Amber Archive Jun 2005 By Thread
- Re: AMBER: Error on restrained MD equilibration (AMBER 7) Shulin Zhuang (Tue May 31 2005 - 18:36:32 PDT)
- Re: AMBER: density problem Shulin Zhuang (Tue May 31 2005 - 18:49:47 PDT)
- Re: AMBER: Is the MD simulation normal JunJun Liu (Tue May 31 2005 - 19:01:07 PDT)
- AMBER: problem in minimization Ananda Rama Krishnan Selvaraj (Wed Jun 01 2005 - 01:48:46 PDT)
- AMBER: Saturated DNA bases L.C. Heady (Wed Jun 01 2005 - 01:55:54 PDT)
- RE: AMBER: Error on restrained MD equilibration (AMBER 7) L Jin (Wed Jun 01 2005 - 03:20:40 PDT)
- AMBER: eigenvalues in vector of ptraj Hwankyu Lee (Wed Jun 01 2005 - 05:53:51 PDT)
- AMBER: stripwater Lukasz Bielecki (Wed Jun 01 2005 - 07:16:05 PDT)
- RE: RE: AMBER: Antechamber RESP failed for large organic molecule Junmei Wang (Wed Jun 01 2005 - 09:54:42 PDT)
- Re: AMBER: mm/pbsa error Eric Hu (Wed Jun 01 2005 - 10:23:53 PDT)
- AMBER: Build of AMBER for YDL ? Gert Kiss (Wed Jun 01 2005 - 16:15:57 PDT)
- Re: AMBER: MM-PBSA calculation Scott Pendley (Wed Jun 01 2005 - 16:44:05 PDT)
- AMBER: gaff.dat typo Brent Krueger (Wed Jun 01 2005 - 18:35:58 PDT)
- AMBER: amber question about leap du yongchun (Wed Jun 01 2005 - 22:12:12 PDT)
- AMBER: amber8 installation problems Zhang Bing (Wed Jun 01 2005 - 23:44:47 PDT)
- AMBER: amber8 installation problems Zhang Bing (Wed Jun 01 2005 - 23:55:48 PDT)
- AMBER: question whem using leap du yongchun (Thu Jun 02 2005 - 00:25:16 PDT)
- RE:AMBER: density problem cristian obiol (Thu Jun 02 2005 - 01:14:21 PDT)
- AMBER: Argon Box Biswaroop Mukherjee (Thu Jun 02 2005 - 01:44:46 PDT)
- AMBER: center-of-mass distance restraints JAVIER PEREZ (Thu Jun 02 2005 - 04:14:15 PDT)
- AMBER: Simon Whitehead (Thu Jun 02 2005 - 05:44:03 PDT)
- AMBER: Protein ions? Anthony Cruz (Thu Jun 02 2005 - 07:12:56 PDT)
- AMBER: How does Amber8 implemnet ntf=4? Li Su (Thu Jun 02 2005 - 08:32:30 PDT)
- Re: AMBER: DNA base-flipping: TI vs PMF Peter Varnai (Thu Jun 02 2005 - 10:21:56 PDT)
- AMBER: checkoverlap Gustavo Pierdominici Sottile (Thu Jun 02 2005 - 10:45:19 PDT)
- AMBER: pressure output Germán Sciaini (Thu Jun 02 2005 - 15:27:13 PDT)
- AMBER: advice needed for minimization and dynamic protocol chaiann ng (Thu Jun 02 2005 - 18:33:44 PDT)
- AMBER: New problem of parallel sander Zhang Bing (Thu Jun 02 2005 - 19:46:13 PDT)
- AMBER: TI in Amber8 ½¨Æ½ ºú (Fri Jun 03 2005 - 02:49:02 PDT)
- AMBER: Nmode with residues excluded Martin Sippel (Fri Jun 03 2005 - 09:56:42 PDT)
- AMBER: Nmode calculations Martin Sippel (Fri Jun 03 2005 - 10:17:48 PDT)
- AMBER: radius parameter for Mg2+ in mm_pbsa calculation Ye Mei (Sat Jun 04 2005 - 07:37:04 PDT)
