005 By ThreadMost recent messages
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Starting: Wed Jun 01 2005 - 03:48:46 CDT
Ending: Thu Jun 30 2005 - 23:33:25 CDT
- AMBER: problem in minimization Ananda Rama Krishnan Selvaraj (Wed Jun 01 2005 - 03:48:46 CDT)
- AMBER: Saturated DNA bases L.C. Heady (Wed Jun 01 2005 - 03:55:54 CDT)
- AMBER: eigenvalues in vector of ptraj Hwankyu Lee (Wed Jun 01 2005 - 07:53:51 CDT)
- AMBER: stripwater Lukasz Bielecki (Wed Jun 01 2005 - 09:16:05 CDT)
- AMBER: Build of AMBER for YDL ? Gert Kiss (Wed Jun 01 2005 - 18:15:57 CDT)
- AMBER: gaff.dat typo Brent Krueger (Wed Jun 01 2005 - 20:35:58 CDT)
- AMBER: amber question about leap du yongchun (Thu Jun 02 2005 - 00:12:12 CDT)
- AMBER: amber8 installation problems Zhang Bing (Thu Jun 02 2005 - 01:44:47 CDT)
- AMBER: amber8 installation problems Zhang Bing (Thu Jun 02 2005 - 01:55:48 CDT)
- AMBER: question whem using leap du yongchun (Thu Jun 02 2005 - 02:25:16 CDT)
- AMBER: Argon Box Biswaroop Mukherjee (Thu Jun 02 2005 - 03:44:46 CDT)
- AMBER: center-of-mass distance restraints JAVIER PEREZ (Thu Jun 02 2005 - 06:14:15 CDT)
- AMBER: Simon Whitehead (Thu Jun 02 2005 - 07:44:03 CDT)
- AMBER: Protein ions? Anthony Cruz (Thu Jun 02 2005 - 09:12:56 CDT)
- AMBER: How does Amber8 implemnet ntf=4? Li Su (Thu Jun 02 2005 - 10:32:30 CDT)
- AMBER: checkoverlap Gustavo Pierdominici Sottile (Thu Jun 02 2005 - 12:45:19 CDT)
- AMBER: pressure output Germán Sciaini (Thu Jun 02 2005 - 17:27:13 CDT)
- AMBER: advice needed for minimization and dynamic protocol chaiann ng (Thu Jun 02 2005 - 20:33:44 CDT)
- AMBER: New problem of parallel sander Zhang Bing (Thu Jun 02 2005 - 21:46:13 CDT)
- AMBER: TI in Amber8 ½¨Æ½ ºú (Fri Jun 03 2005 - 04:49:02 CDT)
- AMBER: Nmode with residues excluded Martin Sippel (Fri Jun 03 2005 - 11:56:42 CDT)
- AMBER: Nmode calculations Martin Sippel (Fri Jun 03 2005 - 12:17:48 CDT)
- AMBER: radius parameter for Mg2+ in mm_pbsa calculation Ye Mei (Sat Jun 04 2005 - 09:37:04 CDT)
- AMBER: SHAKE in md with partial solvation Ye Mei (Sun Jun 05 2005 - 02:30:00 CDT)
- AMBER: fail of minimization in sander wendy (Sun Jun 05 2005 - 22:01:25 CDT)
- Re: AMBER: fail of minimization in sander Bill Ross (Sun Jun 05 2005 - 22:50:48 CDT)
- AMBER: nmode with ibelly Martin Sippel (Mon Jun 06 2005 - 04:38:42 CDT)
- AMBER: Solvate question? Anthony Cruz (Mon Jun 06 2005 - 05:30:44 CDT)
- AMBER: Re: Re: AMBER: SHAKE in md with partial solvation Ye Mei (Mon Jun 06 2005 - 05:49:44 CDT)
- AMBER: Compile question?? Anthony Cruz (Mon Jun 06 2005 - 06:59:13 CDT)
- AMBER: Solvents Anthony Cruz (Mon Jun 06 2005 - 11:00:07 CDT)
- AMBER: GB/SA/LD parallel sander Lwin, ThuZar (Mon Jun 06 2005 - 11:48:27 CDT)
- AMBER: eelnb Stern, Julie (Mon Jun 06 2005 - 15:16:31 CDT)
- AMBER: Protein dynamics. Laurence Lavelle (Mon Jun 06 2005 - 16:43:50 CDT)
- AMBER: segmentation fault in sander Kenley Barrett (Mon Jun 06 2005 - 17:07:59 CDT)
- Re: AMBER: segmentation fault in sander Bill Ross (Mon Jun 06 2005 - 17:18:45 CDT)
- AMBER: Gibbs perturb DNA strands separate ivan_at_mmb.pcb.ub.es (Tue Jun 07 2005 - 06:16:41 CDT)
- AMBER: nucgen problem cbala_at_igib.res.in (Tue Jun 07 2005 - 08:41:27 CDT)