- AMBER: SHAKE in md with partial solvation Ye Mei (Sun Jun 05 2005 - 00:30:00 PDT)
- AMBER: fail of minimization in sander wendy (Sun Jun 05 2005 - 20:01:25 PDT)
- Re: AMBER: fail of minimization in sander Bill Ross (Sun Jun 05 2005 - 20:50:48 PDT)
- AMBER: nmode with ibelly Martin Sippel (Mon Jun 06 2005 - 02:38:42 PDT)
- AMBER: Solvate question? Anthony Cruz (Mon Jun 06 2005 - 03:30:44 PDT)
- AMBER: Re: Re: AMBER: SHAKE in md with partial solvation Ye Mei (Mon Jun 06 2005 - 03:49:44 PDT)
- AMBER: Compile question?? Anthony Cruz (Mon Jun 06 2005 - 04:59:13 PDT)
- AMBER: Error: vlimit exceeded for step Hwankyu Lee (Mon Jun 06 2005 - 06:55:57 PDT)
- AMBER: Solvents Anthony Cruz (Mon Jun 06 2005 - 09:00:07 PDT)
- AMBER: GB/SA/LD parallel sander Lwin, ThuZar (Mon Jun 06 2005 - 09:48:27 PDT)
- AMBER: eelnb Stern, Julie (Mon Jun 06 2005 - 13:16:31 PDT)
- AMBER: Protein dynamics. Laurence Lavelle (Mon Jun 06 2005 - 14:43:50 PDT)
- AMBER: segmentation fault in sander Kenley Barrett (Mon Jun 06 2005 - 15:07:59 PDT)
- Re: AMBER: segmentation fault in sander Bill Ross (Mon Jun 06 2005 - 15:18:45 PDT)
- AMBER: Gibbs perturb DNA strands separate ivan.mmb.pcb.ub.es (Tue Jun 07 2005 - 04:16:41 PDT)
- AMBER: nucgen problem cbala.igib.res.in (Tue Jun 07 2005 - 06:41:27 PDT)
- AMBER: Question about tutorial-9 Varsha Goyal (Tue Jun 07 2005 - 09:27:57 PDT)
- Re: AMBER: nucgen problem Bill Ross (Tue Jun 07 2005 - 09:47:42 PDT)
- AMBER: AMBER frcmod+off input vs. prep input K. Yarem (Tue Jun 07 2005 - 09:57:19 PDT)
- Re: AMBER: quadrupole in resp David A. Case (Tue Jun 07 2005 - 10:30:12 PDT)
- Re: AMBER: AMBER frcmod+off input vs. prep input Bill Ross (Tue Jun 07 2005 - 10:58:06 PDT)
- AMBER: TI calculation using sander Latifa Douali (Tue Jun 07 2005 - 17:10:54 PDT)
- AMBER: How to run amber more efficiently? alice (Tue Jun 07 2005 - 19:59:26 PDT)
- AMBER: Protein dynamics. Laurence Lavelle (Tue Jun 07 2005 - 22:52:00 PDT)
- AMBER: Sander is changing directories Andreas Kerzmann (Wed Jun 08 2005 - 02:39:23 PDT)
- AMBER: Sander is changing directories Andreas Kerzmann (Wed Jun 08 2005 - 02:37:58 PDT)
- AMBER: total energy leaps cristian obiol (Wed Jun 08 2005 - 03:44:18 PDT)
- AMBER: TI tutorial in Amber 8 huhu (Wed Jun 08 2005 - 02:52:24 PDT)
- AMBER: (no subject) Mohammed Mayeed (Wed Jun 08 2005 - 10:26:15 PDT)
- AMBER: Protein-surface interaction Mohammed Mayeed (Wed Jun 08 2005 - 11:37:30 PDT)
- AMBER: GB/SA/LD parallel sander Lwin, ThuZar (Wed Jun 08 2005 - 12:36:41 PDT)
- AMBER: Compile Problems of Parallel Amber8 on Mac G5 Suxin Zheng (Wed Jun 08 2005 - 16:02:23 PDT)