- AMBER: Question about tutorial-9 Varsha Goyal (Tue Jun 07 2005 - 11:27:57 CDT)
- Re: AMBER: nucgen problem Bill Ross (Tue Jun 07 2005 - 11:47:42 CDT)
- AMBER: AMBER frcmod+off input vs. prep input K. Yarem (Tue Jun 07 2005 - 11:57:19 CDT)
- Re: AMBER: AMBER frcmod+off input vs. prep input Bill Ross (Tue Jun 07 2005 - 12:58:06 CDT)
- AMBER: TI calculation using sander Latifa Douali (Tue Jun 07 2005 - 19:10:54 CDT)
- AMBER: How to run amber more efficiently? alice (Tue Jun 07 2005 - 21:59:26 CDT)
- AMBER: Protein dynamics. Laurence Lavelle (Wed Jun 08 2005 - 00:52:00 CDT)
- AMBER: Sander is changing directories Andreas Kerzmann (Wed Jun 08 2005 - 04:37:58 CDT)
- AMBER: Sander is changing directories Andreas Kerzmann (Wed Jun 08 2005 - 04:39:23 CDT)
- AMBER: total energy leaps cristian obiol (Wed Jun 08 2005 - 05:44:18 CDT)
- AMBER: TI tutorial in Amber 8 huhu (Wed Jun 08 2005 - 04:52:24 CDT)
- AMBER: (no subject) Mohammed Mayeed (Wed Jun 08 2005 - 12:26:15 CDT)
- AMBER: Protein-surface interaction Mohammed Mayeed (Wed Jun 08 2005 - 13:37:30 CDT)
- AMBER: GB/SA/LD parallel sander Lwin, ThuZar (Wed Jun 08 2005 - 14:36:41 CDT)
- AMBER: Compile Problems of Parallel Amber8 on Mac G5 Suxin Zheng (Wed Jun 08 2005 - 18:02:23 CDT)
- AMBER: precision switch from 64 to 32 bit (double from single precision) Cordova, Luis E. (Thu Jun 09 2005 - 00:39:59 CDT)
- AMBER: normal mode mm/pbsa interupted Eric Hu (Thu Jun 09 2005 - 13:46:04 CDT)
- AMBER: setting up restraint with ntr option Lwin, ThuZar (Thu Jun 09 2005 - 16:49:04 CDT)
- AMBER: atom type for -CH=CH- Qizhi Cui (Thu Jun 09 2005 - 20:46:13 CDT)
- AMBER: substitute missing residues? Wai Keat Yam (Fri Jun 10 2005 - 03:20:29 CDT)
- AMBER: Vibrational spectrum? milion_at_c-box.cz (Fri Jun 10 2005 - 03:31:27 CDT)
- AMBER: SOURCE3 in gaff.dat Stern, Julie (Fri Jun 10 2005 - 04:40:20 CDT)
- AMBER: vdw for terminal phosphate Rhoad, Jonathan S. (Fri Jun 10 2005 - 11:16:47 CDT)
- Re: AMBER: vdw for terminal phosphate Bill Ross (Fri Jun 10 2005 - 13:10:32 CDT)
- AMBER: Can constant pH be used for minimization? Kenley Barrett (Fri Jun 10 2005 - 16:34:41 CDT)
- AMBER: inpcrd file Douali, Latifa (Fri Jun 10 2005 - 18:04:24 CDT)
- AMBER: Installation problem Sukjoon Yoon (Sun Jun 12 2005 - 04:21:50 CDT)
- AMBER: no corrected reaction field energy in *.out files after running mm_pbsa haixiao jin (Sun Jun 12 2005 - 21:04:40 CDT)
- AMBER: how to pull out frames Vijay Manickam Achari (Mon Jun 13 2005 - 00:23:51 CDT)
- AMBER: leap issues on a powerbook justin litchfield (Sun Jun 12 2005 - 18:21:02 CDT)
- AMBER: Need help in charge fitting through RESP S.Sundar Raman (Mon Jun 13 2005 - 08:55:29 CDT)
- AMBER: Announcing the LMOD website Istvan Kolossvary (Mon Jun 13 2005 - 13:18:52 CDT)
- AMBER: GBSA and thermodynamic ensemble Osmar Norberto de Souza (Mon Jun 13 2005 - 13:29:18 CDT)
- AMBER: atom type question opitz_at_che.udel.edu (Mon Jun 13 2005 - 14:41:30 CDT)
- AMBER: why the dipeptide always moving out the virtual box Li Su (Mon Jun 13 2005 - 16:40:47 CDT)
- AMBER: Restrained-MD Ananda Rama Krishnan Selvaraj (Mon Jun 13 2005 - 18:04:14 CDT)