- AMBER: precision switch from 64 to 32 bit (double from single precision) Cordova, Luis E. (Wed Jun 08 2005 - 22:39:59 PDT)
- AMBER: normal mode mm/pbsa interupted Eric Hu (Thu Jun 09 2005 - 11:46:04 PDT)
- AMBER: setting up restraint with ntr option Lwin, ThuZar (Thu Jun 09 2005 - 14:49:04 PDT)
- AMBER: atom type for -CH=CH- Qizhi Cui (Thu Jun 09 2005 - 18:46:13 PDT)
- AMBER: substitute missing residues? Wai Keat Yam (Fri Jun 10 2005 - 01:20:29 PDT)
- AMBER: Vibrational spectrum? milion.c-box.cz (Fri Jun 10 2005 - 09:53:01 PDT)
- AMBER: SOURCE3 in gaff.dat Stern, Julie (Fri Jun 10 2005 - 02:40:20 PDT)
- AMBER: vdw for terminal phosphate Rhoad, Jonathan S. (Fri Jun 10 2005 - 09:16:47 PDT)
- Re: AMBER: vdw for terminal phosphate Bill Ross (Fri Jun 10 2005 - 11:10:32 PDT)
- AMBER: Can constant pH be used for minimization? Kenley Barrett (Fri Jun 10 2005 - 14:34:41 PDT)
- AMBER: inpcrd file Douali, Latifa (Fri Jun 10 2005 - 16:04:24 PDT)
- AMBER: Installation problem Sukjoon Yoon (Sun Jun 12 2005 - 02:21:50 PDT)
- AMBER: no corrected reaction field energy in *.out files after running mm_pbsa haixiao jin (Sun Jun 12 2005 - 19:04:40 PDT)
- AMBER: how to pull out frames Vijay Manickam Achari (Sun Jun 12 2005 - 22:23:51 PDT)
- AMBER: leap issues on a powerbook justin litchfield (Sun Jun 12 2005 - 16:21:02 PDT)
- AMBER: Need help in charge fitting through RESP S.Sundar Raman (Mon Jun 13 2005 - 06:55:29 PDT)
- AMBER: Announcing the LMOD website Istvan Kolossvary (Mon Jun 13 2005 - 11:18:52 PDT)
- AMBER: GBSA and thermodynamic ensemble Osmar Norberto de Souza (Mon Jun 13 2005 - 11:29:18 PDT)
- AMBER: atom type question opitz.che.udel.edu (Mon Jun 13 2005 - 12:41:30 PDT)
- AMBER: why the dipeptide always moving out the virtual box Li Su (Mon Jun 13 2005 - 14:40:47 PDT)
- AMBER: Restrained-MD Ananda Rama Krishnan Selvaraj (Mon Jun 13 2005 - 16:04:14 PDT)
- AMBER: compiler Zhang Bing (Tue Jun 14 2005 - 01:14:08 PDT)
- AMBER: nmropt =1 AND ntr=1 in pmemd Christoph Brockmann (Tue Jun 14 2005 - 02:33:39 PDT)
- AMBER: creating pdb file.... Vijay Manickam Achari (Tue Jun 14 2005 - 03:49:09 PDT)
- AMBER: compiler Zhang Bing (Tue Jun 14 2005 - 04:13:19 PDT)
- AMBER: time and lifetime in hbond analysis (ptraj) Giulio Rastelli (Tue Jun 14 2005 - 07:23:50 PDT)
- AMBER: Request for g98 (IOP...) Paramasivam Manikandan (Tue Jun 14 2005 - 08:04:30 PDT)
- AMBER: sp2 carbon atom parametrization Gustavo Pierdominici Sottile (Tue Jun 14 2005 - 09:30:16 PDT)
- AMBER: Extended bonds-MD Ananda Rama Krishnan Selvaraj (Tue Jun 14 2005 - 09:29:29 PDT)
- AMBER: Free Energy Calculation torsion missing mrbroad.ilstu.edu (Tue Jun 14 2005 - 11:21:54 PDT)