- AMBER: nmropt =1 AND ntr=1 in pmemd Christoph Brockmann (Tue Jun 14 2005 - 04:33:39 CDT)
- AMBER: compiler Zhang Bing (Tue Jun 14 2005 - 03:14:08 CDT)
- AMBER: creating pdb file.... Vijay Manickam Achari (Tue Jun 14 2005 - 05:49:09 CDT)
- AMBER: compiler Zhang Bing (Tue Jun 14 2005 - 06:13:19 CDT)
- AMBER: time and lifetime in hbond analysis (ptraj) Giulio Rastelli (Tue Jun 14 2005 - 09:23:50 CDT)
- AMBER: Request for g98 (IOP...) Paramasivam Manikandan (Tue Jun 14 2005 - 10:04:30 CDT)
- AMBER: sp2 carbon atom parametrization Gustavo Pierdominici Sottile (Tue Jun 14 2005 - 11:30:16 CDT)
- AMBER: Extended bonds-MD Ananda Rama Krishnan Selvaraj (Tue Jun 14 2005 - 11:29:29 CDT)
- AMBER: Free Energy Calculation torsion missing mrbroad_at_ilstu.edu (Tue Jun 14 2005 - 13:21:54 CDT)
- AMBER: puzzling gaff parameter Oliver Hucke (Tue Jun 14 2005 - 20:16:35 CDT)
- AMBER: Thanks Zhang Bing (Tue Jun 14 2005 - 21:26:23 CDT)
- AMBER: solutions of amber installation problems Zhang Bing (Tue Jun 14 2005 - 21:42:13 CDT)
- AMBER: Extended bonds-MD Ananda Rama Krishnan Selvaraj (Wed Jun 15 2005 - 02:02:25 CDT)
- AMBER: bad atom type: H alice (Wed Jun 15 2005 - 05:53:50 CDT)
- AMBER: Question about "quasih" Yen-Ting Lai (Wed Jun 15 2005 - 11:46:22 CDT)
- AMBER: position of protonation info from constant pH run Kenley Barrett (Wed Jun 15 2005 - 20:27:44 CDT)
- AMBER: Cut pdb files Yogesh Sabnis (Thu Jun 16 2005 - 02:57:18 CDT)
- AMBER: adenine test for LMOD in amber8 Giulio Rastelli (Thu Jun 16 2005 - 04:57:16 CDT)
- AMBER: How to modify force constants and equalibrium values for standard residues Li Su (Thu Jun 16 2005 - 08:30:41 CDT)
- AMBER: Question about GAFF atom types Herbert Georg (Thu Jun 16 2005 - 14:18:50 CDT)
- AMBER: For calculating the energy rised from deviation of equalibrium values of bond angles does amber use degree or radians Li Su (Thu Jun 16 2005 - 16:19:36 CDT)
- AMBER: antechamber problems hj zou (Fri Jun 17 2005 - 08:32:27 CDT)
- AMBER: RE: AMBER :LINMIN problem Ross Walker (Fri Jun 17 2005 - 13:27:25 CDT)
- AMBER: Analysing my simulation data.. Vijay Manickam Achari (Sat Jun 18 2005 - 03:32:13 CDT)
- AMBER: antechamber problems hj zou (Sun Jun 19 2005 - 08:50:08 CDT)
- AMBER: average structure emilia wu (Sun Jun 19 2005 - 19:15:53 CDT)
- AMBER: How to set the virtual box size for a calculation run in vacuum Li Su (Mon Jun 20 2005 - 08:27:33 CDT)
- AMBER: How to turn off pme when using periodic box Li Su (Mon Jun 20 2005 - 13:31:09 CDT)
- AMBER: RESP charges of RNA nucleotides with 3' and 5' ends Ilyas Yildirim (Mon Jun 20 2005 - 20:51:11 CDT)
- AMBER: large std error in entropy estimation Ye Mei (Tue Jun 21 2005 - 21:51:43 CDT)
- AMBER: a question about varying positions of dihedral restraints with step number Li Su (Wed Jun 22 2005 - 14:42:02 CDT)
- AMBER: question about Carnal opitz_at_che.udel.edu (Wed Jun 22 2005 - 15:03:45 CDT)
- Re: AMBER: question about Carnal Bill Ross (Wed Jun 22 2005 - 15:51:34 CDT)
- AMBER: RE: tutorial 8 Ross Walker (Wed Jun 22 2005 - 16:15:33 CDT)
- AMBER: software for real polymer MD simulation xhu1_at_memphis.edu (Wed Jun 22 2005 - 16:31:51 CDT)
- AMBER: how the phosphated threonine to be recognized in leap haixiao jin (Thu Jun 23 2005 - 04:03:26 CDT)