- AMBER: puzzling gaff parameter Oliver Hucke (Tue Jun 14 2005 - 18:16:35 PDT)
- AMBER: Thanks Zhang Bing (Tue Jun 14 2005 - 19:26:23 PDT)
- AMBER: solutions of amber installation problems Zhang Bing (Tue Jun 14 2005 - 19:42:13 PDT)
- AMBER: Extended bonds-MD Ananda Rama Krishnan Selvaraj (Wed Jun 15 2005 - 00:02:25 PDT)
- AMBER: bad atom type: H alice (Wed Jun 15 2005 - 03:53:50 PDT)
- AMBER: Question about "quasih" Yen-Ting Lai (Wed Jun 15 2005 - 09:46:22 PDT)
- AMBER: position of protonation info from constant pH run Kenley Barrett (Wed Jun 15 2005 - 18:27:44 PDT)
- AMBER: Cut pdb files Yogesh Sabnis (Thu Jun 16 2005 - 00:57:18 PDT)
- AMBER: adenine test for LMOD in amber8 Giulio Rastelli (Thu Jun 16 2005 - 02:57:16 PDT)
- AMBER: How to modify force constants and equalibrium values for standard residues Li Su (Thu Jun 16 2005 - 06:30:41 PDT)
- AMBER: Question about GAFF atom types Herbert Georg (Thu Jun 16 2005 - 12:18:50 PDT)
- 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 - 14:19:36 PDT)
- AMBER: antechamber problems hj zou (Fri Jun 17 2005 - 06:32:27 PDT)
- AMBER: RE: AMBER :LINMIN problem Ross Walker (Fri Jun 17 2005 - 11:27:25 PDT)
- AMBER: Analysing my simulation data.. Vijay Manickam Achari (Sat Jun 18 2005 - 01:32:13 PDT)
- AMBER: antechamber problems hj zou (Sun Jun 19 2005 - 06:50:08 PDT)
- AMBER: average structure emilia wu (Sun Jun 19 2005 - 17:15:53 PDT)
- AMBER: How to set the virtual box size for a calculation run in vacuum Li Su (Mon Jun 20 2005 - 06:27:33 PDT)
- RE: AMBER: runtime error in sander? Dave S Walker (Mon Jun 20 2005 - 11:02:16 PDT)
- AMBER: How to turn off pme when using periodic box Li Su (Mon Jun 20 2005 - 11:31:09 PDT)
- AMBER: RESP charges of RNA nucleotides with 3' and 5' ends Ilyas Yildirim (Mon Jun 20 2005 - 18:51:11 PDT)
- AMBER: large std error in entropy estimation Ye Mei (Tue Jun 21 2005 - 19:51:43 PDT)
- AMBER: a question about varying positions of dihedral restraints with step number Li Su (Wed Jun 22 2005 - 12:42:02 PDT)
- AMBER: question about Carnal opitz.che.udel.edu (Wed Jun 22 2005 - 13:03:45 PDT)
- Re: AMBER: question about Carnal Bill Ross (Wed Jun 22 2005 - 13:51:34 PDT)
- AMBER: RE: tutorial 8 Ross Walker (Wed Jun 22 2005 - 14:15:33 PDT)
- AMBER: software for real polymer MD simulation xhu1.memphis.edu (Wed Jun 22 2005 - 14:31:51 PDT)
- AMBER: how the phosphated threonine to be recognized in leap haixiao jin (Thu Jun 23 2005 - 02:03:26 PDT)
- AMBER: Parameters for phosphorylated amino acids Nadine Homeyer (Thu Jun 23 2005 - 06:54:22 PDT)
- AMBER: Parameters for phosphorylated amino acids Nadine Homeyer (Thu Jun 23 2005 - 07:24:08 PDT)
- AMBER: GCC for AMBER on 64 bit machine mfyang (Thu Jun 23 2005 - 10:55:01 PDT)
- AMBER: using xmgrace.... Vijay Manickam Achari (Thu Jun 23 2005 - 19:51:37 PDT)
- AMBER: Have the parameters for dUMP been calculated by somebody? Suxin Zheng (Fri Jun 24 2005 - 18:30:12 PDT)
- AMBER: TI-FEP for ALA --> GLY Jiten (Fri Jun 24 2005 - 22:07:03 PDT)
- AMBER: RED question Kara Di Giorgio (Sat Jun 25 2005 - 15:44:23 PDT)
- AMBER: MM_PBSA ! Pradipta Bandyopadhyay (Sun Jun 26 2005 - 05:43:18 PDT)
- AMBER: Hbond analysis xueping (Sun Jun 26 2005 - 18:27:48 PDT)
- AMBER: mm_pbsa script ! Pradipta Bandyopadhyay (Sun Jun 26 2005 - 23:43:53 PDT)
- AMBER: Request for calculating free energy using AMBER6 S.Sundar Raman (Mon Jun 27 2005 - 04:59:00 PDT)
- AMBER: parallel error Zhang Bing (Mon Jun 27 2005 - 05:36:14 PDT)
- AMBER: INTRA molecular hbonds Giulio Rastelli (Mon Jun 27 2005 - 07:09:23 PDT)
- AMBER: pb_pgb test fail acb15885.uprm.edu (Mon Jun 27 2005 - 11:17:48 PDT)
- AMBER: script for calculating hydrogen bond Vijay Manickam Achari (Mon Jun 27 2005 - 19:57:30 PDT)
- AMBER: questions about RNA xinhuang.indiana.edu (Mon Jun 27 2005 - 20:19:58 PDT)
- AMBER: calculating torsion angles Vijay Manickam Achari (Tue Jun 28 2005 - 01:59:02 PDT)
- AMBER: dielectric constant Germán Sciaini (Wed Jun 29 2005 - 04:02:24 PDT)
- AMBER: compiler error, SGI Octane Peter Gannett (Tue Jun 28 2005 - 05:54:35 PDT)
- AMBER: amber 8 leap topology file dihedral term problem Angela Liu (Tue Jun 28 2005 - 06:59:57 PDT)
- AMBER: Fw: TI tutorial --> ALA --> GLY TI calculation Jiten (Tue Jun 28 2005 - 08:02:42 PDT)
- AMBER: calculating hydrogen bonds Vijay Manickam Achari (Tue Jun 28 2005 - 19:50:36 PDT)
- AMBER: How to read unformatted restart file in PTRAJ ? JunJun Liu (Tue Jun 28 2005 - 23:20:57 PDT)
- Re: [pgannett@hsc.wvu.edu: AMBER: compiler error, SGI Octane] Roberto Gomperts (Wed Jun 29 2005 - 08:01:00 PDT)
- AMBER: error - compiling antechamber Peter Gannett (Wed Jun 29 2005 - 12:30:20 PDT)
- AMBER: Free energy calculation for protein-protein complex using MM_PBSA Zhiguo Liu (Wed Jun 29 2005 - 18:59:01 PDT)
- AMBER: acceptor and donor in hbond calculation Vijay Manickam Achari (Wed Jun 29 2005 - 22:01:58 PDT)
- AMBER: example script for hbond calculation Vijay Manickam Achari (Wed Jun 29 2005 - 23:27:15 PDT)
- AMBER: 10-12 potential and create atom type Fabien CAILLIEZ (Thu Jun 30 2005 - 10:19:41 PDT)
- AMBER: antechamber error Peter Gannett (Thu Jun 30 2005 - 12:05:25 PDT)
- AMBER: Create new Unit Douali, Latifa (Thu Jun 30 2005 - 16:45:37 PDT)
- Last message date: Fri Jul 01 2005 - 02:53:00 PDT
- Archived on: Fri Mar 12 2010 - 05:59:44 PST