- AMBER: Parameters for phosphorylated amino acids Nadine Homeyer (Thu Jun 23 2005 - 08:54:22 CDT)
- AMBER: Parameters for phosphorylated amino acids Nadine Homeyer (Thu Jun 23 2005 - 09:24:08 CDT)
- AMBER: GCC for AMBER on 64 bit machine mfyang (Thu Jun 23 2005 - 12:55:01 CDT)
- AMBER: using xmgrace.... Vijay Manickam Achari (Thu Jun 23 2005 - 21:51:37 CDT)
- AMBER: Have the parameters for dUMP been calculated by somebody? Suxin Zheng (Fri Jun 24 2005 - 20:30:12 CDT)
- AMBER: TI-FEP for ALA --> GLY Jiten (Sat Jun 25 2005 - 00:07:03 CDT)
- AMBER: RED question Kara Di Giorgio (Sat Jun 25 2005 - 17:44:23 CDT)
- AMBER: MM_PBSA ! Pradipta Bandyopadhyay (Sun Jun 26 2005 - 07:43:18 CDT)
- AMBER: Hbond analysis xueping (Sun Jun 26 2005 - 20:27:48 CDT)
- AMBER: mm_pbsa script ! Pradipta Bandyopadhyay (Mon Jun 27 2005 - 01:43:53 CDT)
- AMBER: Request for calculating free energy using AMBER6 S.Sundar Raman (Mon Jun 27 2005 - 06:59:00 CDT)
- AMBER: parallel error Zhang Bing (Mon Jun 27 2005 - 07:36:14 CDT)
- AMBER: INTRA molecular hbonds Giulio Rastelli (Mon Jun 27 2005 - 09:09:23 CDT)
- AMBER: pb_pgb test fail acb15885_at_uprm.edu (Mon Jun 27 2005 - 13:17:48 CDT)
- AMBER: script for calculating hydrogen bond Vijay Manickam Achari (Mon Jun 27 2005 - 21:57:30 CDT)
- AMBER: questions about RNA xinhuang_at_indiana.edu (Mon Jun 27 2005 - 22:19:58 CDT)
- AMBER: calculating torsion angles Vijay Manickam Achari (Tue Jun 28 2005 - 03:59:02 CDT)
- AMBER: dielectric constant Germán Sciaini (Wed Jun 29 2005 - 06:02:24 CDT)
- AMBER: compiler error, SGI Octane Peter Gannett (Tue Jun 28 2005 - 07:54:35 CDT)
- AMBER: amber 8 leap topology file dihedral term problem Angela Liu (Tue Jun 28 2005 - 08:59:57 CDT)
- AMBER: Fw: TI tutorial --> ALA --> GLY TI calculation Jiten (Tue Jun 28 2005 - 10:02:42 CDT)
- AMBER: calculating hydrogen bonds Vijay Manickam Achari (Tue Jun 28 2005 - 21:50:36 CDT)
- AMBER: How to read unformatted restart file in PTRAJ ? JunJun Liu (Wed Jun 29 2005 - 01:20:57 CDT)
- Re: [pgannett@hsc.wvu.edu: AMBER: compiler error, SGI Octane] Roberto Gomperts (Wed Jun 29 2005 - 10:01:00 CDT)
- AMBER: error - compiling antechamber Peter Gannett (Wed Jun 29 2005 - 14:30:20 CDT)
- AMBER: Free energy calculation for protein-protein complex using MM_PBSA Zhiguo Liu (Wed Jun 29 2005 - 20:59:01 CDT)
- AMBER: acceptor and donor in hbond calculation Vijay Manickam Achari (Thu Jun 30 2005 - 00:01:58 CDT)
- AMBER: example script for hbond calculation Vijay Manickam Achari (Thu Jun 30 2005 - 01:27:15 CDT)
- AMBER: 10-12 potential and create atom type Fabien CAILLIEZ (Thu Jun 30 2005 - 12:19:41 CDT)
- AMBER: antechamber error Peter Gannett (Thu Jun 30 2005 - 14:05:25 CDT)
- AMBER: Create new Unit Douali, Latifa (Thu Jun 30 2005 - 18:45:37 CDT)
- AMBER: least square fit of snapshots in md trajectory to a reference frame Ye Mei (Thu Jun 30 2005 - 21:56:08 CDT)
- AMBER: question about spline in sander -- array size of eed_cub Cordova, Luis E. (Thu Jun 30 2005 - 23:33:25 CDT)
Last message date: Sat Dec 31 2005 - 12:51:27 CST
Archived on: Sat Dec 31 2005 - 12:51:45 CST
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